| Previous changeset 28:6aa28a85cc38 (2017-07-10) Next changeset 30:e7c4be523cb7 (2018-06-19) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f |
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modified:
TrackDb.py TrackDb.pyc TrackHub.py TrackHub.pyc hubArchiveCreator.py hubArchiveCreator.xml templates/trackDb/layout.txt tool_dependencies.xml util/Filters.py util/__init__.pyc util/subtools.py util/subtools.pyc |
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added:
datatypes/Datatype.py datatypes/Datatype.pyc datatypes/__init__.py datatypes/__init__.pyc datatypes/binary/Bam.py datatypes/binary/Bam.pyc datatypes/binary/BigBed.py datatypes/binary/BigBed.pyc datatypes/binary/BigWig.py datatypes/binary/BigWig.pyc datatypes/binary/Binary.py datatypes/binary/Binary.pyc datatypes/binary/__init__.py datatypes/binary/__init__.pyc datatypes/converters/DataConversion.py datatypes/converters/DataConversion.pyc datatypes/converters/__init__.py datatypes/converters/__init__.pyc datatypes/interval/Bed.py datatypes/interval/Bed.pyc datatypes/interval/BedBlastAlignments.py datatypes/interval/BedBlastAlignments.pyc datatypes/interval/BedBlatAlignments.py datatypes/interval/BedBlatAlignments.pyc datatypes/interval/BedSimpleRepeats.py datatypes/interval/BedSimpleRepeats.pyc datatypes/interval/BedSpliceJunctions.py datatypes/interval/BedSpliceJunctions.pyc datatypes/interval/BigPsl.py datatypes/interval/BigPsl.pyc datatypes/interval/CytoBand.py datatypes/interval/CytoBand.pyc datatypes/interval/Gff.py datatypes/interval/Gff.pyc datatypes/interval/Gff3.py datatypes/interval/Gff3.pyc datatypes/interval/Gtf.py datatypes/interval/Gtf.pyc datatypes/interval/Interval.py datatypes/interval/Interval.pyc datatypes/interval/Psl.py datatypes/interval/Psl.pyc datatypes/interval/__init__.py datatypes/interval/__init__.pyc datatypes/sequence/Fasta.py datatypes/sequence/Fasta.pyc datatypes/sequence/__init__.py datatypes/sequence/__init__.pyc datatypes/validators/DataValidation.py datatypes/validators/DataValidation.pyc datatypes/validators/Gff3Validation.py datatypes/validators/Gff3Validation.pyc datatypes/validators/GtfValidation.py datatypes/validators/GtfValidation.pyc datatypes/validators/PslValidation.py datatypes/validators/PslValidation.pyc datatypes/validators/__init__.py datatypes/validators/__init__.pyc logging.json macros.xml test-data/all_datatypes/__main__.log test-data/all_datatypes/all_datatypes_trackhub.html test-data/all_datatypes/myHub/Dbia3.html test-data/all_datatypes/myHub/Dbia3/description.html test-data/all_datatypes/myHub/Dbia3/groups.txt test-data/all_datatypes/myHub/Dbia3/trackDb.txt test-data/all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb test-data/all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb test-data/all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb test-data/all_datatypes/myHub/Dbia3/tracks/Cytoband.bb test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb test-data/all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb test-data/all_datatypes/myHub/genomes.txt test-data/all_datatypes/myHub/hub.txt test-data/bam/__main__.log test-data/bam/bam.html test-data/bam/inputs/HISAT2_Accepted_Hits.bai test-data/bam/inputs/HISAT2_Accepted_Hits.bam test-data/bam/myHub/Dbia3.html test-data/bam/myHub/Dbia3/description.html test-data/bam/myHub/Dbia3/groups.txt test-data/bam/myHub/Dbia3/trackDb.txt test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/bam/myHub/genomes.txt test-data/bam/myHub/hub.txt test-data/bed_blast_alignment/__main__.log test-data/bed_blast_alignment/blast_alignment_trackhub.html test-data/bed_blast_alignment/inputs/BLAST_alignment_bigpsl test-data/bed_blast_alignment/myHub/Dbia3.html test-data/bed_blast_alignment/myHub/Dbia3/description.html test-data/bed_blast_alignment/myHub/Dbia3/groups.txt test-data/bed_blast_alignment/myHub/Dbia3/trackDb.txt test-data/bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb test-data/bed_blast_alignment/myHub/genomes.txt test-data/bed_blast_alignment/myHub/hub.txt test-data/bed_blat_alignment/__main__.log test-data/bed_blat_alignment/blat_alignment_trackhub.html test-data/bed_blat_alignment/inputs/BLAT_alignment_bigpsl test-data/bed_blat_alignment/myHub/Dbia3.html test-data/bed_blat_alignment/myHub/Dbia3/description.html test-data/bed_blat_alignment/myHub/Dbia3/groups.txt test-data/bed_blat_alignment/myHub/Dbia3/trackDb.txt test-data/bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb test-data/bed_blat_alignment/myHub/genomes.txt test-data/bed_blat_alignment/myHub/hub.txt test-data/bed_cytoband/__main__.log test-data/bed_cytoband/cytoband_trackhub.html test-data/bed_cytoband/inputs/Cytoband test-data/bed_cytoband/myHub/Dbia3.html test-data/bed_cytoband/myHub/Dbia3/description.html test-data/bed_cytoband/myHub/Dbia3/groups.txt test-data/bed_cytoband/myHub/Dbia3/trackDb.txt test-data/bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb test-data/bed_cytoband/myHub/genomes.txt test-data/bed_cytoband/myHub/hub.txt test-data/bed_generic/__main__.log test-data/bed_generic/bed_generic.html test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins test-data/bed_generic/myHub/Dbia3.html test-data/bed_generic/myHub/Dbia3/description.html test-data/bed_generic/myHub/Dbia3/groups.txt test-data/bed_generic/myHub/Dbia3/trackDb.txt test-data/bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb test-data/bed_generic/myHub/genomes.txt test-data/bed_generic/myHub/hub.txt test-data/bed_simple_repeats/__main__.log test-data/bed_simple_repeats/bed_simple_repeats_trackhub.html test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig test-data/bed_simple_repeats/myHub/Dbia3.html test-data/bed_simple_repeats/myHub/Dbia3/description.html test-data/bed_simple_repeats/myHub/Dbia3/groups.txt test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb test-data/bed_simple_repeats/myHub/genomes.txt test-data/bed_simple_repeats/myHub/hub.txt test-data/bed_splice_junctions/__main__.log test-data/bed_splice_junctions/inputs/regtools_junctions test-data/bed_splice_junctions/myHub/Dbia3.html test-data/bed_splice_junctions/myHub/Dbia3/description.html test-data/bed_splice_junctions/myHub/Dbia3/groups.txt test-data/bed_splice_junctions/myHub/Dbia3/trackDb.txt test-data/bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb test-data/bed_splice_junctions/myHub/genomes.txt test-data/bed_splice_junctions/myHub/hub.txt test-data/bed_splice_junctions/splice_junctions_trackhub.html test-data/big_bed/__main__.log test-data/big_bed/bigbed_trackhub.html test-data/big_bed/inputs/BLAT_alignment_bigbed test-data/big_bed/myHub/Dbia3.html test-data/big_bed/myHub/Dbia3/description.html test-data/big_bed/myHub/Dbia3/groups.txt test-data/big_bed/myHub/Dbia3/trackDb.txt test-data/big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed test-data/big_bed/myHub/genomes.txt test-data/big_bed/myHub/hub.txt test-data/bigwig/__main__.log test-data/bigwig/bigwig.html test-data/bigwig/inputs/RNA-Seq_Alignment_Coverage test-data/bigwig/myHub/Dbia3.html test-data/bigwig/myHub/Dbia3/description.html test-data/bigwig/myHub/Dbia3/groups.txt test-data/bigwig/myHub/Dbia3/trackDb.txt test-data/bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig test-data/bigwig/myHub/genomes.txt test-data/bigwig/myHub/hub.txt test-data/changed_color/__main__.log test-data/changed_color/changed_color_trackhub.html test-data/changed_color/myHub/Dbia3.html test-data/changed_color/myHub/Dbia3/description.html test-data/changed_color/myHub/Dbia3/groups.txt test-data/changed_color/myHub/Dbia3/trackDb.txt test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/changed_color/myHub/genomes.txt test-data/changed_color/myHub/hub.txt test-data/changed_label/__main__.log test-data/changed_label/changed_label_trackhub.html test-data/changed_label/myHub/Dbia3.html test-data/changed_label/myHub/Dbia3/description.html test-data/changed_label/myHub/Dbia3/groups.txt test-data/changed_label/myHub/Dbia3/trackDb.txt test-data/changed_label/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/changed_label/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/changed_label/myHub/genomes.txt test-data/changed_label/myHub/hub.txt test-data/common/Dbia3.2bit test-data/common/dbia3.fa test-data/common/dbia3.sizes test-data/default_color/__main__.log test-data/default_color/default_color_trackhub.html test-data/default_color/myHub/Dbia3.html test-data/default_color/myHub/Dbia3/description.html test-data/default_color/myHub/Dbia3/groups.txt test-data/default_color/myHub/Dbia3/trackDb.txt test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/default_color/myHub/genomes.txt test-data/default_color/myHub/hub.txt test-data/gff3/__main__.log test-data/gff3/gff3_trackhub.html test-data/gff3/inputs/Augustus_Gene_Predictions test-data/gff3/myHub/Dbia3.html test-data/gff3/myHub/Dbia3/description.html test-data/gff3/myHub/Dbia3/groups.txt test-data/gff3/myHub/Dbia3/trackDb.txt test-data/gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb test-data/gff3/myHub/genomes.txt test-data/gff3/myHub/hub.txt test-data/gff3_multi_fasta/__main__.log test-data/gff3_multi_fasta/gff3_multi_fasta_trackhub.html test-data/gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions test-data/gff3_multi_fasta/myHub/Dbia3.html test-data/gff3_multi_fasta/myHub/Dbia3/description.html test-data/gff3_multi_fasta/myHub/Dbia3/groups.txt test-data/gff3_multi_fasta/myHub/Dbia3/trackDb.txt test-data/gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb test-data/gff3_multi_fasta/myHub/genomes.txt test-data/gff3_multi_fasta/myHub/hub.txt test-data/gtf/__main__.log test-data/gtf/gtf_trackhub.html test-data/gtf/inputs/StringTie_Assembled_Transcripts test-data/gtf/myHub/Dbia3.html test-data/gtf/myHub/Dbia3/description.html test-data/gtf/myHub/Dbia3/groups.txt test-data/gtf/myHub/Dbia3/trackDb.txt test-data/gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/gtf/myHub/genomes.txt test-data/gtf/myHub/hub.txt test-data/gtf_gff/__main__.log test-data/gtf_gff/gtf_gff_trackhub.html test-data/gtf_gff/myHub/Dbia3.html test-data/gtf_gff/myHub/Dbia3/description.html test-data/gtf_gff/myHub/Dbia3/groups.txt test-data/gtf_gff/myHub/Dbia3/trackDb.txt test-data/gtf_gff/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb test-data/gtf_gff/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/gtf_gff/myHub/genomes.txt test-data/gtf_gff/myHub/hub.txt test-data/one_group_two_tracks/Hub_Archive_Creator_on_data_15,_data_19,_and_data_1_trackhub.html test-data/one_group_two_tracks/__main__.log test-data/one_group_two_tracks/myHub/Dbia3.html test-data/one_group_two_tracks/myHub/Dbia3/description.html test-data/one_group_two_tracks/myHub/Dbia3/groups.txt test-data/one_group_two_tracks/myHub/Dbia3/trackDb.txt test-data/one_group_two_tracks/myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam test-data/one_group_two_tracks/myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam.bai test-data/one_group_two_tracks/myHub/Dbia3/tracks/StringTie_on_data_15:_Assembled_transcripts.bb test-data/one_group_two_tracks/myHub/genomes.txt test-data/one_group_two_tracks/myHub/hub.txt test-data/only_genome/__main__.log test-data/only_genome/myHub/Dbia3.html test-data/only_genome/myHub/Dbia3/description.html test-data/only_genome/myHub/genomes.txt test-data/only_genome/myHub/hub.txt test-data/only_genome/only_genome.html test-data/psl/__main__.log test-data/psl/inputs/blastXmlToPsl test-data/psl/myHub/Dbia3.html test-data/psl/myHub/Dbia3/description.html test-data/psl/myHub/Dbia3/groups.txt test-data/psl/myHub/Dbia3/trackDb.txt test-data/psl/myHub/Dbia3/tracks/blastXmlToPsl.bb test-data/psl/myHub/genomes.txt test-data/psl/myHub/hub.txt test-data/psl/psl_trackhub.html test-data/stringtie_chromosome_end_coordinates/__main__.log test-data/stringtie_chromosome_end_coordinates/inputs/stringtie_assembled_transcripts test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3.html test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/Dbia3.2bit test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/description.html test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/groups.txt test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/trackDb.txt test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/stringtie_chromosome_end_coordinates/myHub/genomes.txt test-data/stringtie_chromosome_end_coordinates/myHub/hub.txt test-data/stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html test-data/trix_index_files/bigbed_trackhub.html test-data/trix_index_files/blast_alignment_trackhub.html test-data/trix_index_files/blast_out.ix test-data/trix_index_files/blast_out.ixx test-data/trix_index_files/blat_alignment_trackhub.html test-data/trix_index_files/blat_out.ix test-data/trix_index_files/blat_out.ixx test-data/two_groups_multiple_tracks/__main__.log test-data/two_groups_multiple_tracks/myHub/Dbia3.html test-data/two_groups_multiple_tracks/myHub/Dbia3/description.html test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/two_groups_multiple_tracks/myHub/genomes.txt test-data/two_groups_multiple_tracks/myHub/hub.txt test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html test-data/two_groups_no_track/__main__.log test-data/two_groups_no_track/myHub/Dbia3.html test-data/two_groups_no_track/myHub/Dbia3/description.html test-data/two_groups_no_track/myHub/genomes.txt test-data/two_groups_no_track/myHub/hub.txt test-data/two_groups_no_track/two_groups_no_track_trackhub.html test-data/two_groups_one_track_both/__main__.log test-data/two_groups_one_track_both/myHub/Dbia3.html test-data/two_groups_one_track_both/myHub/Dbia3/description.html test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb test-data/two_groups_one_track_both/myHub/genomes.txt test-data/two_groups_one_track_both/myHub/hub.txt test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html test-data/two_groups_one_track_first/__main__.log test-data/two_groups_one_track_first/myHub/Dbia3.html test-data/two_groups_one_track_first/myHub/Dbia3/description.html test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig test-data/two_groups_one_track_first/myHub/genomes.txt test-data/two_groups_one_track_first/myHub/hub.txt test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html tests.xml util/Logger.py util/Logger.pyc util/Reader.py util/Reader.pyc util/index/DatabaseIndex.py util/index/DatabaseIndex.pyc util/index/ExternIndex.py util/index/ExternIndex.pyc util/index/TrixIndex.py util/index/TrixIndex.pyc util/index/__init__.py util/index/__init__.pyc util/log.pyc util/santitizer.py util/santitizer.pyc |
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removed:
Bam.py Bam.pyc Bed.py Bed.pyc BedBlastAlignments.py BedBlastAlignments.pyc BedSimpleRepeats.py BedSimpleRepeats.pyc BedSpliceJunctions.py BedSpliceJunctions.pyc BigBed.py BigWig.py BigWig.pyc Datatype.py Datatype.pyc Gff3.py Gff3.pyc Gtf.py Gtf.pyc Psl.py Psl.pyc Track.py Track.pyc bigPsl.py bigPsl.pyc cytoBand.py util/Fasta.py util/Fasta.pyc util/Filters.pyc |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Bam.py --- a/Bam.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,86 +0,0 @@ -#!/usr/bin/python -# -*- coding: utf8 -*- - -""" -Class to handle Bam files to UCSC TrackHub -""" - -import logging -import os -import shutil - -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb - - - -class Bam( Datatype ): - def __init__(self, input_bam_false_path, data_bam): - super(Bam, self).__init__() - - self.track = None - - self.input_bam_false_path = input_bam_false_path - - self.data_bam = data_bam - # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension - if ".bam" not in self.data_bam["name"]: - self.name_bam = self.data_bam["name"] + ".bam" - else: - self.name_bam = self.data_bam["name"] - - self.priority = self.data_bam["order_index"] - self.index_bam = self.data_bam["index"] - # TODO: Think about how to avoid repetition of the color treatment - self.track_color = self.data_bam["track_color"] - - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = self.data_bam["group_name"] - self.database = self.data_bam["database"] - if self.data_bam["long_label"]: - self.long_label = self.data_bam["long_label"] - else: - self.long_label = self.name_bam - # First: Add the bam file - # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html) - - bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam) - shutil.copyfile(self.input_bam_false_path, bam_file_path) - - # Create and add the bam index file to the same folder - name_index_bam = self.name_bam + ".bai" - bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam) - shutil.copyfile(self.index_bam, bam_index_file_path) - - # Create the Track Object - self.createTrack(file_path=self.name_bam, - track_name=self.name_bam, - long_label=self.long_label, track_type='bam', visibility='pack', priority=self.priority, - track_file=bam_index_file_path, - track_color=self.track_color, - group_name=self.group_name, - database=self.database - ) - # - # dataURL = "tracks/%s" % self.name_bam - # - # trackDb = TrackDb( - # trackName=self.name_bam, - # longLabel=self.name_bam, - # shortLabel=self.getShortName( self.name_bam ), - # trackDataURL=dataURL, - # trackType='bam', - # visibility='pack', - # priority=self.priority, - # ) - # - # # Return the Bam Track Object - # self.track = Track( - # trackFile=bam_index_file_path, - # trackDb=trackDb, - # ) - - print("- Bam %s created" % self.name_bam) - #print("- %s created in %s" % (self.name_bam, bam_file_path)) - #print("- %s created in %s" % (self.index_bam, bam_index_file_path)) |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Bam.pyc |
| b |
| Binary file Bam.pyc has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Bed.py --- a/Bed.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,82 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -# Internal dependencies -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class Bed( Datatype ): - def __init__( self, inputBedGeneric, data_bed_generic): - super(Bed, self).__init__() - - self.track = None - - self.inputBedGeneric = inputBedGeneric - - self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - self.data_bed_generic = data_bed_generic - self.name_bed_generic = self.data_bed_generic["name"] - self.priority = self.data_bed_generic["order_index"] - self.track_color = self.data_bed_generic["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = self.data_bed_generic["group_name"] - self.database = self.data_bed_generic["database"] - if self.data_bed_generic["long_label"]: - self.long_label = self.data_bed_generic["long_label"] - else: - self.long_label = self.name_bed_generic - - # Sort processing - subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb - trackName = "".join( ( self.name_bed_generic, ".bb") ) - - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - with open(myBigBedFilePath, 'w') as self.bigBedFile: - subtools.bedToBigBed(self.sortedBedFile.name, - self.chromSizesFile.name, - self.bigBedFile.name, - typeOption='bed4', - tab='True', - extraIndex='name' - ) - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, track_type='bigBed', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_generic, - # shortLabel=self.getShortName(self.name_bed_generic), - # trackDataURL=dataURL, - # trackType='bigBed', - # visibility='dense', - # thickDrawItem='on', - # priority=self.priority, - # ) - # - # # Return the BigBed track - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- Bed %s created" % self.name_bed_generic) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Bed.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BedBlastAlignments.py --- a/BedBlastAlignments.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,80 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile -import string - -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class BedBlastAlignments( Datatype ): - def __init__(self, input_bed_blast_alignments_false_path, data_bed_blast_alignments): - - super(BedBlastAlignments, self).__init__() - - self.input_bed_blast_alignments_false_path = input_bed_blast_alignments_false_path - self.name_bed_blast_alignments = data_bed_blast_alignments["name"] - self.priority = data_bed_blast_alignments["order_index"] - self.track_color = data_bed_blast_alignments["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_bed_blast_alignments["group_name"] - self.database = data_bed_blast_alignments["database"] - if data_bed_blast_alignments["long_label"]: - self.long_label = data_bed_blast_alignments["long_label"] - else: - self.long_label = self.name_bed_blast_alignments - #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - # Sort processing - #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + .bb - trackName = "".join( ( self.name_bed_blast_alignments, '.bb' ) ) - - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(self.input_bed_blast_alignments_false_path, - self.chromSizesFile.name, - bigBedFile.name, - typeOption='bed12+12', - tab='True', - autoSql=auto_sql_option, - extraIndex='name') - - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, track_type='bigBed 12 +', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database - ) - - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_simple_repeats, - # shortLabel=self.getShortName( self.name_bed_simple_repeats ), - # trackDataURL=dataURL, - # trackType='bigBed 4 +', - # visibility='dense', - # priority=self.priority, - # ) - # - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- Bed Blast alignments %s created" % self.name_bed_blast_alignments) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BedBlastAlignments.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BedSimpleRepeats.py --- a/BedSimpleRepeats.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,78 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class BedSimpleRepeats( Datatype ): - def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats): - - super(BedSimpleRepeats, self).__init__() - - self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path - self.name_bed_simple_repeats = data_bed_simple_repeats["name"] - self.priority = data_bed_simple_repeats["order_index"] - self.track_color = data_bed_simple_repeats["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_bed_simple_repeats["group_name"] - self.database = data_bed_simple_repeats["database"] - if data_bed_simple_repeats["long_label"]: - self.long_label = data_bed_simple_repeats["long_label"] - else: - self.long_label = self.name_bed_simple_repeats - - sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - # Sort processing - subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + .bb - trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) ) - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as') - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(sortedBedFile.name, - self.chromSizesFile.name, - bigBedFile.name, - typeOption='bed4+12', - autoSql=auto_sql_option, - extraIndex='name' - ) - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, track_type='bigBed 4 +', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_simple_repeats, - # shortLabel=self.getShortName( self.name_bed_simple_repeats ), - # trackDataURL=dataURL, - # trackType='bigBed 4 +', - # visibility='dense', - # priority=self.priority, - # ) - # - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- Bed simple repeats %s created" % self.name_bed_simple_repeats) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BedSimpleRepeats.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BedSpliceJunctions.py --- a/BedSpliceJunctions.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,77 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class BedSpliceJunctions( Datatype ): - def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions): - - super(BedSpliceJunctions, self).__init__() - - self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path - self.name_bed_splice_junctions = data_bed_splice_junctions["name"] - self.priority = data_bed_splice_junctions["order_index"] - self.track_color = data_bed_splice_junctions["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_bed_splice_junctions["group_name"] - self.database = data_bed_splice_junctions["database"] - if data_bed_splice_junctions["long_label"]: - self.long_label = data_bed_splice_junctions["long_label"] - else: - self.long_label = self.name_bed_splice_junctions - sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - # Sort processing - subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + .bb - trackName = "".join( ( self.name_bed_splice_junctions, '.bb' ) ) - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as') - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(sortedBedFile.name, - self.chromSizesFile.name, - bigBedFile.name, - typeOption='bed12+1', - autoSql=auto_sql_option, - extraIndex='name' - ) - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, track_type='bigBed 12 +', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_simple_repeats, - # shortLabel=self.getShortName( self.name_bed_simple_repeats ), - # trackDataURL=dataURL, - # trackType='bigBed 4 +', - # visibility='dense', - # priority=self.priority, - # ) - # - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- Bed splice junctions %s created" % self.name_bed_splice_junctions) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BedSpliceJunctions.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BigBed.py --- a/BigBed.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,81 +0,0 @@ -#!/usr/bin/python - -import os -import shutil -from subprocess import Popen, PIPE -import re - -# Internal dependencies -from Datatype import Datatype - -class BigBed(Datatype): - """ Configurations for creating the bigBed evidence track """ - - def __init__(self, input_bigbed_path, data_bigbed): - super(BigBed, self).__init__() - - self.track = None - - self.input_bigbed_path = input_bigbed_path - self.name_bigbed = data_bigbed["name"] - self.priority = data_bigbed["order_index"] - self.track_color = data_bigbed["track_color"] - self.group_name = data_bigbed["group_name"] - self.database = data_bigbed["database"] - - track_name = "".join((self.name_bigbed, ".bigbed")) - if data_bigbed["long_label"]: - self.long_label = data_bigbed["long_label"] - else: - self.long_label = self.name_bigbed - - bigbed_file_path = os.path.join(self.myTrackFolderPath, track_name) - - track_type = self.determine_track_type(input_bigbed_path) - - shutil.copy(self.input_bigbed_path, bigbed_file_path) - - # Create the Track Object - self.createTrack(file_path=track_name, - track_name=track_name, - long_label=self.long_label, - track_type=track_type, - visibility='hide', - priority=self.priority, - track_file=bigbed_file_path, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - print "- BigBed %s created" % self.name_bigbed - - - def determine_track_type(self, bb_file): - """ - Determine the number of standard and extra fields using bigBedSummary - - Implementation of reading from stdout is based on a Stackoverflow post: - http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate - - :param bb_file: path to a bigBed file - - :returns: the bigBed track type - """ - - cmd_ph = Popen(["bigBedSummary", "-fields", bb_file, "stdout"], - stdout=PIPE, bufsize=1) - - pattern = r"(\d+) bed definition fields, (\d+) total fields" - - with cmd_ph.stdout: - for line in iter(cmd_ph.stdout.readline, b''): - match = re.match(pattern, line) - - if match: - extra_mark = "." if match.group(1) == match.group(2) else "+" - bed_type = "bigBed %s %s" % (match.group(1), extra_mark) - break - - cmd_ph.wait() - - return bed_type |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BigWig.py --- a/BigWig.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,76 +0,0 @@ -#!/usr/bin/python - -import os -import shutil -from subprocess import Popen, PIPE -import re - -# Internal dependencies -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb - - -class BigWig( Datatype ): - def __init__(self, input_bigwig_path, data_bigwig): - super(BigWig, self).__init__() - - self.track = None - - self.input_bigwig_path = input_bigwig_path - self.name_bigwig = data_bigwig["name"] - self.priority = data_bigwig["order_index"] - self.track_color = data_bigwig["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_bigwig["group_name"] - self.database = data_bigwig["database"] - if data_bigwig["long_label"]: - self.long_label = data_bigwig["long_label"] - else: - self.long_label = self.name_bigwig - #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig ) - - trackName = "".join( ( self.name_bigwig, ".bigwig" ) ) - - myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName) - shutil.copy(self.input_bigwig_path, myBigWigFilePath) - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, - track_type=self.determine_track_type(myBigWigFilePath), - visibility='full', - priority=self.priority, - track_file=myBigWigFilePath, - track_color=self.track_color, - group_name=self.group_name, - database = self.database) - - print("- BigWig %s created" % self.name_bigwig) - #print("- %s created in %s" % (trackName, myBigWigFilePath)) - - def determine_track_type(self, bw_file): - """ - bigWig tracks must declare the expected signal range for the data - (See https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html). - This method determines the range of values for a bigWig file using - the bigWigInfo program. - - Implementation of reading from stdout is based on a Stackoverflow post: - http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate - - :param bw_file: path to a bigWig file - - :returns: the bigWig track type - """ - cmd_ph = Popen(["bigWigInfo", "-minMax", bw_file], - stdout=PIPE, bufsize=1) - - with cmd_ph.stdout: - for line in iter(cmd_ph.stdout.readline, b''): - bw_type = "bigWig %s" % line.rstrip() - - cmd_ph.wait() - - return bw_type |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 BigWig.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Datatype.py --- a/Datatype.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,118 +0,0 @@ -#!/usr/bin/python -# -*- coding: utf8 -*- - -""" -Super Class of the managed datatype -""" - -import os -import tempfile - -from util import subtools -from Track import Track -from TrackDb import TrackDb - - -class Datatype(object): - - twoBitFile = None - - input_fasta_file = None - extra_files_path = None - tool_directory = None - - mySpecieFolderPath = None - myTrackFolderPath = None - - twoBitFile = None - chromSizesFile = None - - track = None - - def __init__(self): - - not_init_message = "The {0} is not initialized." \ - "Did you use pre_init static method first?" - if Datatype.input_fasta_file is None: - raise TypeError(not_init_message.format('reference genome')) - if Datatype.extra_files_path is None: - raise TypeError(not_init_message.format('track Hub path')) - if Datatype.tool_directory is None: - raise TypeError(not_init_message.format('tool directory')) - - @staticmethod - def pre_init(reference_genome, two_bit_path, chrom_sizes_file, - extra_files_path, tool_directory, specie_folder, tracks_folder): - Datatype.extra_files_path = extra_files_path - Datatype.tool_directory = tool_directory - - # TODO: All this should be in TrackHub and not in Datatype - Datatype.mySpecieFolderPath = specie_folder - Datatype.myTrackFolderPath = tracks_folder - - Datatype.input_fasta_file = reference_genome - - # 2bit file creation from input fasta - Datatype.twoBitFile = two_bit_path - Datatype.chromSizesFile = chrom_sizes_file - - @staticmethod - def get_largest_scaffold_name(self): - # We can get the biggest scaffold here, with chromSizesFile - with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes: - # TODO: Check if exists - return chrom_sizes.readline().split()[0] - - # TODO: Rename for PEP8 - def getShortName( self, name_to_shortify ): - # Slice to get from Long label the short label - short_label_slice = slice(0, 17) - - return name_to_shortify[short_label_slice] - - # TODO: Better handle parameters, use heritance mecanism - # TODO: Use default parameters for some, like visibility - def createTrack(self, - file_path=None, - track_name=None, long_label=None, thick_draw_item='off', - short_label=None, track_type=None, visibility=None, priority=None, - track_file=None, track_color='#000000', group_name="Default", database=""): - - # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath - data_url = "tracks/%s" % file_path - - if not short_label: - short_label = self.getShortName(long_label) - - # Replace '_' by ' ', to invert the sanitization mecanism - # TODO: Find a better way to manage the sanitization of file path - long_label = long_label.replace("_", " ") - short_label = short_label.replace("_", " ") - - #TODO: Check if rgb or hexa - # Convert hexa to rgb array - hexa_without_sharp = track_color.lstrip('#') - rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)] - rgb_ucsc = ','.join(map(str, rgb_array)) - - #sanitize the track_name - sanitized_name = subtools.fixName(track_name) - track_db = TrackDb( - trackName=sanitized_name, - longLabel=long_label, - shortLabel=short_label, - trackDataURL=data_url, - trackType=track_type, - visibility=visibility, - thickDrawItem=thick_draw_item, - priority=priority, - track_color=rgb_ucsc, - group_name=group_name, - database=database - ) - - # Return the Bam Track Object - self.track = Track( - trackFile=track_file, - trackDb=track_db, - ) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Datatype.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Gff3.py --- a/Gff3.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,73 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -# Internal dependencies -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class Gff3( Datatype ): - def __init__(self, input_Gff3_false_path, data_gff3): - super( Gff3, self ).__init__() - - self.track = None - - self.input_Gff3_false_path = input_Gff3_false_path - self.name_gff3 = data_gff3["name"] - self.priority = data_gff3["order_index"] - self.track_color = data_gff3["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_gff3["group_name"] - self.database = data_gff3["database"] - if data_gff3["long_label"]: - self.long_label = data_gff3["long_label"] - else: - self.long_label = self.name_gff3 - # TODO: See if we need these temporary files as part of the generated files - unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") - unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") - sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") - - # gff3ToGenePred processing - subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name) - - # genePredToBigGenePred - subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name) - - # Sort processing - subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name) - - # TODO: Check if no errors - - # bedToBigBed processing - trackName = "".join( (self.name_gff3, ".bb" ) ) - - auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as') - - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(sorted_biGenePred_file.name, - self.chromSizesFile.name, - bigBedFile.name, - autoSql=auto_sql_option, - typeOption='bed12+8', - tab=True, - extraIndex='name') - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, - track_type='bigGenePred', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - print("- Gff3 %s created" % self.name_gff3) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Gff3.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Gtf.py --- a/Gtf.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,162 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -# Internal dependencies -from Datatype import Datatype -from util import subtools - -class InfoModifiedGtf(): - def __init__(self, is_modified=False, array_modified_lines=[]): - self.is_modified = is_modified - self.array_modified_lines = array_modified_lines - - def get_str_modified_lines(self): - return ','.join(map(str, self.array_modified_lines)) - -class Gtf( Datatype ): - def __init__( self, input_gtf_false_path, data_gtf): - - super(Gtf, self).__init__() - - self.track = None - - self.input_gtf_false_path = input_gtf_false_path - self.name_gtf = data_gtf["name"] - self.priority = data_gtf["order_index"] - self.track_color = data_gtf["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_gtf["group_name"] - self.database = data_gtf["database"] - if data_gtf["long_label"]: - self.long_label = data_gtf["long_label"] - else: - self.long_label = self.name_gtf - #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) - - # TODO: See if we need these temporary files as part of the generated files - genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") - unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") - sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sortedBed.bigGenePred") - - # GtfToGenePred - ## Checking the integrity of the inputs - modified_gtf = self._checkAndFixGtf() - - ## Processing the gtf - subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name) - - # TODO: From there, refactor because common use with Gff3.py - # genePredToBigGenePred processing - subtools.genePredToBigGenePred(genePredFile.name, unsorted_bigGenePred_file.name) - - # Sort processing - subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name) - - # bedToBigBed processing - trackName = "".join( ( self.name_gtf, ".bb") ) - - auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as') - - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(sorted_bigGenePred_file.name, - self.chromSizesFile.name, - bigBedFile.name, - autoSql=auto_sql_option, - typeOption='bed12+8', - tab=True, - extraIndex='name') - - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, track_type='bigGenePred', - visibility='dense', priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - # TODO: Use Logging instead of print - if modified_gtf.is_modified: - print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues." - % self.name_gtf) - print("Here are the lines removed: " + modified_gtf.get_str_modified_lines()) - else: - print("- Gtf %s created" % self.name_gtf) - - def _checkAndFixGtf(self): - """ - Call _checkAndFixGtf, check the integrity of gtf file, - if coordinates exceed chromosome size, either removed the whole line(s) or truncated to the end of the scaffold - depending on the user choice - default: remove the whole line(s) - """ - # Set the boolean telling if we had to modify the file - modified_gtf = InfoModifiedGtf() - - # Create a temp gtf just in case we have issues - temp_gtf = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gtf", delete=False) - - # TODO: Get the user choice and use it - # TODO: Check if the start > 0 and the end <= chromosome size - # Get the chrom.sizes into a dictionary to have a faster access - # TODO: Think about doing this in Datatype.py, so everywhere we have access to this read-only dictionary - dict_chrom_sizes = {} - with open(self.chromSizesFile.name, 'r') as chromSizes: - lines = chromSizes.readlines() - for line in lines: - fields = line.split() - # fields[1] should be the name of the scaffold - # fields[2] should be the size of the scaffold - # TODO: Ensure this is true for all lines - dict_chrom_sizes[fields[0]] = fields[1] - - # Parse the GTF and check each line using the chrom sizes dictionary - with open(temp_gtf.name, 'a+') as tmp: - with open(self.input_gtf_false_path, 'r') as gtf: - lines = gtf.readlines() - for index, line in enumerate(lines): - # If this is not a comment, we check the fields - if not line.startswith('#'): - fields = line.split() - # We are interested in fields[0] => Seqname (scaffold) - # We are interested in fields[3] => Start of the scaffold - # We are interested in fields[4] => End of the scaffold - scaffold_size = dict_chrom_sizes[fields[0]] - start_position = fields[3] - end_position = fields[4] - - if start_position > 0 and end_position <= scaffold_size: - # We are good, so we copy this line - tmp.write(line) - tmp.write(os.linesep) - - - # The sequence is not good, we are going to process it regarding the user choice - # TODO: Process the user choice - # By default, we are assuming the user choice is to remove the lines: We don't copy it - - # If we are here, it means the gtf has been modified - else: - # We save the line for the feedback to the user - modified_gtf.array_modified_lines.append(index + 1) - - if modified_gtf.is_modified is False: - modified_gtf.is_modified = True - else: - pass - else: - tmp.write(line) - tmp.write(os.linesep) - - # Once the process it completed, we just replace the path of the gtf - self.input_gtf_false_path = temp_gtf.name - - # TODO: Manage the issue with the fact the dataset is going to still exist on the disk because of delete=False - - return modified_gtf |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Gtf.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Psl.py --- a/Psl.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,66 +0,0 @@ -import logging -import os -import tempfile - -# Internal dependencies -from Datatype import Datatype -from util import subtools - - -class Psl(Datatype): - def __init__(self, input_psl_path, data_psl): - super(Psl, self).__init__() - - self.track = None - - self.input_psl_path = input_psl_path - self.name_psl = data_psl["name"] - self.priority = data_psl["order_index"] - self.track_color = data_psl["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_psl["group_name"] - self.database = data_psl["database"] - if data_psl["long_label"]: - self.long_label = data_psl["long_label"] - else: - self.long_label = self.name_psl - # Temporary files - unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl') - sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl') - - # Get the bed12+12 with pslToBigPsl - subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name) - - # Sort the formatted psl into sorted_bed_formatted_psl_file - subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name) - - # Get the binary indexed bigPsl with bedToBigBed - trackName = "".join((self.name_psl, ".bb")) - - auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') - - my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName) - - logging.debug("Hello") - - with open(my_big_psl_file_path, 'w') as big_psl_file: - subtools.bedToBigBed(sorted_bed_formatted_psl_file.name, - self.chromSizesFile.name, - big_psl_file.name, - autoSql=auto_sql_option, - typeOption='bed12+12', - tab=True, - extraIndex='name') - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, - track_type='bigPsl', visibility='dense', - priority=self.priority, - track_file=my_big_psl_file_path, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - print("- BigPsl %s created" % self.name_psl) \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Psl.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Track.py --- a/Track.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -#!/usr/bin/python - -# TODO: Is this still useful? -class Track(object): - """Class to manage the track informations needed for Track Hub, in the TrackDb text file""" - - def __init__(self, trackFile=None, trackDb=None): - self.trackFile = trackFile - - self.trackDb = trackDb |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 Track.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 TrackDb.py --- a/TrackDb.py Mon Jul 10 17:08:38 2017 -0400 +++ b/TrackDb.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -1,21 +1,80 @@ #!/usr/bin/python +import collections +from util import santitizer class TrackDb(object): """docstring for TrackDb""" + def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", extraSettings=None): + #super(TrackDb, self).__init__() + not_init_message = "The {0} is not initialized." + if trackName is None: + raise TypeError(not_init_message.format('trackName')) + if longLabel is None: + raise TypeError(not_init_message.format('longLabel')) + if trackType is None: + raise TypeError(not_init_message.format('trackType')) + if trackDataURL is None: + raise TypeError(not_init_message.format('trackDataURL')) + + self.createTrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extraSettings) - def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", visibility="", - thickDrawItem='off', priority="0", track_color="#000000", group_name="Default", database=""): - super(TrackDb, self).__init__() + def createTrackDb(self, track_name, long_label, short_label, file_path, track_type, extraSettings = None): + + # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath + data_url = "tracks/%s" % track_name + if not short_label: + short_label = TrackDb.getShortName(long_label) + # Replace '_' by ' ', to invert the sanitization mecanism + # TODO: Find a better way to manage the sanitization of file path + long_label = long_label.replace("_", " ") + short_label = short_label.replace("_", " ") + + #sanitize the track_name + sanitized_name = santitizer.prefixTrackName(track_name) - self.trackName = trackName - self.longLabel = longLabel - self.shortLabel = shortLabel - self.trackDataURL = trackDataURL - self.trackType = trackType - self.visibility = visibility - self.thickDrawItem = thickDrawItem - self.priority = priority - self.track_color = track_color - self.group_name = group_name - self.database = database - \ No newline at end of file + self.track_db = collections.OrderedDict([("track",sanitized_name), + ("type",track_type), + ("shortLabel",short_label), + ("longLabel",long_label), + ("bigDataUrl",data_url)] + ) + + + TrackDb.prepareExtraSetting(extraSettings) + self.track_db.update(extraSettings) + #print self.track_db + + # TODO: Rename for PEP8 + @staticmethod + def getShortName(name_to_shortify): + # Slice to get from Long label the short label + short_label_slice = slice(0, 17) + return name_to_shortify[short_label_slice] + + @staticmethod + def getRgb(track_color): + #TODO: Check if rgb or hexa + # Convert hexa to rgb array + hexa_without_sharp = track_color.lstrip('#') + rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)] + rgb_ucsc = ','.join(map(str, rgb_array)) + return rgb_ucsc + + @staticmethod + def prepareExtraSetting(extraSettings): + if not extraSettings: + extraSettings = collections.OrderedDict() + if not "color" in extraSettings: + extraSettings["color"] = "#000000" + extraSettings["color"] = TrackDb.getRgb(extraSettings["color"]) + if not "group" in extraSettings or not extraSettings["group"]: + extraSettings["group"] = "Default group" + if not "thickDrawItem" in extraSettings: + extraSettings["thickDrawItem"] = "off" + + def get(self, item_name): + if item_name in self.track_db: + return self.track_db[item_name] + return None + + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 TrackDb.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 TrackHub.py --- a/TrackHub.py Mon Jul 10 17:08:38 2017 -0400 +++ b/TrackHub.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -6,12 +6,14 @@ import tempfile import shutil import zipfile +from mako.lookup import TemplateLookup # Internal dependencies -from Datatype import Datatype +from datatypes.Datatype import Datatype from util import subtools +from util import santitizer -from mako.lookup import TemplateLookup + class TrackHub(object): @@ -19,7 +21,6 @@ def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory): super(TrackHub, self).__init__() - self.rootAssemblyHub = None self.mySpecieFolderPath = None @@ -68,7 +69,7 @@ Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile, self.extra_files_path, self.tool_directory, self.mySpecieFolderPath, self.myTracksFolderPath) - + ''' def createZip(self): for root, dirs, files in os.walk(self.rootAssemblyHub): # Get all files and construct the dir at the same time @@ -76,29 +77,30 @@ self.outputZip.write(os.path.join(root, file)) self.outputZip.close() - + ''' def addTrack(self, trackDbObject=None): # Create the trackDb.txt file in the specie folder, if not exists # Else append the new track # TODO: Get this out of the function trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt') - # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object with open(trackDbTxtFilePath, 'a+') as trackDbFile: + group_name = trackDbObject["group"] + trackDbObject["group"] = santitizer.sanitize_group_name(trackDbObject["group"]) trackDbs = [trackDbObject] - # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label # Add the group as well, if exists in trackDbObject - self.addGroup(trackDbObject.group_name) + self.addGroup(group_name) htmlMakoRendered = self.trackDbTemplate.render( trackDbs=trackDbs ) trackDbFile.write(htmlMakoRendered) - logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName, - trackDbObject.group_name.lower().replace(' ', '_'))) - + #logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName, + # trackDbObject.group_name.lower().replace(' ', '_'))) + logging.debug("We just added track {0} (in group {1})".format(trackDbObject.get("track"), + trackDbObject.get("group").lower().replace(' ', '_'))) def addGroup(self, group_name="Default"): # If not already present in self.groups, add to groups.txt # Create the trackDb.txt file in the specie folder, if not exists @@ -168,6 +170,7 @@ ) htmlOutput.write(htmlMakoRendered) + def __createAssemblyHub__(self, extra_files_path): # Get all necessaries infos first # 2bit file creation from input fasta |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 TrackHub.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 bigPsl.py --- a/bigPsl.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,79 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile -import string - -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class bigPsl( Datatype ): - def __init__(self, input_bigpsl_false_path, data_bigpsl): - - super(bigPsl, self).__init__() - - self.input_bigpsl_false_path = input_bigpsl_false_path - self.name_bigpsl = data_bigpsl["name"] - self.priority = data_bigpsl["order_index"] - self.track_color = data_bigpsl["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_bigpsl["group_name"] - self.database = data_bigpsl["database"] - if data_bigpsl["long_label"]: - self.long_label = data_bigpsl["long_label"] - else: - self.long_label = self.name_bigpsl - #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - # Sort processing - #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + .bb - trackName = "".join( ( self.name_bigpsl, '.bb' ) ) - - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(self.input_bigpsl_false_path, - self.chromSizesFile.name, - bigBedFile.name, - typeOption='bed12+12', - tab='True', - autoSql=auto_sql_option, - extraIndex='name') - - self.createTrack(file_path=trackName, - track_name=trackName, - long_label=self.long_label, track_type='bigPsl', visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_simple_repeats, - # shortLabel=self.getShortName( self.name_bed_simple_repeats ), - # trackDataURL=dataURL, - # trackType='bigBed 4 +', - # visibility='dense', - # priority=self.priority, - # ) - # - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- bigPsl %s created" % self.name_bigpsl) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 bigPsl.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 cytoBand.py --- a/cytoBand.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,78 +0,0 @@ -#!/usr/bin/python - -import os -import tempfile - -from Datatype import Datatype -from Track import Track -from TrackDb import TrackDb -from util import subtools - - -class cytoBand( Datatype ): - def __init__(self, input_bed_cytoBand_false_path, data_bed_cytoBand): - - super(cytoBand, self).__init__() - - self.input_bed_cytoBand_false_path = input_bed_cytoBand_false_path - self.name_bed_cytoBand = data_bed_cytoBand["name"] - self.priority = data_bed_cytoBand["order_index"] - self.track_color = data_bed_cytoBand["track_color"] - # TODO: Think about how to avoid repetition of the group_name everywhere - self.group_name = data_bed_cytoBand["group_name"] - self.database = data_bed_cytoBand["database"] - if data_bed_cytoBand["long_label"]: - self.long_label = data_bed_cytoBand["long_label"] - else: - self.long_label = self.name_bed_cytoBand - sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - - # Sort processing - subtools.sort(self.input_bed_cytoBand_false_path, sortedBedFile.name) - - # bedToBigBed processing - # TODO: Change the name of the bb, to tool + genome + .bb - trackName = "".join( ( self.name_bed_cytoBand, '.bb' ) ) - myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) - - auto_sql_option = os.path.join(self.tool_directory, 'cytoBandIdeo.as') - - with open(myBigBedFilePath, 'w') as bigBedFile: - subtools.bedToBigBed(sortedBedFile.name, - self.chromSizesFile.name, - bigBedFile.name, - typeOption='bed4+1', - tab='True', - autoSql=auto_sql_option) - - # Create the Track Object - self.createTrack(file_path=trackName, - track_name='cytoBandIdeo', - long_label=self.long_label, - track_type='bigBed', - visibility='dense', - priority=self.priority, - track_file=myBigBedFilePath, - track_color=self.track_color, - group_name=self.group_name, - database=self.database) - - # dataURL = "tracks/%s" % trackName - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bed_simple_repeats, - # shortLabel=self.getShortName( self.name_bed_simple_repeats ), - # trackDataURL=dataURL, - # trackType='bigBed 4 +', - # visibility='dense', - # priority=self.priority, - # ) - # - # self.track = Track( - # trackFile=myBigBedFilePath, - # trackDb=trackDb, - # ) - - print("- Bed splice junctions %s created" % self.name_bed_cytoBand) - #print("- %s created in %s" % (trackName, myBigBedFilePath)) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/Datatype.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/Datatype.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,98 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +Super Class of the managed datatype +""" + +import os +import tempfile +import collections +import util +import logging +import abc +from abc import ABCMeta +from TrackDb import TrackDb +from datatypes.validators.DataValidation import DataValidation + + +class Datatype(object): + __metaclass__ = ABCMeta + + twoBitFile = None + chromSizesFile = None + input_fasta_file = None + extra_files_path = None + tool_directory = None + + mySpecieFolderPath = None + myTrackFolderPath = None + + + def __init__(self): + not_init_message = "The {0} is not initialized." \ + "Did you use pre_init static method first?" + if Datatype.input_fasta_file is None: + raise TypeError(not_init_message.format('reference genome')) + if Datatype.extra_files_path is None: + raise TypeError(not_init_message.format('track Hub path')) + if Datatype.tool_directory is None: + raise TypeError(not_init_message.format('tool directory')) + self.inputFile = None + self.trackType = None + self.dataType = None + self.track = None + self.trackSettings = dict() + self.extraSettings = collections.OrderedDict() + + @staticmethod + def pre_init(reference_genome, two_bit_path, chrom_sizes_file, + extra_files_path, tool_directory, specie_folder, tracks_folder): + Datatype.extra_files_path = extra_files_path + Datatype.tool_directory = tool_directory + + # TODO: All this should be in TrackHub and not in Datatype + Datatype.mySpecieFolderPath = specie_folder + Datatype.myTrackFolderPath = tracks_folder + + Datatype.input_fasta_file = reference_genome + + # 2bit file creation from input fasta + Datatype.twoBitFile = two_bit_path + Datatype.chromSizesFile = chrom_sizes_file + + def generateCustomTrack(self): + self.validateData() + self.initSettings() + #Create the track file + self.createTrack() + # Create the TrackDb Object + self.createTrackDb() + logging.debug("- %s %s created", self.dataType, self.trackName) + + + @abc.abstractmethod + def validateData(self): + """validate the input data with DataValidation""" + + def initSettings(self): + #Initialize required fields: trackName, longLabel, shortLable + self.trackName = self.trackSettings["name"] + if self.trackSettings["long_label"]: + self.longLabel = self.trackSettings["long_label"] + else: + self.longLabel = self.trackName + if not "short_label" in self.trackSettings: + self.shortLabel = "" + else: + self.shortLabel = self.trackSettings["short_label"] + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + + + @abc.abstractmethod + def createTrack(self): + """Create the final track file""" + + def createTrackDb(self): + self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings) + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/Bam.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/binary/Bam.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,53 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +Class to handle Bam files to UCSC TrackHub +""" + +import logging +import os +import shutil + +from Binary import Binary +from datatypes.validators.DataValidation import DataValidation + + + +class Bam(Binary): + def __init__(self, input_bam_false_path, data_bam): + super(Bam, self).__init__() + self.inputFile = input_bam_false_path + self.trackSettings = data_bam + self.dataType = "bam" + self.trackType = "bam" + + + def initSettings(self): + super(Bam, self).initSettings() + if ".bam" not in self.trackName: + self.trackName = self.trackName + ".bam" + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "pack" + self.extraSettings["priority"] = self.trackSettings["order_index"] + + def validateData(self): + self.validator = DataValidation(self.inputFile, self.dataType, self.chromSizesFile.name) + self.validator.validate() + + def createTrack(self): + super(Bam, self).createTrack() + self._moveBamIndex() + + def _moveBamIndex(self): + # Create and add the bam index file to the same folder + self.index_bam = self.trackSettings["index"] + name_index_bam = self.trackName + ".bai" + bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam) + shutil.copyfile(self.index_bam, bam_index_file_path) + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/Bam.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/BigBed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/binary/BigBed.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,83 @@ +#!/usr/bin/python + +import os +import shutil +from subprocess import Popen, PIPE +import re +import logging + +# Internal dependencies +from Binary import Binary +from datatypes.validators.DataValidation import DataValidation +from util.index.DatabaseIndex import DatabaseIndex +from util.index.TrixIndex import TrixIndex + + +class BigBed(Binary): + def __init__(self, input_bigbed_path, data_bigbed): + super(BigBed, self).__init__() + self.inputFile = input_bigbed_path + self.trackSettings = data_bigbed + self.trackType = self._determine_track_type(self.inputFile) + self.dataType = self.trackType.replace(' ', '') + self.seqType = None + self.logger = logging.getLogger(__name__) + + def initSettings(self): + super(BigBed, self).initSettings() + self.trackName = "".join( ( self.trackName, ".bigbed" ) ) + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "dense" + self.extraSettings["priority"] = self.trackSettings["order_index"] + if "database" in self.trackSettings: + self.database_settings = DatabaseIndex(database=self.trackSettings["database"], seqType=self.seqType).setExtLink() + self.extraSettings.update(self.database_settings) + if "index_ix" in self.trackSettings and "index_ixx" in self.trackSettings: + self.trix_id = self.trackSettings.get("trix_id") + if not self.trix_id: + self.logger.info("Didn't specify the ID for Trix index for BigBed file: %s. \n Will use \"name\" as default", self.trackName) + self.trix_id = "name" + self.trix_settings = TrixIndex(indexIx=self.trackSettings["index_ix"], indexIxx=self.trackSettings["index_ixx"], trackName=self.trackName, mySpecieFolderPath=self.mySpecieFolderPath, trixId=self.trix_id).setExtLink() + self.extraSettings.update(self.trix_settings) + + def validateData(self): + self.validator = DataValidation(self.inputFile, self.dataType, self.chromSizesFile.name) + self.validator.validate() + + + def getValidateType(self): + return self._determine_track_type(self.inputFile) + + def _determine_track_type(self, bb_file): + """ + Determine the number of standard and extra fields using bigBedSummary + + Implementation of reading from stdout is based on a Stackoverflow post: + http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate + + :param bb_file: path to a bigBed file + + :returns: the bigBed track type + """ + + cmd_ph = Popen(["bigBedSummary", "-fields", bb_file, "stdout"], + stdout=PIPE, bufsize=1) + + pattern = r"(\d+) bed definition fields, (\d+) total fields" + + with cmd_ph.stdout: + for line in iter(cmd_ph.stdout.readline, b''): + match = re.match(pattern, line) + + if match: + extra_mark = "." if match.group(1) == match.group(2) else "+" + bed_type = "bigBed %s %s" % (match.group(1), extra_mark) + break + + cmd_ph.wait() + + return bed_type |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/BigBed.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/BigWig.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/binary/BigWig.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,65 @@ +#!/usr/bin/python + +import os +import shutil +from subprocess import Popen, PIPE +import re + +# Internal dependencies +from Binary import Binary +from datatypes.validators.DataValidation import DataValidation + + + +class BigWig(Binary): + def __init__(self, input_bigwig_path, data_bigwig): + super(BigWig, self).__init__() + self.inputFile = input_bigwig_path + self.trackSettings = data_bigwig + self.dataType = "bigWig" + self.trackType=self._determine_track_type(self.inputFile) + + def initSettings(self): + super(BigWig, self).initSettings() + self.trackName = "".join( ( self.trackName, ".bigwig" ) ) + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "dense" + self.extraSettings["priority"] = self.trackSettings["order_index"] + self.extraSettings["autoScale"] = "on" + self.extraSettings["maxHeightPixels"] = "100:32:8" + self.extraSettings["windowingFunction"] = "mean+whiskers" + + def validateData(self): + self.validator = DataValidation(self.inputFile, self.dataType, self.chromSizesFile.name) + self.validator.validate() + + def _determine_track_type(self, bw_file): + """ + bigWig tracks must declare the expected signal range for the data + (See https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html). + This method determines the range of values for a bigWig file using + the bigWigInfo program. + + Implementation of reading from stdout is based on a Stackoverflow post: + http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate + + :param bw_file: path to a bigWig file + + :returns: the bigWig track type + """ + cmd_ph = Popen(["bigWigInfo", "-minMax", bw_file], + stdout=PIPE, bufsize=1) + + with cmd_ph.stdout: + for line in iter(cmd_ph.stdout.readline, b''): + bw_type = "bigWig %s" % line.rstrip() + + cmd_ph.wait() + + return bw_type + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/BigWig.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/Binary.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/binary/Binary.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,31 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +Super Class of the managed datatype +""" + +import os +import tempfile +import collections +import shutil +import util +from TrackDb import TrackDb +from datatypes.Datatype import Datatype + + +class Binary(Datatype): + + def __init__(self): + super(Binary, self).__init__() + + + def createTrack(self): + shutil.copy(self.inputFile, self.trackDataURL) + + + + + + + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/binary/Binary.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/converters/DataConversion.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/converters/DataConversion.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,75 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +This class handles the subprocess calls of the different tools used +in HubArchiveCreator +""" + +import logging +import os +import subprocess +import sys +import string +import tempfile + +from util import subtools + +class DataConversion(object): + + CONVERT_OPERATIONS = {("bed", "bigbed"): "bedtobigbed", + ("bed", "bigpsl"): "bedtobigbed", + ("psl", "bigpsl"): "psltobigbed", + ("fasta", "twobit"): "fatotwobit", + ("gtf", "biggenepred"): "gtftobiggenepred", + ("gff3", "biggenepred"): "gff3tobiggenepred" + } + + + def __init__(self, inputFile, outputFile, chromSizesFile, operateType, options=None): + self.chromSizesFile = chromSizesFile + self.inputFile = inputFile + self.outputFile = outputFile + self.operateType = operateType + self.options = options + if not self.operateType or not self.inputFile: + raise TypeError("the operateType or the input file is not specified!\n") + + def convertFormats(self): + convertMethod = self.CONVERT_OPERATIONS[self.operateType] + if convertMethod == "bedtobigbed": + sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") + subtools.sort(self.inputFile, sortedBedFile.name) + subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile, self.outputFile, self.options) + + elif convertMethod == "psltobigbed": + unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl') + sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl') + subtools.pslToBigPsl(self.inputFile, unsorted_bed_formatted_psl_file.name) + subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name) + subtools.bedToBigBed(sorted_bed_formatted_psl_file.name, self.chromSizesFile, self.outputFile, self.options) + + elif convertMethod == "fatotwobit": + subtools.faToTwoBit(self.inputFile, self.outputFile) + + elif convertMethod == "gtftobiggenepred": + unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") + unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") + sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") + subtools.gtfToGenePred(self.inputFile, unsorted_genePred_file.name) + subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name) + subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name) + subtools.bedToBigBed(sorted_bigGenePred_file.name, self.chromSizesFile, self.outputFile, self.options) + + elif convertMethod == "gff3tobiggenepred": + unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") + unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") + sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") + subtools.gff3ToGenePred(self.inputFile, unsorted_genePred_file.name) + subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name) + subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name) + subtools.bedToBigBed(sorted_bigGenePred_file.name, self.chromSizesFile, self.outputFile, self.options) + + else: + raise Exception("the operation is not defined!\n") + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Bed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/Bed.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,70 @@ +#!/usr/bin/python + +import os +import tempfile +import logging + +# Internal dependencies +from Interval import Interval +from datatypes.validators.DataValidation import DataValidation +from datatypes.converters.DataConversion import DataConversion + +class Bed(Interval): + def __init__(self, inputBedGeneric, data_bed_generic): + super(Bed, self).__init__() + self.inputFile = inputBedGeneric + self.trackSettings = data_bed_generic + self.bedFields = None + self.extFields = None + self.dataType = "bed" + + + def initSettings(self): + super(Bed, self).initSettings() + self.trackType = self._determine_track_type() + self.trackName = "".join( ( self.trackName, ".bb") ) + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "dense" + self.extraSettings["priority"] = self.trackSettings["order_index"] + + def createTrack(self): + #self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") + #subtools.sort(self.inputFile, self.sortedBedFile.name) + self.convertType = self.getConvertType() + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType) + self.converter.convertFormats() + + def validateData(self): + self.validator = DataValidation(self.inputFile, self.getValidateType(), self.chromSizesFile.name) + self.validator.validate() + + def _getBedFields(self): + """count number of bed fields for generic bed format""" + with open(self.inputFile, 'r') as bed: + l = bed.readline().split() + return len(l) + + def getValidateType(self): + if not self.bedFields: + logging.debug("bedFields is not defined, consider the file as Bed generic format, datatype = bed%s", str(self.bedFields)) + self.bedFields = self._getBedFields() + return self.dataType + str(self.bedFields) + elif not self.extFields: + return self.dataType + str(self.bedFields) + else: + return self.dataType + str(self.bedFields) + "+" + str(self.extFields) + + def _determine_track_type(self): + if not self.bedFields: + return "bigBed" + else: + if not self.extFields: + extra_mark = "." + else: + extra_mark = "+" + return "bigBed %s %s" % (str(self.bedFields), extra_mark) + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Bed.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/BedBlastAlignments.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/BedBlastAlignments.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,17 @@ +#!/usr/bin/python + +import os +import tempfile +import string + +from BigPsl import BigPsl +from util import subtools + + +class BedBlastAlignments( BigPsl ): + def __init__(self, input_bed_blast_alignments_false_path, data_bed_blast_alignments): + + super(BedBlastAlignments, self).__init__(input_bed_blast_alignments_false_path, data_bed_blast_alignments) + self.seqType = 2 + self.trackType = "bigBed 12 +" + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/BedBlatAlignments.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/BedBlatAlignments.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,17 @@ +#!/usr/bin/python + +import os +import tempfile +import string + +from BigPsl import BigPsl +from util import subtools + + +class BedBlatAlignments( BigPsl ): + def __init__(self, input_bed_blast_alignments_false_path, data_bed_blast_alignments): + + super(BedBlatAlignments, self).__init__(input_bed_blast_alignments_false_path, data_bed_blast_alignments) + self.seqType = 1 + + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/BedSimpleRepeats.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/BedSimpleRepeats.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,30 @@ +#!/usr/bin/python + +import os +import tempfile + +from Bed import Bed +from datatypes.validators.DataValidation import DataValidation +from datatypes.converters.DataConversion import DataConversion + + +class BedSimpleRepeats( Bed ): + def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats): + + super(BedSimpleRepeats, self).__init__(input_bed_simple_repeats_false_path, data_bed_simple_repeats) + self.bedFields = 4 + self.extFields = 12 + self.autoSql = os.path.join(self.tool_directory, 'trf_simpleRepeat.as') + + def validateData(self): + self.validateOptions = self.getValidateOptions(tab="True", autoSql=self.autoSql) + self.validator = DataValidation(self.inputFile, self.getValidateType(), self.chromSizesFile.name, self.validateOptions) + self.validator.validate() + + + def createTrack(self): + self.convertType = self.getConvertType() + self.options = self.getConvertOptions(typeOption=self.getValidateType(), tab="True", autoSql=self.autoSql) + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType, self.options) + self.converter.convertFormats() + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/BedSpliceJunctions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/BedSpliceJunctions.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,30 @@ +#!/usr/bin/python + +import os +import tempfile + +from Bed import Bed +from datatypes.validators.DataValidation import DataValidation +from datatypes.converters.DataConversion import DataConversion + + + +class BedSpliceJunctions( Bed ): + def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions): + + super(BedSpliceJunctions, self).__init__(input_bed_splice_junctions_false_path, data_bed_splice_junctions) + self.bedFields = 12 + self.extFields = 1 + self.autoSql = os.path.join(self.tool_directory, 'spliceJunctions.as') + + def validateData(self): + self.validateOptions = self.getValidateOptions(tab="True", autoSql=self.autoSql) + self.validator = DataValidation(self.inputFile, self.getValidateType(), self.chromSizesFile.name, self.validateOptions) + self.validator.validate() + + def createTrack(self): + self.convertType = self.getConvertType() + self.options = self.getConvertOptions(typeOption=self.getValidateType(), tab="True", autoSql=self.autoSql) + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType, self.options) + self.converter.convertFormats() + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/BigPsl.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/BigPsl.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,79 @@ +#!/usr/bin/python + +import os +import tempfile +import string +import logging + +from Interval import Interval +from util.index.DatabaseIndex import DatabaseIndex +from util.index.TrixIndex import TrixIndex +from datatypes.validators.DataValidation import DataValidation +from datatypes.converters.DataConversion import DataConversion + + +class BigPsl(Interval): + def __init__(self, input_bigpsl_false_path, data_bigpsl): + + super(BigPsl, self).__init__() + self.inputFile = input_bigpsl_false_path + self.trackSettings = data_bigpsl + self.trackType = "bigPsl" + self.dataType = "bed" + self.bedFields = 12 + self.extFields = 12 + self.seqType = None + self.autoSql = os.path.join(self.tool_directory, 'bigPsl.as') + self.logger = logging.getLogger(__name__) + + def initSettings(self): + super(BigPsl, self).initSettings() + self.trackName = "".join( ( self.trackName, ".bb") ) + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "dense" + self.extraSettings["priority"] = self.trackSettings["order_index"] + if self.seqType is None: + self.seqType = self._getSeqType() + if "database" in self.trackSettings: + self.database_settings = DatabaseIndex(database=self.trackSettings["database"], seqType=self.seqType).setExtLink() + self.extraSettings.update(self.database_settings) + if "index_ix" in self.trackSettings and "index_ixx" in self.trackSettings: + self.trix_id = self.extraSettings.get("trix_id") + if not self.trix_id: + self.logger.info("Didn't specify the ID for Trix index for BigBed file: %s. \n Will use \"name\" as default", self.trackName) + self.trix_id = "name" + self.trix_settings = TrixIndex(indexIx=self.trackSettings["index_ix"], indexIxx=self.trackSettings["index_ixx"], trackName=self.trackName, mySpecieFolderPath=self.mySpecieFolderPath, trixId=self.trix_id).setExtLink() + self.extraSettings.update(self.trix_settings) + self.extraIndex = self.trix_id + else: + self.extraIndex = "name" + self.extraSettings["searchIndex"] = "name" + + + def validateData(self): + self.validateOptions = self.getValidateOptions(tab="True", autoSql=self.autoSql) + self.validator = DataValidation(self.inputFile, self.getValidateType(), self.chromSizesFile.name, self.validateOptions) + self.validator.validate() + + def createTrack(self): + self.convertType = self.getConvertType() + self.options = self.getConvertOptions(typeOption=self.getValidateType(), tab="True", autoSql=self.autoSql, extraIndex=self.extraIndex) + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType, self.options) + self.converter.convertFormats() + + def getValidateType(self): + if not self.bedFields or not self.extFields: + raise Exception("Invalid bigPsl format, no {0} or {1}".format("bedFields", "extFields")) + return self.dataType + str(self.bedFields) + "+" + str(self.extFields) + + def _getSeqType(self): + with open(self.inputFile, "r") as bigpsl: + sampleSeq = bigpsl.readline().split() + if len(sampleSeq) == 25: + return sampleSeq[-1] + else: + return None |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/CytoBand.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/CytoBand.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,32 @@ +#!/usr/bin/python + +import os +import tempfile + +from Bed import Bed +from TrackDb import TrackDb +from datatypes.validators.DataValidation import DataValidation +from datatypes.converters.DataConversion import DataConversion + + +class CytoBand( Bed ): + def __init__(self, input_bed_cytoBand_false_path, data_bed_cytoBand): + + super(CytoBand, self).__init__(input_bed_cytoBand_false_path, data_bed_cytoBand) + self.bedFields = 4 + self.extFields = 1 + self.autoSql = os.path.join(self.tool_directory, 'cytoBandIdeo.as') + + def validateData(self): + self.validateOptions = self.getValidateOptions(tab="True", autoSql=self.autoSql) + self.validator = DataValidation(self.inputFile, self.getValidateType(), self.chromSizesFile.name, self.validateOptions) + self.validator.validate() + + def createTrack(self): + self.convertType = self.getConvertType() + self.options = self.getConvertOptions(typeOption=self.getValidateType(), tab="True", autoSql=self.autoSql) + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType, self.options) + self.converter.convertFormats() + + def createTrackDb(self): + self.track = TrackDb('cytoBandIdeo', self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/CytoBand.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Gff.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/Gff.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,52 @@ +#!/usr/bin/python + +import os +import tempfile +import abc + +# Internal dependencies +from Interval import Interval +from datatypes.validators.DataValidation import DataValidation +from datatypes.converters.DataConversion import DataConversion + +class Gff(Interval): + def __init__(self): + super(Gff, self).__init__() + self.trackType = "bigGenePred" + self.autoSql = os.path.join(self.tool_directory, 'bigGenePred.as') + + def initSettings(self): + super(Gff, self).initSettings() + self.trackName = "".join( ( self.trackName, ".bb") ) + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "dense" + self.extraSettings["priority"] = self.trackSettings["order_index"] + + def createTrack(self): + self.convertType = self.getConvertType() + self.options = self.getConvertOptions(typeOption="bed12+8", tab="True", autoSql=self.autoSql) + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType, self.options) + self.converter.convertFormats() + + + @abc.abstractmethod + def getConvertType(self): + """return tuple: (dataType, trackType)""" + return (self.dataType.lower(), self.trackType.lower()) + + + def getConvertOptions(self, typeOption=None, tab=None, autoSql=None, extraIndex=None): + options = dict() + if typeOption: + options["typeOption"] = typeOption + if tab: + options["tab"] = tab + if autoSql: + options["autoSql"] = autoSql + if extraIndex: + options["extraIndex"] = extraIndex + return options \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Gff.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Gff3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/Gff3.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,24 @@ +#!/usr/bin/python + +import os +import tempfile + +# Internal dependencies +from Gff import Gff +from datatypes.validators.Gff3Validation import Gff3Validation + + +class Gff3( Gff ): + def __init__(self, input_Gff3_false_path, data_gff3): + super( Gff3, self ).__init__() + self.inputFile = input_Gff3_false_path + self.trackSettings = data_gff3 + self.dataType = "gff3" + + def getConvertType(self): + return (self.dataType.lower(), self.trackType.lower()) + + def validateData(self): + self.validator = Gff3Validation(self.inputFile, self.dataType, self.chromSizesFile.name) + self.inputFile = self.validator.validate() + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Gff3.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Gtf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/Gtf.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,25 @@ +#!/usr/bin/python + +import os +import tempfile + +# Internal dependencies +from Gff import Gff +from datatypes.validators.GtfValidation import GtfValidation + + +class Gtf(Gff): + def __init__( self, input_gtf_false_path, data_gtf): + + super(Gtf, self).__init__() + self.inputFile = input_gtf_false_path + self.trackSettings = data_gtf + self.dataType = "gtf" + + def getConvertType(self): + return (self.dataType.lower(), self.trackType.lower()) + + def validateData(self): + self.validator = GtfValidation(self.inputFile, self.dataType, self.chromSizesFile.name) + self.inputFile = self.validator.validate() + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Gtf.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Interval.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/Interval.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,50 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +Super Class of the managed datatype +""" + +import os +import tempfile +import collections +import shutil +import abc +import util +from TrackDb import TrackDb +from datatypes.Datatype import Datatype + + +class Interval(Datatype): + + def __init__(self): + super(Interval, self).__init__() + + def getConvertType(self): + return (self.dataType.lower(), self.trackType.split()[0].lower()) + + def getValidateOptions(self, tab=None, autoSql=None): + options = dict() + if tab: + options["tab"] = tab + if autoSql: + options["autoSql"] = autoSql + return options + + def getConvertOptions(self, typeOption=None, tab=None, autoSql=None, extraIndex=None): + options = dict() + if typeOption: + options["typeOption"] = typeOption + if tab: + options["tab"] = tab + if autoSql: + options["autoSql"] = autoSql + if extraIndex: + options["extraIndex"] = extraIndex + return options + + + + + + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Interval.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/interval/Psl.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/interval/Psl.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,42 @@ +import logging +import os +import tempfile + +# Internal dependencies +from Interval import Interval +from datatypes.validators.PslValidation import PslValidation +from datatypes.converters.DataConversion import DataConversion + + +class Psl(Interval): + def __init__(self, input_psl_path, data_psl): + super(Psl, self).__init__() + self.inputFile = input_psl_path + self.trackSettings = data_psl + self.dataType = "psl" + self.trackType = "bigPsl" + self.autoSql = os.path.join(self.tool_directory, 'bigPsl.as') + + def initSettings(self): + super(Psl, self).initSettings() + self.trackName = "".join( ( self.trackName, ".bb") ) + self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) + if "track_color" in self.trackSettings: + self.extraSettings["color"] = self.trackSettings["track_color"] + if "group_name" in self.trackSettings: + self.extraSettings["group"] = self.trackSettings["group_name"] + self.extraSettings["visibility"] = "dense" + self.extraSettings["priority"] = self.trackSettings["order_index"] + + def validateData(self): + self.validator = PslValidation(self.inputFile, self.dataType, self.chromSizesFile) + self.validator.validate() + + def createTrack(self): + self.convertType = self.getConvertType() + self.options = self.getConvertOptions("bed12+12", tab="True", autoSql=self.autoSql, extraIndex="name") + self.converter = DataConversion(self.inputFile, self.trackDataURL, self.chromSizesFile.name, self.convertType, self.options) + self.converter.convertFormats() + + def getConvertType(self): + return (self.dataType.lower(), self.trackType.lower()) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/sequence/Fasta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/sequence/Fasta.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,16 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +Class describing the Fasta format +(As of the 07/20/2016, only used with the reference genome) +""" + +class Fasta(object): + def __init__(self, false_path, name, assembly_id): + self.false_path = false_path + self.name = name + + if not assembly_id: + assembly_id = "unknown" + self.assembly_id = assembly_id \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/sequence/Fasta.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/sequence/__init__.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/DataValidation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/validators/DataValidation.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,43 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +This class handles the subprocess calls of the different tools used +in HubArchiveCreator +""" + +import logging +import os +import subprocess +import sys +import string +import tempfile +import re + +from util import subtools + + +class DataValidation(object): + BED_TYPE = re.compile(r'bed([1-9][0-9]?)\+?([1-9][0-9]?)?$') + BIGBED_TYPE = re.compile(r'bigBed([1-9][0-9]?)\+?([1-9][0-9]?)?$') + FILE_TYPE = ["fasta", "fastq", "bam", "bigwig", "bed", "bigbed", "bedgraph"] + + def __init__(self, inputFile, fileType, chromSizesFile, options=None): + self.inputFile = inputFile + self.fileType = fileType + self.chromSizesFile = chromSizesFile + self.options = options + + def validate(self): + """validate input file format""" + if self._checkDatatype(): + subtools.validateFiles(self.inputFile, self.chromSizesFile, self.fileType, self.options) + else: + raise TypeError("validateFiles cannot validate format {0}. Only the following formats can be validated by this tool: \n{1}\n".format(self.fileType, self.FILE_TYPE)) + + def _checkDatatype(self): + if re.match(self.BED_TYPE, self.fileType) or re.match(self.BIGBED_TYPE, self.fileType): + return True + elif self.fileType.lower() in self.FILE_TYPE: + return True + return False |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/DataValidation.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/Gff3Validation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/validators/Gff3Validation.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,48 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +This class handles the subprocess calls of the different tools used +in HubArchiveCreator +""" + +import logging +import os +import subprocess +import sys +import string +import tempfile +import re + +from DataValidation import DataValidation + + + +class Gff3Validation(DataValidation): + + def __init__(self, inputFile, fileType, chromSizesFile, options=None): + super(Gff3Validation, self).__init__(inputFile, fileType, chromSizesFile, options) + + def validate(self): + """validate input file format""" + if self._removeExtraHeader() > 1: + print("- Warning: Gff3 created with a modified version of your Gff3 by removing extra headers '##gff-version 3'.") + return self.inputFile + + def _removeExtraHeader(self): + """ + Remove extra meta line: ##gff-version 3 + """ + valid_gff3_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gff3", delete=False) + valid = open(valid_gff3_file.name, 'w') + num = 0 + with open(self.inputFile, 'r') as f: + for line in f: + if '##gff-version 3' in line: + if num == 0: + num += 1 + else: + continue + valid.write(line) + self.inputFile = valid_gff3_file.name + return num |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/Gff3Validation.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/GtfValidation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/validators/GtfValidation.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,108 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +This class handles the subprocess calls of the different tools used +in HubArchiveCreator +""" + +import logging +import os +import subprocess +import sys +import string +import tempfile +import re + +from DataValidation import DataValidation + + +class GtfValidation(DataValidation): + + def __init__(self, inputFile, fileType, chromSizesFile, options=None): + super(GtfValidation, self).__init__(inputFile, fileType, chromSizesFile, options) + + def validate(self): + """validate input file format""" + self._checkAndFixGtf() + if self.is_modified: + print("- Warning: Gtf created with a modified version of your Gtf because of start/end coordinates issues.") + print("Here are the lines removed: " + self._get_str_modified_lines()) + return self.inputFile + + + + def _checkAndFixGtf(self): + """ + Call _checkAndFixGtf, check the integrity of gtf file, + if coordinates exceed chromosome size, either removed the whole line(s) or truncated to the end of the scaffold + depending on the user choice + default: remove the whole line(s) + """ + # Set the boolean telling if we had to modify the file + self.is_modified = False + self.array_modified_lines = [] + # Create a temp gtf just in case we have issues + temp_gtf = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gtf", delete=False) + + # TODO: Get the user choice and use it + # TODO: Check if the start > 0 and the end <= chromosome size + # Get the chrom.sizes into a dictionary to have a faster access + # TODO: Think about doing this in Datatype.py, so everywhere we have access to this read-only dictionary + dict_chrom_sizes = {} + with open(self.chromSizesFile, 'r') as chromSizes: + lines = chromSizes.readlines() + for line in lines: + fields = line.split() + # fields[1] should be the name of the scaffold + # fields[2] should be the size of the scaffold + # TODO: Ensure this is true for all lines + dict_chrom_sizes[fields[0]] = fields[1] + + # Parse the GTF and check each line using the chrom sizes dictionary + with open(temp_gtf.name, 'a+') as tmp: + with open(self.inputFile, 'r') as gtf: + lines = gtf.readlines() + for index, line in enumerate(lines): + # If this is not a comment, we check the fields + if not line.startswith('#'): + fields = line.split() + # We are interested in fields[0] => Seqname (scaffold) + # We are interested in fields[3] => Start of the scaffold + # We are interested in fields[4] => End of the scaffold + scaffold_size = dict_chrom_sizes[fields[0]] + start_position = fields[3] + end_position = fields[4] + + if start_position > 0 and end_position <= scaffold_size: + # We are good, so we copy this line + tmp.write(line) + tmp.write(os.linesep) + + + # The sequence is not good, we are going to process it regarding the user choice + # TODO: Process the user choice + # By default, we are assuming the user choice is to remove the lines: We don't copy it + + # If we are here, it means the gtf has been modified + else: + # We save the line for the feedback to the user + self.array_modified_lines.append(index + 1) + + if self.is_modified is False: + self.is_modified = True + else: + pass + else: + tmp.write(line) + tmp.write(os.linesep) + + # Once the process it completed, we just replace the path of the gtf + self.inputFile = temp_gtf.name + + # TODO: Manage the issue with the fact the dataset is going to still exist on the disk because of delete=False + #return modified_gtf + + def _get_str_modified_lines(self): + return ','.join(map(str, self.array_modified_lines)) + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/PslValidation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes/validators/PslValidation.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,31 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +This class handles the subprocess calls of the different tools used +in HubArchiveCreator +""" + +import logging +import os +import subprocess +import sys +import string +import tempfile +import re + +from util import subtools +from datatypes.validators.DataValidation import DataValidation + + +class PslValidation(DataValidation): + + def __init__(self, inputFile, fileType, chromSizesFile, options=None): + super(PslValidation, self).__init__(inputFile, fileType, chromSizesFile, options) + + def validate(self): + """validate input file format""" + self.pslCheck() + + def pslCheck(self): + subtools.pslCheck(self.inputFile) |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 datatypes/validators/PslValidation.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 hubArchiveCreator.py --- a/hubArchiveCreator.py Mon Jul 10 17:08:38 2017 -0400 +++ b/hubArchiveCreator.py Wed May 16 18:04:20 2018 -0400 |
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| b'@@ -5,7 +5,7 @@\n This Galaxy tool permits to prepare your files to be ready for\n Assembly Hub visualization.\n Program test arguments:\n-hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html\n+hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f \'{"false_path": "./test-data/common/dbia3.fa", "name":"dbia3"}\' -d . -u ./tools -o output.html\n """\n \n import argparse\n@@ -16,324 +16,75 @@\n import sys\n \n # Internal dependencies\n-from Bam import Bam\n-from BedSimpleRepeats import BedSimpleRepeats\n-from BedSpliceJunctions import BedSpliceJunctions\n-from Bed import Bed\n-from cytoBand import cytoBand\n-from BigWig import BigWig\n-from util.Fasta import Fasta\n-from util.Filters import TraceBackFormatter\n-from Gff3 import Gff3\n-from Gtf import Gtf\n-from Psl import Psl\n+from util.Reader import Reader\n+from util.Logger import Logger\n from TrackHub import TrackHub\n-from bigPsl import bigPsl\n-from BedBlastAlignments import BedBlastAlignments\n-from BigBed import BigBed\n+\n+\n \n # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort\n \n \n def main(argv):\n+ \n # Command Line parsing init\n parser = argparse.ArgumentParser(description=\'Create a foo.txt inside the given folder.\')\n-\n- # Reference genome mandatory\n- parser.add_argument(\'-f\', \'--fasta\', help=\'Fasta file of the reference genome\')\n-\n- # GFF3 Management\n- parser.add_argument(\'--gff3\', action=\'append\', help=\'GFF3 format\')\n-\n- # GTF Management\n- parser.add_argument(\'--gtf\', action=\'append\', help=\'GTF format\')\n-\n- # Bed4+12 (TrfBig)\n- parser.add_argument(\'--bedSimpleRepeats\', action=\'append\', help=\'Bed4+12 format, using simpleRepeats.as\')\n-\n- # Bed12+1 (regtools)\n- parser.add_argument(\'--bedSpliceJunctions\', action=\'append\', help=\'Bed12+1 format, using spliceJunctions.as\')\n-\n- # Generic Bed (Blastx transformed to bed)\n- parser.add_argument(\'--bed\', action=\'append\', help=\'Bed generic format\')\n-\n- #cytoBandIdeo\n- parser.add_argument(\'--cytoBand\', action=\'append\', help=\'Cytoband Track, using cytoBandIdeo.as\')\n-\n- # BigPsl (blat alignment)\n- parser.add_argument(\'--bigpsl\', action=\'append\', help=\'bigPsl format, using bigPsl.as\')\n-\n- # Bed12+12 (tblastn alignment)\n- parser.add_argument(\'--bedBlastAlignments\', action=\'append\', help=\'Bed12+12 format, using bigPsl.as\')\n+ parser.add_argument(\'-j\', \'--data_json\', help=\'JSON file containing the metadata of the inputs\')\n+ parser.add_argument(\'-o\', \'--output\', help=\'Name of the HTML summarizing the content of the Track Hub Archive\')\n+ \n+ # Get the args passed in parameter\n+ args = parser.parse_args()\n+ json_inputs_data = args.data_json\n+ outputFile = args.output\n \n- # BigWig Management\n- parser.add_argument(\'--bigwig\', action=\'append\', help=\'BigWig format\')\n-\n- # Bam Management\n- parser.add_argument(\'--bam\', action=\'append\', help=\'Bam format\')\n-\n- # Psl Management\n- parser.add_argument(\'--psl\', action=\'append\', help=\'Psl format\')\n-\n- # BigBed Management\n- parser.add_argument(\'--bigbed\', action=\'append\', help=\'BigBed format\')\n-\n- # TODO: Check if the running directory can have issues if we run the tool outside\n- parser.add_argument(\'-d\', \'--directory\',\n- help=\'Running tool directory, where to find the templates. Default is running directory\')\n- parser.add_argument(\'-u\', \'--ucsc_tools_path\',\n- help=\'Directory where to find the executables needed to run this tool\')\n- parser.add_argument(\'-e\', \'--extra_files_path\',\n- help=\'Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive\')\n- parser.add_argument(\'-o\', \'--output\', help=\'Name of the HTML summarizing the content of the Track Hub Archive\')\n-\n- parser.add_argument(\'-j\', \'--data_json\', help=\'Json containing the metadata of the inputs\')\n-\n- parser.add_argumen'..b'output from Galaxy, or even just file name, from user inputs, have spaces.\n- Also, it can contain \'/\' character and could break the use of os.path function.\n-\n- :param inputs_data: dict[string, dict[string, string]]\n- """\n- for key in inputs_data:\n- inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])\n-\n-\n-def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):\n- """\n- Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub\n- and update the dictionary of datatype\n-\n- :param ExtensionClass:\n- :param array_inputs:\n- :param inputs_data:\n- :type ExtensionClass: Datatype\n- :type array_inputs: list[string]\n- :type inputs_data: dict\n- :rtype: dict\n- """\n-\n- datatype_dictionary = {}\n-\n- # TODO: Optimize this double loop\n- for input_false_path in array_inputs:\n- for key, data_value in inputs_data.items():\n- if key == input_false_path:\n- logging.debug("input_false_path: " + input_false_path)\n- logging.debug("data_value: " + str(data_value))\n- extensionObject = ExtensionClass(input_false_path, data_value)\n- datatype_dictionary.update({data_value["order_index"]: extensionObject})\n- return datatype_dictionary\n-\n-def configure_logger(extra_files_path=None, debug=False):\n- if not extra_files_path:\n- raise Exception("Extra files path is not set. Stopping the application")\n-\n-\n- # All case log: log everything in a .log file\n- logger_file_name = \'\'.join([__name__, \'.log\'])\n- logging_file_path = os.path.join(extra_files_path, logger_file_name)\n-\n- logging.basicConfig(filename=logging_file_path, level=logging.DEBUG)\n-\n- log_stdout = logging.StreamHandler(sys.stdout)\n- if not debug:\n- configure_logger_user(log_stdout)\n- else:\n- configure_logger_dev(log_stdout)\n-\n- # stderr configuration\n- configure_logger_stderr()\n-\n- logging.debug(\'#### Welcome in HubArchiveCreator Debug Mode ####\\n\')\n-\n-def configure_logger_user(log_stdout=None):\n- """\n- User Logger is defined as following:\n- - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback\n- in STDOUT\n- - Still access to full, brute and traceback for errors\n- in STDERR\n- - And further access to debug if needed\n- in .log\n-\n- """\n-\n- if not log_stdout:\n- raise Exception("No log_stdout given. Stopping the application")\n-\n- # stdout for INFO / WARN / ERROR / CRITICAL\n- log_stdout.setLevel(logging.INFO)\n-\n- formatter = TraceBackFormatter(\'%(message)s\')\n-\n- log_stdout.setFormatter(formatter)\n-\n- logging.getLogger().addHandler(log_stdout)\n-\n-def configure_logger_dev(log_stdout=None):\n- """\n- Dev Logger is defined as following:\n- - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout\n- - Still access to full, brute and traceback in stderr for errors\n- - And further access to debug if needed\n-\n- """\n- if not log_stdout:\n- raise Exception("No log_stdout given. Stopping the application")\n- log_format = \'%(message)s\'\n-\n- # stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL\n- log_stdout.setLevel(logging.DEBUG)\n-\n- formatter = logging.Formatter(log_format)\n-\n- log_stdout.setFormatter(formatter)\n-\n- logging.getLogger().addHandler(log_stdout)\n-\n-def configure_logger_stderr():\n- """\n- Configure what should be logged in stderr\n- """\n- log_error = logging.StreamHandler(sys.stderr)\n- log_error.setLevel(logging.ERROR)\n- log_error_format = \'%(message)s\'\n-\n- formatter_error = logging.Formatter(log_error_format)\n-\n- log_error.setFormatter(formatter_error)\n-\n- logging.getLogger().addHandler(log_error)\n-\n if __name__ == "__main__":\n- logging.getLogger(__name__)\n main(sys.argv)\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 hubArchiveCreator.xml --- a/hubArchiveCreator.xml Mon Jul 10 17:08:38 2017 -0400 +++ b/hubArchiveCreator.xml Wed May 16 18:04:20 2018 -0400 |
| [ |
| b'@@ -1,8 +1,11 @@\n-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2">\n+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0">\n <description>\n This Galaxy tool permits to prepare your files to be ready for\n Assembly Hub visualization.\n </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n \n <requirements>\n <requirement type="package" version="340">ucsc_hac</requirement>\n@@ -23,156 +26,192 @@\n <!-- Idea: python \\ -augustus [parameters] \\ -trfBig [parameters] -->\n <command detect_errors="exit_code"><![CDATA[\n mkdir -p $output.extra_files_path;\n+ \n+ ## Dump the tool parameters into a JSON file \n+ python $json_file parameters.json;\n \n- python $__tool_directory__/hubArchiveCreator.py\n+ python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output;\n+\n \n- ## Ask the user to enter the genome name\n- --genome_name \'$genome_name\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="json_file">\n+import json\n+import sys\n \n- #import json\n+file_path = sys.argv[1]\n+#set global $data_parameter_dict = {}\n \n- #set global data_parameter_dict = {}\n+## Ask the user to enter the genome name\n+#silent $data_parameter_dict.update({"genome_name": str($genome_name)})\n+\n+## Function to retrieve the data of the inputs\n+#def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})\n+ #set false_path = str($input_to_prepare)\n+ #set $data_dict = {"false_path": $false_path}\n \n- ## Function to retrieve the data of the inputs\n- #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})\n- #set false_path = str($input_to_prepare)\n- #set name = $input_to_prepare.name\n+ #set name = str($input_to_prepare.name)\n+ #silent $data_dict.update({"name": $name})\n+ #silent $data_dict.update($extra_data_dict)\n+ ## Add the ordering by taking the tool form indexes\n+ #silent $data_dict.update({"order_index": $order_index})\n \n- #set data_dict = {"name": $name}\n- #silent data_dict.update($extra_data_dict)\n+ #if $datatype in $data_parameter_dict\n+ #silent $data_parameter_dict[$datatype].append($data_dict)\n+ #else\n+ #set array_inputs = []\n+ #silent $array_inputs.append($data_dict)\n+ #silent $data_parameter_dict.update({$datatype: $array_inputs})\n+ #end if \n+#end def\n \n- ## Add the ordering by taking the tool form indexes\n- #silent $data_dict.update({"order_index": $order_index})\n+## Get the number of digits from tracks, to have a unique integer from group index and track index\n+\n+#set temp_max_digit = 0\n \n- #silent $data_parameter_dict.update({$false_path: $data_dict})\n-\n- #end def\n+#for $g in $group\n+ #if len($g.format) > $temp_max_digit\n+ #silent temp_max_digit = len($g.format)\n+ #end if\n+#end for\n \n \n- ## Get the number of digits from tracks, to have a unique integer from group index and track index\n+#set nb_digits_max_track = len(str($temp_max_digit))\n \n- #set temp_max_digit = 0\n+## END Get the number of digits\n \n- #for $g in $group\n- #if len($g.format) > $temp_max_digit\n- #silent temp_max_digit = len($g.format)\n- #end if\n- #end for\n-\n- #set nb_digits_max_track = len(str($temp_max_digit))\n-\n- ## END Get the number of digits\n+#for $i_g, $g in enumerate( $group )\n+ #for $i, $f in enumerate( $g.format )\n+ ## Create the order index using index_group+1 concatenated with index_track\n+ #set index_group_final = str($i_g + 1)\n+ #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)\n \n- #for $i_g, $g in enumerate( $group )\n- #for $i, $f in enumerate( $g.format )\n- ## Create the order index using index_group+1 co'..b'"trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <param name="debug_mode" value="true" />\n+ <output name="output" file="trix_index_files/blast_alignment_trackhub.html">\n+ <extra_files type="file"\n+ name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"\n+ value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"\n+ compare="sim_size"\n+ />\n+ <expand macro="verify_hub_structure" test="bed_blast_alignment" />\n+ <!-- check additional trackDb settings for BLAST -->\n+ <extra_files type="file" name="myHub/Dbia3/trackDb.txt">\n+ <assert_contents>\n+ <has_text text="searchIndex"/>\n+ <has_text text="searchTrix"/>\n+ <has_text text="url"/>\n+ <has_text text="urlLabel"/>\n+ <has_text text="iframeUrl"/>\n+ <has_text text="iframeOptions"/>\n+ </assert_contents>\n+ </extra_files>\n+ <!-- check Trix index directory -->\n+ <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"\n+ value="trix_index_files/blast_out.ix" />\n+ <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"\n+ value="trix_index_files/blast_out.ixx" />\n+ </output>\n+ </test>\n \n+ <!-- Test TrixIndex for BigBed -->\n+ <test>\n+ <param name="genome_name" value="Dbia3"/>\n+ <param name="fasta_file" value="common/dbia3.fa"/>\n+ <repeat name="group">\n+ <param name="group_name" value="Default group"/>\n+ <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="bigbed"/>\n+ <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />\n+ <param name="longLabel" value="bigBed" />\n+ <param name="track_color" value="#000000"/>\n+ <conditional name="add_trix_index">\n+ <param name="add_trix_index_selector" value="yes" />\n+ <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />\n+ <param name="trix_id" value="name" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <param name="debug_mode" value="true" />\n+ <output name="output" file="trix_index_files/bigbed_trackhub.html">\n+ <extra_files type="file"\n+ name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"\n+ value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"\n+ compare="sim_size"\n+ />\n+ <expand macro="verify_hub_structure" test="big_bed">\n+ <has_text text="searchIndex"/>\n+ <has_text text="searchTrix"/>\n+ </expand>\n+\n+ <!-- check Trix index directory -->\n+ <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"\n+ value="trix_index_files/blat_out.ix" />\n+ <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"\n+ value="trix_index_files/blat_out.ixx" />\n+ </output>\n+ </test>\n+ \n </tests>\n \n <help>\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 logging.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/logging.json Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,48 @@ +{ + "version": 1, + "disable_existing_loggers": false, + "formatters": { + "simple": { + "format": "%(asctime)s - %(name)s - %(levelname)s - %(message)s" + } + }, + + "handlers": { + "console": { + "class": "logging.StreamHandler", + "level": "INFO", + "formatter": "simple", + "stream": "ext://sys.stdout" + }, + + "console_stderr": { + "class": "logging.StreamHandler", + "level": "ERROR", + "formatter": "simple", + "stream": "ext://sys.stderr" + }, + + "debug_file_handler": { + "class": "logging.handlers.RotatingFileHandler", + "level": "DEBUG", + "formatter": "simple", + "filename": "__main__.log", + "maxBytes": 10485760, + "backupCount": 20, + "encoding": "utf8" + } + }, + + "loggers": { + "Reader": { + "level": "INFO", + "handlers": ["console"], + "propagate": "yes" + } + }, + + "root": { + "level": "DEBUG", + "handlers": ["console", "console_stderr", "debug_file_handler"] + } +} \ No newline at end of file |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,79 @@ +<macros> + <xml name="verify_hub_structure" token_genome="Dbia3" token_test="common"> + <!--genomes.txt --> + <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" /> + + <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/> + <!-- hub.txt --> + <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <!-- 2bit file --> + <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" /> + <!-- groups.txt --> + <extra_files type="file" name="myHub/@GENOME@/groups.txt" value="@TEST@/myHub/@GENOME@/groups.txt" /> + <!-- description.html --> + <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/> + <!-- trackDb.txt --> + <extra_files type="file" name="myHub/@GENOME@/trackDb.txt"> + <assert_contents> + <has_text text="track"/> + <has_text text="longLabel"/> + <has_text text="shortLabel"/> + <has_text text="bigDataUrl"/> + <has_text text="type"/> + <has_text text="visibility"/> + <has_text text="thickDrawItem"/> + <has_text text="priority"/> + <has_text text="color"/> + <has_text text="group"/> + <yield /> + </assert_contents> + </extra_files> + </xml> + + <xml name="verify_hub_structure_no_track" token_genome="Dbia3" token_test="common"> + <!--genomes.txt --> + <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" /> + + <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/> + <!-- hub.txt --> + <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <!-- 2bit file --> + <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" /> + <!-- description.html --> + <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/> + </xml> + + + <xml name="add_trix_file"> + <conditional name="add_trix_index"> + <param name="add_trix_index_selector" type="select" label="Add Trix index that allow for fast look-up of free text associated with a list of identifiers." help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="trix_index" + type="data" + format="txt" + multiple="true" + min="2" + max="2" + label="Specify Trix index" + help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator" + /> + <yield /> + </when> + <when value="no"> + </when> + </conditional> + </xml> + + +</macros> \ No newline at end of file |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 templates/trackDb/layout.txt --- a/templates/trackDb/layout.txt Mon Jul 10 17:08:38 2017 -0400 +++ b/templates/trackDb/layout.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -1,92 +1,7 @@ % for trackDb in trackDbs: - % if "bigWig" in trackDb.trackType: - -track ${trackDb.trackName} -longLabel ${trackDb.longLabel} -shortLabel ${trackDb.shortLabel} -bigDataUrl ${trackDb.trackDataURL} -visibility ${trackDb.visibility} -priority ${trackDb.priority} -color ${trackDb.track_color} -group ${trackDb.group_name.lower().replace(' ', '_')} -type ${trackDb.trackType} -autoScale on -maxHeightPixels 100:32:8 -windowingFunction mean+whiskers - - % elif "bigBed 12 +" in trackDb.trackType and trackDb.database: +## See this http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html + % for key in trackDb: +${key} ${trackDb.get(key)} + % endfor -track ${trackDb.trackName} -longLabel ${trackDb.longLabel} -shortLabel ${trackDb.shortLabel} -bigDataUrl ${trackDb.trackDataURL} -type ${trackDb.trackType} -visibility ${trackDb.visibility} -thickDrawItem ${trackDb.thickDrawItem} -priority ${trackDb.priority} -color ${trackDb.track_color} -group ${trackDb.group_name.lower().replace(' ', '_')} -searchIndex name - % if "NCBI" in trackDb.database: -url https://www.ncbi.nlm.nih.gov/protein/$$ -urlLabel ${trackDb.database} Details: -iframeUrl https://www.ncbi.nlm.nih.gov/protein/$$ -iframeOptions height='600' width='800' - % elif "UniProt" in trackDb.database: -url http://www.uniprot.org/uniprot/$$ -urlLabel ${trackDb.database} Details: -iframeUrl http://www.uniprot.org/uniprot/$$ -iframeOptions height='600' width='800' - % elif "FlyBase" in trackDb.database: -url http://flybase.org/reports/$$ -urlLabel ${trackDb.database} Details: -iframeUrl http://flybase.org/reports/$$ -iframeOptions height='600' width='800' - % else: -url https://www.ncbi.nlm.nih.gov/gquery/?term=$$ -urlLabel NCBI Details: -iframeUrl https://www.ncbi.nlm.nih.gov/gquery/?term=$$ -iframeOptions height='600' width='800' - % endif - - % elif "bigPsl" in trackDb.trackType and trackDb.database: - -track ${trackDb.trackName} -longLabel ${trackDb.longLabel} -shortLabel ${trackDb.shortLabel} -bigDataUrl ${trackDb.trackDataURL} -type ${trackDb.trackType} -visibility ${trackDb.visibility} -thickDrawItem ${trackDb.thickDrawItem} -priority ${trackDb.priority} -color ${trackDb.track_color} -group ${trackDb.group_name.lower().replace(' ', '_')} -searchIndex name - % if "NCBI" in trackDb.database: -url https://www.ncbi.nlm.nih.gov/nuccore/$$ -urlLabel NCBI Details: -iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$ -iframeOptions height='600' width='800' - % else: -url https://www.ncbi.nlm.nih.gov/gquery/?term=$$ -urlLabel NCBI Details: -iframeUrl https://www.ncbi.nlm.nih.gov/gquery/?term=$$ -iframeOptions height='600' width='800' - % endif - - % else: - -## See this http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html -track ${trackDb.trackName} -longLabel ${trackDb.longLabel} -shortLabel ${trackDb.shortLabel} -bigDataUrl ${trackDb.trackDataURL} -type ${trackDb.trackType} -visibility ${trackDb.visibility} -thickDrawItem ${trackDb.thickDrawItem} -priority ${trackDb.priority} -color ${trackDb.track_color} -group ${trackDb.group_name.lower().replace(' ', '_')} -searchIndex name - % endif % endfor |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| b"@@ -0,0 +1,178 @@\n+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####\n+\n+DEBUG:root:Calling faToTwoBit:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:Calling twoBitInfo:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:Calling sort:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat\n+DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_6.dat', u'long_label': u'', u'name': u'HISAT2_Accepted_Hits', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'100'}\n+DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_207.dat\n+DEBUG:root:data_value: {u'long_label': u'', u'name': u'TBLASTN_Alignment_to_proteins', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'101'}\n+DEBUG:root:Calling sort:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:sorted_bed_file_name: /tmp/tmp1sO3E0.sortedBed\n+DEBUG:root:chrom_sizes_file_name: /tmp/tmp6FxMJO.chrom.sizes\n+DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb\n+DEBUG:root:typeOption: None\n+DEBUG:root:autoSql: None\n+DEBUG:root:tab option: False\n+DEBUG:root:Calling bedToBigBed:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_203.dat\n+DEBUG:root:data_value: {u'long_label': u'', u'name': u'Cytoband', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'107'}\n+DEBUG:root:Calling sort:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:sorted_bed_file_name: /tmp/tmpqqVa9O.sortedBed\n+DEBUG:root:chrom_sizes_file_name: /tmp/tmp6FxMJO.chrom.sizes\n+DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/tracks/Cytoband.bb\n+DEBUG:root:typeOption: bed4+1\n+DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/cytoBandIdeo.as\n+DEBUG:root:tab option: True\n+DEBUG:root:Calling bedToBigBed:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_157.dat\n+DEBUG:root:data_value: {u'long_label': u'', u'name': u'RNA-Seq_Alignment_Coverage', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'104'}\n+DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_146.dat\n+DEBUG:root:data_value: {u'long_label': u'', u'name': u'Repeating_Elements_by_TrfBig', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'102'}\n+DEBUG:root:Calling sort:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:sorted_bed_file_name: /tmp/tmpkAWfa_.sortedBed\n+DEBUG:root:chrom_sizes_file_name: /tmp/tmp6FxMJO.chrom.sizes\n+DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb\n+DEBUG:root:typeOption: bed4+12\n+DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/trf_simpleRepeat.as\n+DEBUG:root:tab option: False\n+DEBUG:root:Calling bedToBigBed:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_160.dat\n+DEBUG:root:data_value: {u'long_label': u'', u'name': u'regtools_junctions', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'108'}\n+DEBUG:root:Calling sort:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:sorted_bed_file_name: /tmp/tmpNMo1LO.sortedBed\n+DEBUG:root:chrom_sizes_file_name: /tmp/tmp6FxMJO.chrom.sizes\n+DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/tracks/regtools_junctions.bb\n+DEBUG:root:typeOp"..b", u'name': u'BLAST_alignment_bigpsl', u'database': u'NCBI', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'109'}\n+DEBUG:root:sorted_bed_file_name: /home/galaxy/galaxy/database/datasets/000/dataset_199.dat\n+DEBUG:root:chrom_sizes_file_name: /tmp/tmp6FxMJO.chrom.sizes\n+DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb\n+DEBUG:root:typeOption: bed12+12\n+DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigPsl.as\n+DEBUG:root:tab option: True\n+DEBUG:root:Calling bedToBigBed:\n+DEBUG:root:---------\n+DEBUG:root:\t\n+DEBUG:root:----- End of all_datatype_dictionary processing -----\n+DEBUG:root:all_datatype_ordered_dictionary keys are: [<BedSpliceJunctions.BedSpliceJunctions object at 0x7f780e58c9d0>, <BedBlastAlignments.BedBlastAlignments object at 0x7f780e58cf50>, <bigPsl.bigPsl object at 0x7f780e58cdd0>, <BedSimpleRepeats.BedSimpleRepeats object at 0x7f780e58cb10>, <Psl.Psl object at 0x7f780e58ce10>, <Bam.Bam object at 0x7f780e58c6d0>, <Bed.Bed object at 0x7f780e58c790>, <Gtf.Gtf object at 0x7f780e58cbd0>, <cytoBand.cytoBand object at 0x7f780e58c810>, <BigWig.BigWig object at 0x7f780e58ca10>, <Gff3.Gff3 object at 0x7f780e58cc10>]\n+DEBUG:root:----- Beginning of Track adding processing -----\n+DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_regtools_junctions_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_BLAST_alignment_bigpsl_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_BLAT_alignment_bigpsl_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_Repeating_Elements_by_TrfBig_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_blastXmlToPsl_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_HISAT2_Accepted_Hits_bam (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_TBLASTN_Alignment_to_proteins_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_StringTie_Assembled_Transcripts_bb (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track cytoBandIdeo (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_RNA_Seq_Alignment_Coverage_bigwig (in group default_group)\n+DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/185/dataset_210_files/myHub/Dbia3/groups.txt the group Default group\n+DEBUG:root:We just added track gonramp_Augustus_Gene_Predictions_bb (in group default_group)\n+DEBUG:root:----- End of Track adding processing -----\n+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####\n" |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/all_datatypes_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/all_datatypes_trackhub.html Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,103 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Cytoband.bb">Cytoband.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig">RNA-Seq_Alignment_Coverage.bigwig</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb">Repeating_Elements_by_TrfBig.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb">TBLASTN_Alignment_to_proteins.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/blastXmlToPsl.bb">blastXmlToPsl.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb">BLAT_alignment_bigpsl.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb">BLAST_alignment_bigpsl.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/regtools_junctions.bb">regtools_junctions.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,144 @@ + +track gonramp_regtools_junctions_bb +longLabel regtools junctions +shortLabel regtools junction +bigDataUrl tracks/regtools_junctions.bb +type bigBed 12 + +visibility dense +thickDrawItem off +priority 108 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_BLAST_alignment_bigpsl_bb +longLabel BLAST alignment bigpsl +shortLabel BLAST alignment b +bigDataUrl tracks/BLAST_alignment_bigpsl.bb +type bigBed 12 + +visibility dense +thickDrawItem off +priority 109 +color 0,0,0 +group default_group +searchIndex name +url https://www.ncbi.nlm.nih.gov/protein/$$ +urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/protein/$$ +iframeOptions height='600' width='800' + + +track gonramp_BLAT_alignment_bigpsl_bb +longLabel BLAT alignment bigpsl +shortLabel BLAT alignment bi +bigDataUrl tracks/BLAT_alignment_bigpsl.bb +type bigPsl +visibility dense +thickDrawItem off +priority 110 +color 0,0,0 +group default_group +searchIndex name +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$ +iframeOptions height='600' width='800' + + +track gonramp_Repeating_Elements_by_TrfBig_bb +longLabel Repeating Elements by TrfBig +shortLabel Repeating Element +bigDataUrl tracks/Repeating_Elements_by_TrfBig.bb +type bigBed 4 + +visibility dense +thickDrawItem off +priority 102 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_blastXmlToPsl_bb +longLabel blastXmlToPsl +shortLabel blastXmlToPsl +bigDataUrl tracks/blastXmlToPsl.bb +type bigPsl +visibility dense +thickDrawItem off +priority 103 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_HISAT2_Accepted_Hits_bam +longLabel HISAT2 Accepted Hits.bam +shortLabel HISAT2 Accepted H +bigDataUrl tracks/HISAT2_Accepted_Hits.bam +type bam +visibility pack +thickDrawItem off +priority 100 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_TBLASTN_Alignment_to_proteins_bb +longLabel TBLASTN Alignment to proteins +shortLabel TBLASTN Alignment +bigDataUrl tracks/TBLASTN_Alignment_to_proteins.bb +type bigBed +visibility dense +thickDrawItem off +priority 101 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_StringTie_Assembled_Transcripts_bb +longLabel StringTie Assembled Transcripts +shortLabel StringTie Assembl +bigDataUrl tracks/StringTie_Assembled_Transcripts.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 106 +color 0,0,0 +group default_group +searchIndex name + +track cytoBandIdeo +longLabel Cytoband +shortLabel Cytoband +bigDataUrl tracks/Cytoband.bb +type bigBed +visibility dense +thickDrawItem off +priority 107 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_RNA_Seq_Alignment_Coverage_bigwig +longLabel RNA-Seq Alignment Coverage +shortLabel RNA-Seq Alignment +bigDataUrl tracks/RNA-Seq_Alignment_Coverage.bigwig +visibility full +priority 104 +color 0,0,0 +group default_group +type bigWig 1.000000 39.000000 +autoScale on +maxHeightPixels 100:32:8 +windowingFunction mean+whiskers + + +track gonramp_Augustus_Gene_Predictions_bb +longLabel Augustus Gene Predictions +shortLabel Augustus Gene Pre +bigDataUrl tracks/Augustus_Gene_Predictions.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 105 +color 0,0,0 +group default_group +searchIndex name |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/Cytoband.bb |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb |
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| Binary file test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/all_datatypes/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_datatypes/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_6.dat', u'long_label': u'HISAT sequence alignment', u'name': u'HISAT2_Accepted_Hits', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x7f0ce436b650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/160/dataset_187_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_HISAT2_Accepted_Hits_bam (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/bam.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam/bam.html Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,73 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/inputs/HISAT2_Accepted_Hits.bai |
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| Binary file test-data/bam/inputs/HISAT2_Accepted_Hits.bai has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/inputs/HISAT2_Accepted_Hits.bam |
| b |
| Binary file test-data/bam/inputs/HISAT2_Accepted_Hits.bam has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_HISAT2_Accepted_Hits_bam +longLabel HISAT sequence alignment +shortLabel HISAT sequence al +bigDataUrl tracks/HISAT2_Accepted_Hits.bam +type bam +visibility pack +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam |
| b |
| Binary file test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai |
| b |
| Binary file test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bam/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,29 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_199.dat +DEBUG:root:data_value: {u'long_label': u'BLAST alignment', u'name': u'BLAST_alignment_bigpsl', u'database': u'NCBI', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:sorted_bed_file_name: /home/galaxy/galaxy/database/datasets/000/dataset_199.dat +DEBUG:root:chrom_sizes_file_name: /tmp/tmpqOqZkp.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/174/dataset_200_files/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb +DEBUG:root:typeOption: bed12+12 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigPsl.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BedBlastAlignments.BedBlastAlignments object at 0x7fef7001b410>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/174/dataset_200_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_BLAST_alignment_bigpsl_bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/blast_alignment_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/blast_alignment_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb">BLAST_alignment_bigpsl.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/inputs/BLAST_alignment_bigpsl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/inputs/BLAST_alignment_bigpsl Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,20 @@ +contig14 31613 32039 FBpp0070070 1000 - 31613 32039 0 4 141,69,156,39, 0,147,219,387, 822 1227 - 1623 396,537,606,762, 45010 129 276 0 0 +contig14 32918 33596 FBpp0070070 1000 - 32918 33596 0 6 99,57,324,18,45,126, 0,99,156,480,507,552, 153 834 - 1623 789,891,951,1278,1296,1344, 45010 276 357 36 0 +contig15 1606 2032 FBpp0070070 1000 - 1606 2032 0 4 141,69,156,39, 0,147,219,387, 822 1227 - 1623 396,537,606,762, 50014 129 276 0 0 +contig15 2911 3589 FBpp0070070 1000 - 2911 3589 0 6 99,57,324,18,45,126, 0,99,156,480,507,552, 153 834 - 1623 789,891,951,1278,1296,1344, 50014 276 357 36 0 +contig36 38740 38977 FBpp0070566 1000 + 38740 38977 0 2 213,24, 0,213, 165 405 + 2046 165,381, 45010 135 102 0 0 +contig36 38740 38977 FBpp0070567 1000 + 38740 38977 0 2 213,24, 0,213, 165 405 + 1986 165,381, 45010 135 102 0 0 +contig36 40303 40558 FBpp0070566 1000 + 40303 40558 0 1 255, 0, 606 861 + 2046 606, 45010 99 156 0 0 +contig36 40303 40558 FBpp0070567 1000 + 40303 40558 0 1 255, 0, 606 861 + 1986 606, 45010 99 156 0 0 +contig36 41724 42168 FBpp0070566 1000 + 41724 42168 0 4 102,87,30,162, 0,165,252,282, 873 1386 + 2046 873,975,1116,1224, 45010 204 177 0 0 +contig36 41724 42168 FBpp0070567 1000 + 41724 42168 0 5 102,93,9,15,162, 0,165,258,267,282, 873 1326 + 1986 873,975,1086,1131,1164, 45010 207 174 0 0 +contig36 42322 42514 FBpp0070566 1000 + 42322 42514 0 2 39,150, 0,42, 1476 1665 + 2046 1476,1515, 45010 96 93 0 0 +contig36 42322 42514 FBpp0070567 1000 + 42322 42514 0 2 39,150, 0,42, 1416 1605 + 1986 1416,1455, 45010 96 93 0 0 +contig37 8733 8970 FBpp0070566 1000 + 8733 8970 0 2 213,24, 0,213, 165 405 + 2046 165,381, 50013 135 102 0 0 +contig37 8733 8970 FBpp0070567 1000 + 8733 8970 0 2 213,24, 0,213, 165 405 + 1986 165,381, 50013 135 102 0 0 +contig37 10296 10551 FBpp0070566 1000 + 10296 10551 0 1 255, 0, 606 861 + 2046 606, 50013 99 156 0 0 +contig37 10296 10551 FBpp0070567 1000 + 10296 10551 0 1 255, 0, 606 861 + 1986 606, 50013 99 156 0 0 +contig37 11717 12161 FBpp0070566 1000 + 11717 12161 0 4 102,87,30,162, 0,165,252,282, 873 1386 + 2046 873,975,1116,1224, 50013 204 177 0 0 +contig37 11717 12161 FBpp0070567 1000 + 11717 12161 0 5 102,93,9,15,162, 0,165,258,267,282, 873 1326 + 1986 873,975,1086,1131,1164, 50013 207 174 0 0 +contig37 12315 12507 FBpp0070566 1000 + 12315 12507 0 2 39,150, 0,42, 1476 1665 + 2046 1476,1515, 50013 96 93 0 0 +contig37 12315 12507 FBpp0070567 1000 + 12315 12507 0 2 39,150, 0,42, 1416 1605 + 1986 1416,1455, 50013 96 93 0 0 |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,17 @@ + +track gonramp_BLAST_alignment_bigpsl_bb +longLabel BLAST alignment +shortLabel BLAST alignment +bigDataUrl tracks/BLAST_alignment_bigpsl.bb +type bigBed 12 + +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name +url https://www.ncbi.nlm.nih.gov/protein/$$ +urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/protein/$$ +iframeOptions height='600' width='800' + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb |
| b |
| Binary file test-data/bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blast_alignment/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blast_alignment/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,29 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_196.dat +DEBUG:root:data_value: {u'long_label': u'BLAT alignment', u'name': u'BLAT_alignment_bigpsl', u'database': u'NCBI', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:sorted_bed_file_name: /home/galaxy/galaxy/database/datasets/000/dataset_196.dat +DEBUG:root:chrom_sizes_file_name: /tmp/tmphDNrBt.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/172/dataset_198_files/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb +DEBUG:root:typeOption: bed12+12 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigPsl.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<bigPsl.bigPsl object at 0x7f9da3bd9690>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/172/dataset_198_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_BLAT_alignment_bigpsl_bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/blat_alignment_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/blat_alignment_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb">BLAT_alignment_bigpsl.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/inputs/BLAT_alignment_bigpsl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/inputs/BLAT_alignment_bigpsl Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,20 @@\n+contig1\t651\t13048\tNM_001258471\t1000\t-\t651\t13042\t0\t5\t1627,925,2096,325,177,\t0,1725,2662,11889,12220,\t348\t5635\t+\t7050\t1415,3155,4089,6185,6525,\ttaataatctgctctaggactgatagtgtacacacaacgtttgagcgttgcctaagaagttttttttaaataaatatttgtttacattgactaatcgattttttgtgttaaacaaccttataaaaaatgcgctaaacctaaaatagccaaatggatcattttaatttaaaaatatttatgcacctacagtgaatcagcggcatataaaattaattcgcattaaattcaatcgatattaaaaagtttatatattaaggagagagaatgtagagctaaataataataaaaatgacatatggggaattgatgcccaaactcaactacaaactgatcatacacaaaaccacaaataaatatgttgcgaaaggaattgtattgtgcaaacattatacatgttttacatgtactgtgtattattatcatactcggttctcagcattattgcgttaactgcattgaagaactgccggctcaggcgttatctcccttaaatgacatagtcgcccagtttaacttgccatcaataccagttcaatcaacagcttccagctatggcaatcgatcaattggaaacaatatagaaagtgttagagactctcaatctaaaaattattttactcacatgagcttcgactttatgcacaatgttttgtttgcgggtgctacaaataaaatacttaaacttaacgaaaaccttcgagtgctggccgaggctgttactgggccgttacatgattccccgcaatgtcacgctggaggctgtccggaagatattgagacatcgcttgtcaataacttcaacaaaattctagtagtaagctacgctcacgatggtattctcatagcgtgtggaagcattcgacaaggagcctgcgaaatttacagcctgccacgttttccggcaacgccccagttttttgcagttccattggctgctaacgatgaaaacgcgtctacatatgcatttgtaggtccggcgagatatgcgtggaaagaagaggatattttatatgtggggacaacatttacgaatgttggtgattatcgtcatgacgtgccagccatttcgtcccgccgacttgatgatttaaactatgctgaattttcaatacagcagtcaattataaatatcgatgtaaaatatcgggatcattttctagtcgattatatttacggctttaattcttctgaatatgcgtacttcataattgttcaaaaaaaatcacatttagctgatgaggccggttatgtaacacgcttggcacgcatttgcattacagatcctaattacgacagctatactgaaataactgttcaatgcactgcaactgaaaacaatgttgactacaatattgtaagggatgcgaaagtaactccagccagccacaaattggcgcaaaaaatgggcataaaaaaagacgatcacgttttagtaacggttttttcgccctcaagagaaataagtaatcagccagaaagtaagtctgctatgtgtatatatagcattaaagatattgaagacatgttcattgaaaatatccatctgtgttttaacggaaccacaaaagatcgaaatttgggctatatatccggcaccattaatgatggcagatgtccaatagttggttcgctcggtaacatttacaacttttgctctgtgggacttaaaataagcggagtatccccaatcactgcacacgcactttttcattttgataatgtttcagttacgtcagtcacagcaacttcaacgactgatcagcagcattctcttgcatttcttggaacgaacatgggagtaatcaaaaaagttttattatctggccaaagtccgggcgagtacgaggaaatagttgtggatgctggaaatcgtatactaccaaatacaatgatgtcgccaaaaaaagattttctttacgtactttctcaacgaaaaataactaagcttagaatcgaacactgttctgtgtacacgaattgttccgcttgcttagagtctcgggatcctttttgtggatggtgttccttggagaagcggtgcactgtacgatcaacatgccagcgagatacatctgcgtcgagatggctttcattaggtagtggacagcaatgcatagaatttgaatctattatcccagagaaaataccaatttctgaattatcgcacctgcatttaataattcgaactttgcccgaaccttttaatgcaaaataccgatgtgtttttggaaattccacccccattgatgccgaaattctggaaaacggactcggatgtgctactcccccattagatgaaagaccattaataccaacaaacactgatcatattttggtgccattgtcagtaagaagttcggagacaaataaggattttgtatcaaggaattttgctttttttgactgctcacatcatggaaattgccaggagtgtctacaaagttcctggggttgcaactggtgtatttttgataataagtgcgttcacaagtctttgcaatgccgtaacatagaaaatgctgtaagtactgttggtcactgcccccacttaaaaaaaaatcgtccggaaatacttctacccgtaagagtgccaatagaaattcggctagagattgaaaatttaccaaaacccaagagcgcacatgctggttttttatgtacaatacatattgaagctgctcagatgctactccctgctcacgttgagtcaaataaaattgtagtttgcgaaaaaacaccatatttctacgagattaatacacatgaatatcaggcgaaggttgtagttacatggaacttccagcattatgtggacaccgcaattgttacattatacaagtgtgacgtgttgggctcccatcgggaacaccctgattgcagtttgtgcgtaactcgagatccaaaatataaatgtgcttggtgcagcaactcatgtgtatataatgaaacttgcatagctgataaaaattctatcagctcaggatctaaatccgctatagaaaacgagtgcccattaccacggattgatattattaaaccattatctgggccagtcgagggtggaactcttattacaattgaaggaagtaatttgggcataagggaggaagatgttcgtggcaaaatatttattggttctgtgccttgtgaactagaaaattatcaaatatcggtaaaaattgaatgccggactggagcatcactgtacgaaatgtctgcacccataaaagttgcaaatgatgcagggtttactgaatcaagtgttcagtttcattttaagaatgtgctgttaacaggtttatatcccacaattggccctaggtcgggagggacacaattgtctttaattgggaagtttttgaacattggctcaactatgcgagcatttttagatgagtatgagtgtcatatagatgttacacaagcttcatcatcccaagttagttgtactacatcagaagcgacccaacctgaaccaatacggtcccttcatctagttattgatggtgcgaacagaacgctagaatgccagatctcaaccccaagcattaccaatacaaatccgactcgaagtaattttggttcttatcaactccgttcgctaccacggcaaccctgctctatttttaactatacacaggacccgcgtataatgcaaattaagccattgcgtagttttaaaagtggtggtcgagtcctcaccgttcatggaatatatcttaattccatccaaaaacctgaactagaagtgttttatgacaatgaaagagtaaataaaacatcttgtgtggtgatcaactctaatcaaatggaatgtccatctcctcctgtaaattacaa'..b'caattagccttcgtgcagtgccagtggtcacacctaactgtgatatagttgtaccaaaacttacattgtgcatagagcctggtgtgcacttgttaataactgggccaaatggatgtggaaaatcgagcttgtttagaatactaagtggactttggcctatatacgcaggggagttgcacataccaaggcctgtgaaagacgttccatgtatgttttacattccccaacgtccatatatgtcaatcggcagcctgtgtgatcaaattatataccctgacacgagggaagatatgaaacgcaagcatataactgaaaacgagctaagatccattttgaaaatggtcagccttgagcacatcgctcaacgggatagctttgacgttgttcgtgattggaaggatatattatccggaggtgaaaaacaacgtatggcgatagcccgtttgttttatcatagaccgcgctatgcccttcttgatgaatgcaccagtgcagtatctatagatgttgaaagctcgatttatgaaattgctaaaggaatgggaattactttgttaaccataacacacaggcctactttgtggaaatatcacacacatattttggagtttgacggtcttggaaactggcagtttagaaaaatgaattcagatgaagaacaaaaaggacaatttctatcgtagtacaaagttgtttcggggaaccgaagcttttatacccgtgcagttttgacataaacttacttatcaagattgtgtacacaacagtaatagaatacagtcttccgatttataagcaaattccacaaatcgtcaggtttttaaaatcttatataaatattataattatataattattatatataatttaaactccttttattttatttttacaattttttttaaacataactaaaaatatgattttatgcataggtgtgagcaatattaaaaaaccttaaaattttaatttg\t132..2324\t35013\t1839\t314\t0\t0\n+contig11\t22940\t30319\tNM_143649\t1000\t-\t22943\t30314\t0\t10\t103,129,86,866,171,144,95,325,88,146,\t0,156,1133,1279,6185,6416,6630,6784,7109,7233,\t274\t2475\t+\t2762\t287,390,519,605,1471,1642,1786,1881,2209,2342,\tttcggtcatagccttagattctttcacttgcctggcagtatccttcggggactgtctattctaacagtacaaatcgtttataaacattgccgtcaagtagtcattcatagtttattttcctgacgtataaaattttctaacaaaaagcggagatgtaggacgtattgcgaaggaatataagccgtacgcagccgcttagtactttgtaggtccgatttttcataaactgttttgtgcaacgataaatccaaacgtcaaagaactattatactgtcaacaatgagtgttttatcaaaatatgttgaccggattgcagaaaagtgtgaacataatgggtttacaaaacacgcttttagctatgctctagtaactagtgctatcctagcacttaccattaaagttactatcccttacgtaaaaaacgtaaatactacgtctagtgtaaggacccaaaaaggaaaaaccaatggccaactttcaccatcgacaagagatagctcagaagaggatttcaagcttgcagaggccgaaaagttattggttgcacagcagcttaaaaaaaaagctacaaataatttagttgagcctggtctaaataaggagtttttaaaacatttgcaaatgttggccaaaataatgattcctcaggccttctgctatgaaacaggattactaagcgttcatactttttgcttgatttctcgaacatttcttagtatttatgttgccgcattggagggagctcttgttaaatttatagttcgaaaggatattaagcaatttgcccttgtattgcttaaatggtttggaattgctatccctgctactttcgttaattctatgatacggtttctcgaaagtaaactgtctctggcgtttcgaactcggcttgtgcgtcactcatatcggctctattttaaaaaccaaaattactacagagtatcaaatttggacggacgcattgaaaacgcggatcatagacttacggaagatatttctgtgttcgcaaattctgtagctcatttgtatagtagcctgactaaaccatgcttcgatctgatgcttattggcttggcactaatgagatcgtctaaaaaaatgaaagctaacattataactggaccagcattatcaatcggggttattgcccttacagcccatatattaagaattgtttcaccgaagttcggacagctggtatcggaagaagcaaatagatatgggtatttaagacatatacactcccgcataataacaaatgcggaagaaattgctttttacggaggtcataaggtggaaatgcagcagctaaggcaggcatacaaccgcctggtaaatcaaatgactacaatttttaaccaaaagctttggtttataatgcttgaacaattttttatgaaatacgtttggtcgggtactggaatgattatggtatcacttccaattttgaccggcagtgacgtaggacttggaaccgttcccaacacggccatatcggaatcccgagttagcgaacgcactcaatatctaactactgctagaaatttactaatttccgcagcagacgcgattgagcgattaatgtcttcttacaaggaaatcgtgtcgcttgctggctacacatttagagtggctggtatgatggatgtctttgaggaaactgctttgggagtttattgcaagacaagtgtaatggaatccaatcagtcgaacggtattattgagtttcgtaatggaaaaccaatagcaaagggtcgcataatctattcagatgatccgaaaaatatgtcaattagccttcgtgcagtgccagtggtcacacctaactgtgatatagttgtaccaaaacttacattgtgcatagagcctggtgtgcacttgttaataactgggccaaatggatgtggaaaatcgagcttgtttagaatactaagtggactttggcctatatacgcaggggagttgcacataccaaggcctgtgaaagacgttccatgtatgttttacattccccaacgtccatatatgtcaatcggcagcctgtgtgatcaaattatataccctgacacgagggaagatatgaaacgcaagcatataactgaaaacgagctaagatccattttgaaaatggtcagccttgagcacatcgctcaacgggatagctttgacgttgttcgtgattggaaggatatattatccggaggtgaaaaacaacgtatggcgatagcccgtttgttttatcatagaccgcgctatgcccttcttgatgaatgcaccagtgcagtatctatagatgttgaaagctcgatttatgaaattgctaaaggaatgggaattactttgttaaccataacacacaggcctactttgtggaaatatcacacacatattttggagtttgacggtcttggaaactggcagtttagaaaaatgaattcagatgaagaacaaaaaggacaatttctatcgtagtacaaagttgtttcggggaaccgaagcttttatacccgtgcagttttgacataaacttacttatcaagattgtgtacacaacagtaatagaatacagtcttccgatttataagcaaattccacaaatcgtcaggtttttaaaatcttatataaatattataattatataattattatatataatttaaactccttttattttatttttacaattttttttaaacataactaaaaatatgattttatgcataggtgtgagcaatattaaaaaaccttaaaattttaatttg\t280..2472\t35013\t1839\t314\t0\t0\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,17 @@ + +track gonramp_BLAT_alignment_bigpsl_bb +longLabel BLAT alignment +shortLabel BLAT alignment +bigDataUrl tracks/BLAT_alignment_bigpsl.bb +type bigPsl +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$ +iframeOptions height='600' width='800' + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb |
| b |
| Binary file test-data/bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_blat_alignment/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_blat_alignment/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,32 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_203.dat +DEBUG:root:data_value: {u'long_label': u'Cytoband', u'name': u'Cytoband', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpyrZVK2.sortedBed +DEBUG:root:chrom_sizes_file_name: /tmp/tmpw2rT8T.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/178/dataset_204_files/myHub/Dbia3/tracks/Cytoband.bb +DEBUG:root:typeOption: bed4+1 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/cytoBandIdeo.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<cytoBand.cytoBand object at 0x7f3458e87750>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/178/dataset_204_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track cytoBandIdeo (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/cytoband_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/cytoband_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Cytoband.bb">Cytoband.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/inputs/Cytoband --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/inputs/Cytoband Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ +contig1 0 45179 contig1 gneg +contig10 0 43013 contig10 gneg +contig11 0 35013 contig11 gneg +contig12 0 56019 contig12 gneg +contig13 0 45015 contig13 gneg +contig14 0 45010 contig14 gneg +contig15 0 50014 contig15 gneg +contig16 0 45017 contig16 gneg +contig17 0 40013 contig17 gneg +contig18 0 40012 contig18 gneg +contig19 0 45013 contig19 gneg +contig2 0 45017 contig2 gneg +contig20 0 50014 contig20 gneg +contig21 0 50011 contig21 gneg +contig22 0 60010 contig22 gneg +contig23 0 50012 contig23 gneg +contig24 0 40010 contig24 gneg +contig25 0 75023 contig25 gneg +contig26 0 40013 contig26 gneg +contig27 0 50016 contig27 gneg +contig28 0 50013 contig28 gneg +contig29 0 50006 contig29 gneg +contig3 0 40006 contig3 gneg +contig30 0 70018 contig30 gneg +contig31 0 40012 contig31 gneg +contig32 0 40014 contig32 gneg +contig33 0 40016 contig33 gneg +contig34 0 50012 contig34 gneg +contig35 0 48011 contig35 gneg +contig36 0 45010 contig36 gneg +contig37 0 50013 contig37 gneg +contig38 0 50017 contig38 gneg +contig39 0 45019 contig39 gneg +contig4 0 55011 contig4 gneg +contig40 0 60015 contig40 gneg +contig41 0 60014 contig41 gneg +contig42 0 70020 contig42 gneg +contig43 0 50016 contig43 gneg +contig44 0 50013 contig44 gneg +contig45 0 50013 contig45 gneg +contig46 0 50012 contig46 gneg +contig47 0 35007 contig47 gneg +contig48 0 65012 contig48 gneg +contig49 0 30003 contig49 gneg +contig5 0 50018 contig5 gneg +contig50 0 40009 contig50 gneg +contig51 0 50015 contig51 gneg +contig52 0 40012 contig52 gneg +contig53 0 50013 contig53 gneg +contig54 0 35008 contig54 gneg +contig55 0 40015 contig55 gneg +contig56 0 55020 contig56 gneg +contig57 0 60013 contig57 gneg +contig58 0 50011 contig58 gneg +contig59 0 40011 contig59 gneg +contig6 0 40015 contig6 gneg +contig60 0 50013 contig60 gneg +contig61 0 40008 contig61 gneg +contig62 0 50017 contig62 gneg +contig63 0 55021 contig63 gneg +contig64 0 40016 contig64 gneg +contig65 0 45013 contig65 gneg +contig66 0 45011 contig66 gneg +contig67 0 44531 contig67 gneg +contig68 0 25628 contig68 gneg +contig69 0 44962 contig69 gneg +contig7 0 50017 contig7 gneg +contig70 0 55020 contig70 gneg +contig8 0 35012 contig8 gneg +contig9 0 60018 contig9 gneg |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track cytoBandIdeo +longLabel Cytoband +shortLabel Cytoband +bigDataUrl tracks/Cytoband.bb +type bigBed +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb |
| b |
| Binary file test-data/bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_cytoband/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cytoband/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,32 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1199.dat +DEBUG:root:data_value: {u'order_index': u'10', u'name': u'TBLASTN_Alignment_to_proteins', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpmC5L13.sortedBed +DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmphIusrY.chrom.sizes +DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/905/dataset_1273_files/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb +DEBUG:root:typeOption: None +DEBUG:root:autoSql: None +DEBUG:root:tab option: False +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bed.Bed object at 0x2cbbd10>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/905/dataset_1273_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track TBLASTN_Alignment_to_proteins.bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/bed_generic.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/bed_generic.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb">TBLASTN_Alignment_to_proteins.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,40 @@ +contig2 16199 18659 ci-PA 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295, +contig2 18939 20598 ci-PA 604 - 18939 20598 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485, +contig2 18712 18877 ci-PA 964 - 18712 18877 0 1 165, 0, +contig1 31366 33826 ci-PA 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295, +contig1 34106 35765 ci-PA 604 - 34106 35765 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485, +contig1 33879 34044 ci-PA 964 - 33879 34044 0 1 165, 0, +contig24 12402 12561 ci-PA 0 - 12402 12561 0 2 63,96, 0,63, +contig24 12402 12570 ci-PA 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153, +contig23 32405 32564 ci-PA 0 - 32405 32564 0 2 63,96, 0,63, +contig23 32405 32573 ci-PA 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153, +contig67 20513 20759 ci-PA 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153, +contig67 20531 20753 ci-PA 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186, +contig67 18177 18309 ci-PA 0 - 18177 18309 0 1 132, 0, +contig67 20471 20660 ci-PA 0 - 20471 20660 0 1 189, 0, +contig66 35516 35762 ci-PA 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153, +contig66 35534 35756 ci-PA 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186, +contig66 33180 33312 ci-PA 0 - 33180 33312 0 1 132, 0, +contig66 35474 35663 ci-PA 0 - 35474 35663 0 1 189, 0, +contig2 18711 20598 ci-PC 584 - 18711 20598 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716, +contig2 18601 18889 ci-PC 0 - 18601 18889 0 5 63,36,51,54,45, 0,75,123,180,243, +contig1 33878 35765 ci-PC 584 - 33878 35765 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716, +contig1 33768 34056 ci-PC 0 - 33768 34056 0 5 63,36,51,54,45, 0,75,123,180,243, +contig2 16199 18659 ci-PB 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295, +contig2 18939 20268 ci-PB 560 - 18939 20268 0 4 510,210,432,51, 0,564,774,1278, +contig2 18712 18877 ci-PB 964 - 18712 18877 0 1 165, 0, +contig1 31366 33826 ci-PB 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295, +contig1 34106 35435 ci-PB 560 - 34106 35435 0 4 510,210,432,51, 0,564,774,1278, +contig1 33879 34044 ci-PB 964 - 33879 34044 0 1 165, 0, +contig24 12402 12561 ci-PB 0 - 12402 12561 0 2 63,96, 0,63, +contig24 12402 12570 ci-PB 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153, +contig23 32405 32564 ci-PB 0 - 32405 32564 0 2 63,96, 0,63, +contig23 32405 32573 ci-PB 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153, +contig67 20513 20759 ci-PB 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153, +contig67 20531 20753 ci-PB 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186, +contig67 18177 18309 ci-PB 0 - 18177 18309 0 1 132, 0, +contig67 20471 20660 ci-PB 0 - 20471 20660 0 1 189, 0, +contig66 35516 35762 ci-PB 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153, +contig66 35534 35756 ci-PB 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186, +contig66 33180 33312 ci-PB 0 - 33180 33312 0 1 132, 0, +contig66 35474 35663 ci-PB 0 - 35474 35663 0 1 189, 0, |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + track TBLASTN_Alignment_to_proteins.bb + longLabel TBLASTN Alignment to proteins + shortLabel TBLASTN Alignme + bigDataUrl tracks/TBLASTN_Alignment_to_proteins.bb + type bigBed + visibility dense + thickDrawItem off + priority 10 + color 0,0,0 + group default_group + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb |
| b |
| Binary file test-data/bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_generic/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_generic/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email rmarenco@gwu.edu +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,32 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_146.dat +DEBUG:root:data_value: {u'long_label': u'Simple repeat', u'name': u'TrfBig_on_data_1', u'database': u'', u'track_color': u'#f79646', u'group_name': u'Simple repeats', u'order_index': u'10'} +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmptOTxHF.sortedBed +DEBUG:root:chrom_sizes_file_name: /tmp/tmpr8MCAz.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/142/dataset_169_files/myHub/Dbia3/tracks/TrfBig_on_data_1.bb +DEBUG:root:typeOption: bed4+12 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/trf_simpleRepeat.as +DEBUG:root:tab option: False +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BedSimpleRepeats.BedSimpleRepeats object at 0x7f4713fe8690>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/142/dataset_169_files/myHub/Dbia3/groups.txt the group Simple repeats +DEBUG:root:We just added track gonramp_TrfBig_on_data_1_bb (in group simple_repeats) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/bed_simple_repeats_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/bed_simple_repeats_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb">Repeating_Elements_by_TrfBig.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,602 @@\n+contig1\t9130\t9428\ttrf\t163\t1.8\t164\t86\t2\t438\t36\t12\t13\t37\t1.82\tAAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT\n+contig1\t15707\t15757\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig1\t16261\t16302\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig1\t23387\t23483\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig1\t23451\t23520\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig1\t24200\t24233\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig1\t29159\t29628\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig1\t37571\t37606\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig1\t38436\t38491\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig1\t38436\t38491\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig1\t38436\t38491\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig1\t43116\t43168\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t540\t590\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig2\t1094\t1135\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig2\t8220\t8316\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig2\t8284\t8353\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig2\t9033\t9066\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig2\t13992\t14461\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig2\t22404\t22439\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig2\t23269\t23324\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig2\t23269\t23324\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig2\t23269\t23324\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig2\t27949\t28001\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t38280\t38311\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t3265\t3296\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t17933\t17958\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig3\t19067\t19124\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig3\t23368\t23418\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig3\t24889\t25322\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig3\t26816\t26900\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig3\t26816\t26887\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig3\t26816\t26900\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT\n+contig3\t26820\t26887\ttrf\t17\t3.7\t19\t80\t20\t74\t20\t4\t0\t74\t0.99\tTTTATATATTTTTTTTTCA\n+contig3\t29468\t29515\ttrf\t25\t2.0\t23\t84\t12\t60\t34\t0\t17\t48\t1.47\tATTATAATTATGATGTTATGATG\n+contig3\t38756\t38791\ttrf\t10\t3.6\t10\t92\t7\t63\t40\t0\t0\t60\t0.97\tATTTATTTAA\n+contig3\t38758\t38788\ttrf\t9\t3.2\t9\t95\t4\t51\t40\t0\t0\t60\t0.97\tTTATTTAAA\n+contig4\t7931\t7956\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig4\t9065\t9122\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig4\t13366\t13416\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig4\t14887\t15320\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig4\t16814\t16898\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig4\t16814\t16885\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig4\t16814\t16898\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT'..b'\n+contig69\t18503\t18850\ttrf\t163\t2.1\t163\t88\t3\t502\t36\t12\t16\t35\t1.86\tCTTTGGTGCTATTTGACATATAACCTCCTAAGCTTGGAAATATCATTTTTTAATTGATTTTGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAG\n+contig69\t18536\t18888\ttrf\t163\t2.2\t161\t85\t4\t472\t36\t9\t16\t37\t1.82\tTTGGAAATACAATTTTTTATATTTATGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAGCTTTGGAGCTGTTTGACATATAACCCTATAAGA\n+contig69\t19781\t19812\ttrf\t15\t2.1\t14\t94\t5\t53\t58\t0\t0\t41\t0.98\tATATAATTATAATA\n+contig69\t23637\t24060\ttrf\t162\t2.7\t156\t83\t6\t496\t37\t11\t12\t38\t1.79\tAAAAAAATTATATCTTCGGTGCTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTAATTAGTTCTGAATTTCAATTAAATTTTATCAAAATCGGACGACTTATAGCTGCCATAGGAACGATCGAAAAATTGATGGGAAAATAAATAT\n+contig69\t36863\t36892\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+contig69\t38645\t39124\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+contig69\t43653\t44084\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t6910\t6939\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+contig70\t8692\t9171\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+contig70\t13700\t14131\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t17962\t18295\ttrf\t161\t2.1\t160\t83\t5\t413\t37\t12\t13\t35\t1.84\tAAAAAATTATATCTCTGGTGTTTTTAAACATATAACCTCCTAAACTTGGAAATAACATTTTATAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAACCCGACGACTATATCATACATGTAACTGTAACGATCGGAAAATTGATGGGAAAATAATATG\n+contig70\t19030\t19306\ttrf\t137\t2.0\t137\t94\t1\t482\t39\t13\t13\t34\t1.83\tTTTAACACATACCTTTCTAAGCTTGGATATAACATTTTTAAACTGGTTCTGAATTTCAAATTAAATTCAATTAAAATCGGACGACTATATCATATAGCTCCCATAGGAAAAATCGGAAAATTAGTGAGAAAATAATA\n+contig70\t22269\t22308\ttrf\t19\t2.1\t19\t100\t0\t78\t58\t15\t15\t10\t1.62\tAACTAAGGAAATACCAGAA\n+contig70\t22812\t23252\ttrf\t162\t2.8\t156\t84\t5\t562\t37\t11\t13\t37\t1.81\tTTCTAAGCTTGAAATAACATTTTTTAATTAGTTCTGAATTTCGAATTTAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAAATAAAAATTATATTTGTATTTTTAACATATAACC\n+contig70\t23421\t23486\ttrf\t13\t4.7\t13\t70\t20\t51\t38\t0\t0\t61\t0.96\tATATATATAATTT\n+contig70\t23426\t23479\ttrf\t7\t7.4\t7\t79\t12\t54\t35\t0\t0\t64\t0.94\tTATATTT\n+contig70\t23430\t23486\ttrf\t27\t2.0\t27\t83\t10\t69\t35\t0\t0\t64\t0.94\tATTTATATATTTATTAATATATTTTAT\n+contig70\t25576\t25606\ttrf\t12\t2.5\t12\t94\t0\t51\t33\t26\t36\t3\t1.73\tACGGACGGACAG\n+contig70\t27263\t27382\ttrf\t63\t1.9\t63\t85\t3\t168\t27\t25\t21\t26\t1.99\tATTTTTCCAAGCACTTTCCTGTACAAGGGAAACGTCCCAGGGAAAGCCTATCGGAATTTCAAA\n+contig70\t27353\t27406\ttrf\t25\t2.1\t25\t85\t0\t70\t30\t26\t32\t11\t1.91\tGGAAACGTCCCAGGGAAAGCCCATC\n+contig70\t27848\t27878\ttrf\t12\t2.5\t12\t88\t0\t51\t30\t30\t40\t0\t1.57\tACGGACGGACAG\n+contig70\t35504\t35713\ttrf\t102\t2.0\t102\t99\t0\t409\t37\t12\t13\t36\t1.82\tAAAACGATGGTAGACAAATATGCATATATTTTTTACACAAAACGAAATATAATGGACTTTTAAAAATTCTTTTTTCTATCTTTCCTGGTGGGAGATATATAT\n+contig70\t43333\t43446\ttrf\t57\t2.0\t57\t94\t0\t199\t30\t17\t22\t29\t1.97\tAATATTGGGAATAACATATTATCTTATAATATGGGAGCGCGAAGGCTCCTCGCCCAT\n+contig70\t44242\t44281\ttrf\t7\t5.7\t7\t81\t6\t53\t28\t20\t12\t38\t1.89\tTACATGT\n+contig70\t44241\t44281\ttrf\t13\t2.9\t14\t85\t7\t55\t27\t22\t12\t37\t1.90\tCTACATGTTACATG\n+contig70\t44485\t44531\ttrf\t14\t3.3\t14\t84\t0\t65\t41\t21\t10\t26\t1.86\tAACCGTATATGACT\n+contig70\t45147\t45181\ttrf\t16\t2.0\t17\t88\t11\t52\t52\t0\t2\t44\t1.16\tAAATATTAGTAATATAT\n+contig70\t46706\t46990\ttrf\t147\t1.9\t147\t100\t0\t568\t39\t10\t9\t40\t1.72\tTTCTTTATTTTTTTTATTTTAAAATACTTAGTACTTAGTAATGTCGCTAAAACCAATATAATATTCTTTAAAATTTAGAAAATATATTCAGACTTCGAATTACAAGGTGTATTAGAAGATAAATTAAACTCTAAAGCTTAATTTATC\n+contig70\t53900\t53978\ttrf\t28\t2.8\t28\t80\t5\t97\t15\t43\t5\t35\t1.69\tCTCTGTCACCCTCTCTTTACCTACCTCA\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_Repeating_Elements_by_TrfBig_bb +longLabel Simple repeat +shortLabel Simple repeat +bigDataUrl tracks/Repeating_Elements_by_TrfBig.bb +type bigBed 4 + +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb |
| b |
| Binary file test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_simple_repeats/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_simple_repeats/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,32 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_160.dat +DEBUG:root:data_value: {u'long_label': u'Splice junctions', u'name': u'regtools_junctions', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpNmrPuS.sortedBed +DEBUG:root:chrom_sizes_file_name: /tmp/tmpKM2jLb.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/175/dataset_201_files/myHub/Dbia3/tracks/regtools_junctions.bb +DEBUG:root:typeOption: bed12+1 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/spliceJunctions.as +DEBUG:root:tab option: False +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BedSpliceJunctions.BedSpliceJunctions object at 0x7f3fc157f690>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/175/dataset_201_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_regtools_junctions_bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/inputs/regtools_junctions --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/inputs/regtools_junctions Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,38 @@ +contig16 1843 11364 JUNC00000001 1000 - 1843 11364 255,0,0 2 54,80 0,9441 13 +contig16 11386 11595 JUNC00000003 1000 - 11386 11595 255,0,0 2 77,78 0,131 13 +contig16 11617 11783 JUNC00000004 1000 - 11617 11783 255,0,0 2 65,25 0,141 1 +contig16 11624 11834 JUNC00000005 1000 - 11624 11834 255,0,0 2 81,76 0,134 20 +contig16 11782 11975 JUNC00000006 1000 - 11782 11975 255,0,0 2 76,54 0,139 10 +contig16 11806 11956 JUNC00000007 1000 - 11806 11956 255,0,0 2 55,35 0,115 1 +contig16 11921 12673 JUNC00000008 1000 - 11921 12673 255,0,0 2 54,73 0,679 13 +contig16 11939 17275 JUNC00000009 1000 - 11939 17275 255,0,0 2 36,54 0,5282 1 +contig16 12733 17294 JUNC00000011 1000 - 12733 17294 255,0,0 2 78,73 0,4488 10 +contig16 12782 21003 JUNC00000012 1000 - 12782 21003 255,0,0 2 29,61 0,8160 1 +contig16 12796 21322 JUNC00000013 1000 - 12796 21322 255,0,0 2 15,75 0,8451 1 +contig16 17254 17474 JUNC00000014 1000 - 17254 17474 255,0,0 2 83,69 0,151 15 +contig16 17307 21307 JUNC00000015 1000 - 17307 21307 255,0,0 2 30,60 0,3940 1 +contig16 21007 21283 JUNC00000016 1000 - 21007 21283 255,0,0 2 54,36 0,240 1 +contig16 21263 22512 JUNC00000017 1000 - 21263 22512 255,0,0 2 73,58 0,1191 7 +contig16 21316 23083 JUNC00000018 1000 - 21316 23083 255,0,0 2 20,70 0,1697 1 +contig16 22206 25361 JUNC00000019 1000 + 22206 25361 255,0,0 2 39,51 0,3104 1 +contig16 27016 27178 JUNC00000021 1000 + 27016 27178 255,0,0 2 33,70 0,92 2 +contig16 27196 34369 JUNC00000022 1000 + 27196 34369 255,0,0 2 57,32 0,7141 1 +contig16 29358 34416 JUNC00000023 1000 + 29358 34416 255,0,0 2 11,79 0,4979 1 +contig16 34568 34752 JUNC00000024 1000 + 34568 34752 255,0,0 2 51,68 0,116 2 +contig16 34573 34763 JUNC00000025 1000 + 34573 34763 255,0,0 2 46,44 0,146 1 +contig16 34782 34954 JUNC00000026 1000 + 34782 34954 255,0,0 2 53,66 0,106 4 +contig16 35110 42519 JUNC00000027 1000 + 35110 42519 255,0,0 2 64,64 0,7345 4 +contig16 42508 43097 JUNC00000029 1000 + 42508 43097 255,0,0 2 82,65 0,524 6 +contig16 43274 43495 JUNC00000030 1000 + 43274 43495 255,0,0 2 80,75 0,146 10 +contig17 1255 2504 JUNC00000031 1000 - 1255 2504 255,0,0 2 73,58 0,1191 7 +contig17 1308 3075 JUNC00000032 1000 - 1308 3075 255,0,0 2 20,70 0,1697 1 +contig17 2198 5353 JUNC00000033 1000 + 2198 5353 255,0,0 2 39,51 0,3104 1 +contig17 7008 7170 JUNC00000035 1000 + 7008 7170 255,0,0 2 33,70 0,92 2 +contig17 7188 14361 JUNC00000036 1000 + 7188 14361 255,0,0 2 57,32 0,7141 1 +contig17 9350 14408 JUNC00000037 1000 + 9350 14408 255,0,0 2 11,79 0,4979 1 +contig17 14560 14744 JUNC00000038 1000 + 14560 14744 255,0,0 2 51,68 0,116 2 +contig17 14565 14755 JUNC00000039 1000 + 14565 14755 255,0,0 2 46,44 0,146 1 +contig17 14774 14946 JUNC00000040 1000 + 14774 14946 255,0,0 2 53,66 0,106 4 +contig17 15102 22511 JUNC00000041 1000 + 15102 22511 255,0,0 2 64,64 0,7345 4 +contig17 22500 23089 JUNC00000043 1000 + 22500 23089 255,0,0 2 82,65 0,524 6 +contig17 23265 23487 JUNC00000044 1000 + 23265 23487 255,0,0 2 81,75 0,147 11 |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_regtools_junctions_bb +longLabel Splice junctions +shortLabel Splice junctions +bigDataUrl tracks/regtools_junctions.bb +type bigBed 12 + +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb |
| b |
| Binary file test-data/bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bed_splice_junctions/splice_junctions_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_splice_junctions/splice_junctions_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/regtools_junctions.bb">regtools_junctions.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/big_bed/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_205.dat +DEBUG:root:data_value: {u'long_label': u'bigBed ', u'name': u'BLAT_alignment_bigbed', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigBed.BigBed object at 0x7fe280ba0710>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/180/dataset_206_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_BLAT_alignment_bigbed_bigbed (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/bigbed_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/big_bed/bigbed_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed">BLAT_alignment_bigbed.bigbed</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/inputs/BLAT_alignment_bigbed |
| b |
| Binary file test-data/big_bed/inputs/BLAT_alignment_bigbed has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/big_bed/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/big_bed/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_BLAT_alignment_bigbed_bigbed +longLabel bigBed +shortLabel bigBed +bigDataUrl tracks/BLAT_alignment_bigbed.bigbed +type bigBed 12 + +visibility hide +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed |
| b |
| Binary file test-data/big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/big_bed/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/big_bed/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/big_bed/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwig/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_157.dat +DEBUG:root:data_value: {u'long_label': u'RNA-Seq Coverage', u'name': u'RNA-Seq_Alignment_Coverage', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigWig.BigWig object at 0x7f8c591d1650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/167/dataset_193_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_RNA_Seq_Alignment_Coverage_bigwig (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/bigwig.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwig/bigwig.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig">RNA-Seq_Alignment_Coverage.bigwig</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/inputs/RNA-Seq_Alignment_Coverage |
| b |
| Binary file test-data/bigwig/inputs/RNA-Seq_Alignment_Coverage has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwig/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwig/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ + +track gonramp_RNA_Seq_Alignment_Coverage_bigwig +longLabel RNA-Seq Coverage +shortLabel RNA-Seq Coverage +bigDataUrl tracks/RNA-Seq_Alignment_Coverage.bigwig +visibility full +priority 10 +color 0,0,0 +group default_group +type bigWig 1.000000 39.000000 +autoScale on +maxHeightPixels 100:32:8 +windowingFunction mean+whiskers + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig |
| b |
| Binary file test-data/bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwig/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/bigwig/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwig/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_color/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_6.dat', u'long_label': u'', u'name': u'HISAT2_Accepted_Hits', u'database': u'', u'track_color': u'#8064a2', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x7f5e7d7eb650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/190/dataset_215_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_HISAT2_Accepted_Hits_bam (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/changed_color_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_color/changed_color_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,73 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_color/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_color/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_HISAT2_Accepted_Hits_bam +longLabel HISAT2 Accepted Hits.bam +shortLabel HISAT2 Accepted H +bigDataUrl tracks/HISAT2_Accepted_Hits.bam +type bam +visibility pack +thickDrawItem off +priority 10 +color 128,100,162 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam |
| b |
| Binary file test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai |
| b |
| Binary file test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_color/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_color/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_color/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_label/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_6.dat', u'long_label': u'HISAT sequence alignment', u'name': u'HISAT2_Accepted_Hits', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x7fb6792b0650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/191/dataset_216_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_HISAT2_Accepted_Hits_bam (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/changed_label_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_label/changed_label_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,73 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_label/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_label/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_HISAT2_Accepted_Hits_bam +longLabel HISAT sequence alignment +shortLabel HISAT sequence al +bigDataUrl tracks/HISAT2_Accepted_Hits.bam +type bam +visibility pack +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam |
| b |
| Binary file test-data/changed_label/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai |
| b |
| Binary file test-data/changed_label/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_label/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/changed_label/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/changed_label/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/common/Dbia3.2bit |
| b |
| Binary file test-data/common/Dbia3.2bit has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/common/dbia3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/common/dbia3.fa Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,66784 @@\n+>contig1\n+AAAACTAATTTTATCAAAATCGGACAACTATATCATATAGCTGCCATACG\n+AACGATCGGAAAATTGGTAAGTAAATAATTAAAAATATTATATCTTTGGT\n+GTGTTTTTGGAAATAACATTTTTTAATATGTTTTGAATTTTGAATTAAAT\n+TCTATCAAAATCGGACGACTATATCATATAGCTGCCATACAAACGATCGG\n+AAAATTGGTGAATAAATAATATGAAAAAATTATATCTTTGGTTATTTTTT\n+AGACAAATAACCTCCAACGCTTGGAAATAACATTTTTTAATTAGTTATAA\n+ATTTGATATTTTAATTTTATCAAAATCGGACGAATATAGCATATAGCTGT\n+TAAAATAATATGAAACAAATTATAGCTCCGGTGTTTTTTACATATTATCT\n+TATACTATTGGGAAAATAGTTTATTATATTTTAAAGAATTTCCAATTAAA\n+CTCTAACATATAGCTTTCAAAGAAACGGTCAAAAAAGTAAAGAAATCATT\n+TTTTTTTAACATCACTGAAGCTAGAAACAATCCTTAAAAATGTAACATGG\n+TGTTAGTAGCATTGAAAATTGCTTATAACTGCAAAGGGAAAACAAACATC\n+GGCTTGCCGAATGTAATTTCCATTCTTGTTTGACTTGAGTTTATAACTTA\n+CAATTATGGTAAGGTGCCTGATTTTGGTTTTTGCCATACGGTATGTGGTA\n+GTTATCATTTTGCCGTGCTATAAGTGACATCACAGCCGATTCTTTTACTC\n+CATAATGGGCCAATGTGTTGAGGCGTTTCCATCCATTTATTGTTTTTGTA\n+GTTAGGTCTTCATCTTGTAATGTGAGATGACCTCCTCTTCCATGCCTCCA\n+TTCTAAGTCAACTTCGTGCACAGATGGTCTCATAGAAAACGGAGTATTTT\n+TAAAAATTGCGTCCAAAATTTTTAATTTAACTTGCGATATGGTATCCAAA\n+TCGTTTACACGACATTGGACTTTTTCATCAAGATCATCTTGTAAAATGTG\n+CAAAATTACAACAGAATGGGTAACTTGTTCGTGGAGAAGTCGTTCCTCTG\n+AAAGTGAATAACGAGCATCGTGGGTTATTGCGTCCACCAAACCCTTTTCA\n+ATTTGATGCTTAATTGCCTTGAACAGCAAAAATAAATTAGATCCAGCATA\n+TTCTTTTAGGTAGTCGTACATACAAATTGCTAAGTAGTTTGTTAACATTT\n+TTTCAACTACGCTCTCAGTGCGTCGTAGCATTAGCTGAGGATGCTTGCTG\n+GCGAGCGATTTGTCAATTAATCGCAATAAAAGGGACTTTAAAATTTCCGT\n+CGCATATTCCATTTTGTTCATTAGAACAACCATAAGTAAAGAGGCGACGT\n+TAACTCGATCGCGAATTGAGAAAGATGACCGTTGAGCTTCTAAAGTTTCT\n+ATGAACAATAGTAAAAAATATTTGTTTCCAATAAGTTGCTCGAATTGTAT\n+CATAGCTGCATCATAGTTAGTGTGCGGGCTACTTCCACAAAATTTTCGGG\n+AGTTTAGAATAGGATGATCTGATACACCGGGAAAGAAAACTTTCATAATG\n+TAATTGACGTGATCTAACGTTGGTATACCGGTGCTCTCCAAATCTGCTGT\n+TAGATCGGTCATGTCCGTTTGGAGCTCAGCAAATGCCTGTTTACACTCAG\n+AACGAACGTTGCTTTCCAATGTTATCATCTGTATCTGAATTCGTTTGTAT\n+TCCCGTTCTGCTTGGGTCGATTTCCTTCTAAATATTATTAGTACGACAAC\n+CAAAACGATGACAAGCACTGCAACTGTCAATATAACGACAAACATGGCAT\n+GTGAAAAAACATAGGGTTTATTTAAATCATATTTCAAATATCCTATGGCG\n+AAACGAAGATTTCGCCCTACTTTAACCACAACTAGAGGTAAATCTGTCGA\n+TTGATCCACACCATTTTCATCAGTTGGGAGTGGTTGATGTTCCGGTGGAA\n+TGCACAAAAGTTGAGTTAGTGTAAGGCTTGTTATATTGCATTGAGTAGTA\n+CCAATGGTTACATTAACGTCGTATTCATCAGCTGCCAAATTTAGTAGCTC\n+GCCTTCAATAACCAAGCTGTCACCCTTGTATAGTTTAATTCCGTCATTTG\n+GAAATGGTAAATATTTTGGATCGGCTAAATAAACAATAGTGCTCCTGATA\n+TCATGAAAGTATTTATTTAGATCTCGAACAAGCTGTACATTGTCCATTAC\n+AAAACTAAGTTGTAAATTCAGTTGCGTTTCATGGACCTTTACAAAAGTTG\n+TAACATCCATATTATTATTGACGAAATAGCTAGGCGCAGTTCCCCCTGTT\n+GTGTATATATGAAAGTTGTCTACGAAGTCTGCTTTTCGCTTTCGTCTAGA\n+ATATTCGTTCTGATGCGCACTTTCATTTTTAAAGTCAAATTCCGAATCCA\n+TCACTCTGTTAGAACTTTTAAATGCTTGAAATTTATCATTTACCGGAGGA\n+GATGGGCATTCCATTTGATTTGAATTGATTACTACGCAAGATGTTTTGTT\n+TACTCTTTCATTATCAAAAAAAACTTCAAGTTCAGGCTTTTGAATTGAAT\n+TAAGATACATTCCATGAACGGTCAGAACGCGACCACCACTTACAAAACTG\n+CGTAAAGGCTTAATCTGCATTATACGCGGGTCTTGGGTATAGTTAAAAAT\n+AGAACAGGGCTGCCTTGGTAACGTACGAAATTGGTATGAACCGAAATTAC\n+TTCGAGTTAGATTTTTATTGGGTATAGTTGCGGGTGAGATATGACATTCT\n+AAAGTTCGGTTGGCACCGTCAATAAGAAGGTGTAGAGACCGTATTGGTTC\n+TGGCTGGGTCGCCTCTGATGTAGTACTACTAACTTGAGTTGAAGAAGCTT\n+GTGTAACGTTTATATGACACTCGTACTCATCTAAATATGCTCGCATGGTT\n+GATCCAATGTTCAAAAACTTTCCTATTAACGACAATTGTGTTCCTCCCGA\n+CCTGGGCCCAATCGTGGGATATAATCCTGTTAGCAAAACATTCTTAAAGT\n+GAAATTGTACACTAGATTCAGTATACCCTGCATCATTTGCAACCTTTATA\n+GGCGCTGACATTTCATACATCACTGCTCCAGTGCGGCATTCGATCTTTAC\n+AGAAATTTGGTAGTTGACTAGTTCACAAGGCACAGACCCAATAAATATTT\n+TTCCACGCACATCTCCTTCGCGAATGCCCAAATTACTGCCTTCAATTGTA\n+ATAAGGGTACCACCCTCAATAGGTCCAGATAACGGTTTAATAATATCGAT\n+CCTTGGTAAAGGGCACTCGTTTTCTTTAGTTGTTTTTGATCCTGCACTAA\n+TAGCACGATCACTGTCTGCTATGCAAGTCTCGTTATATACACATGAGTTG\n+CTGCACCAAGCACATTGGTATTTTGGATCACGAGTGACACACAAACTGCA\n+ATCAGCATGATCCCGATGTGAGCCCAGTACGTCGCATTTATATAATGTAA\n+CAATCGCCGTGTCCACATAGTGCTGGAAATTCCATGTAATTACAACCTTT\n+GCTTGGTATTCATGTGTATTAGTCTCGTAGAAATAAGGTGTTTTTTCACA\n+AACAACAATCTTGTTTGACTCAATGTGGGCAGGCAATAGCATCTGAGCAG\n+CTTCAATATGAACTGTACACAAGAATCCAGCGTGAGCGCTTTTGGGTTTT\n+GGTAAGTTTTCTATCTCTAAACGAATTTCTTTTGGCACCCGCACCGGTAA\n+AAGAATCGCCGGACGATTGCTTTTTAAATGGGGGCATTGACCAACACTAG\n+TTACCGAATTTTCTATATTACGACATTGTATTGATTGATGGACACATTTA\n+TTGTCAAAAATACACC'..b'CCACTGGACCCGTTGGATAGCGTC\n+GGCACTTTTCTGTTTGGTGCCATTCACTGGTCACTAGTAGGACCGCTCTG\n+CCTATTAAAATAGGAGTGCTGCTTAGAATTTATTTCAGCAAGACAGCCGT\n+AAGATATATATGAATAGTATTTAACGGCAGTGGCAGAGGCCTTTACAATA\n+TAAGGCTTTACGGGATTTTAAACAATGAAAAACAAAAATATTTTTATAGA\n+GTCGAGATAAAATACTTTTTACAATAAATACTAAGTATTTTTAAAAGATA\n+AAAATATTTAAAAGTAAATACTGAATATTTTAACAGGTGTTAAGTACTGG\n+GAACTGTGACTAAGGACGGCGGTATATCGCTACCATAATATTTTTAAAGG\n+AACTGAATACTGAAAGATGTGACCAAAATGGTAGAATATCGCTAACGAAA\n+ATCACAGACGCAAATATCGATAGTGGCCTAGAGACCCGATATCGCCGCCG\n+TGATTATCGATGAAACTACAGCTGAGCTGCTTGTTTACATTCTAAAGTTA\n+AAATTTTTAAAAATTTCCAATACAAAAAAAAATTCTTCGTATTAACACGG\n+CTGTTTGCCGGTAAGATCTGAAGTGGATTCAAGTTGCAGCACCCTCAGGA\n+AAAGAATAAATTATTATAATATAATAATATAATATAAAGAATTTAAATTC\n+GAACCAAACGCGGTATGTCACTCTTCATTTAGAGAATTTGTGGCTTTGTT\n+TTGTACAAAAAACTATTCTTTTTTCTTGAAAATTAGCATCAAGAATTTAT\n+TGCCAAAACAGAACGCAATTCTGCTAAATCTGGTTACCCTGCCAAATGGC\n+TGGCCGTTCTGTGCATTCAATAACACAAGCTAACGGCTTACGGCACATTC\n+GGAAAGATCCAAAAGAATTTCTATTCCGGCATTTTTTATGTATTATCGTC\n+CAATTTTTGTATGTGTATTCATTCTTTTGGCTGTCCGTTATTAAGCTTTT\n+CTTATCCACATAAGCTGACCAGCTGCCAAAAAGCCGACCGTTTTGTGCAG\n+CCAATAACCCAAGCTAACTATCAACAGCAATTTCGAAAAATCCAGAAGAA\n+GCTATCCTTCGGCAATTTTTTCTTATATTATAATTTTTTTGTCACAATTT\n+TTTGTCAAAAAATCGACAATAATTAAGTGTTTACATTTTAATGCGATTTA\n+ATTGGAAATTTGAATTCGAATCAAACGCGGTGTCACTCTACATATGGACA\n+ATTTGTGGCTACAAAATTAGTTGAAAGTGCATGTTTTTTTTTAAGTGAAA\n+TAAAACAAAAACAGCAATAACAGGCCAAAATGTTGTTTTATAAATAAATA\n+CTTACATATCCGCATATAAATATGAATGAAAAAAAAAACAGCAAGACTGG\n+GCCAAAATATTGTTCTTTAATATGTAAATAAATACATATCTACATATACA\n+TATGTGGACAAAAGTGTTAAAATTAGTTAATAGTGCATGTTTTTTAAATG\n+AAAAAATAAAACAAAAAAAGCAAGCAAATATAAATTATATTCCACACACA\n+TTTACAATAATTTCAAACTACGCTAAAAATACCCAACAGAAAAAACATAG\n+AAAGGTAAACAAAATACAAGAATATCAAAAAAAATCTAATTTTCACGTTG\n+TTGTGGCCGGTACCACCGGTCATACATACATATAGATACATATTTAGATT\n+CTCACAAAAAGAATAGAAAATTACCGCTAATTTCCTTATATACGTTTTTG\n+TTTTCAGTGTTTTGAAATAGTATTTTTCAAACAAAAAACAATACAAAAGG\n+GTTAAAAAAATTGTTCGATTGGCTTTAACATACTAATTAAAAAAAATCAC\n+AATTTTTTGGCAAAATATCGAAAAAAATTAAGTGTTTACATTTTTATGCG\n+AATTATTTGGAAATTTAAATAAGAACCCAACGCGGTTTGTCACTCTACAT\n+ATGGACAATTTGTGGCTTTGTTTTGAACAAAAAATGAATTTTTTTTTACT\n+CAAAATTAACAAGAAGAAACAGTAATGCGGGTTTTGATCGCAATTCTGCT\n+AAATCGAATTTCCGTGCCCAAAGGCTGACCTTTTTGTGCAGCAAATAGCC\n+CAAGCTAATAATCTACAGCAATTTCTTAAAGACCGAAAATGTATCAACTT\n+CGGCAAAATATGAAAATTTAACATTTATTTTTCAACATTTTTTGCCAAAT\n+AATCGACAAAAATTTCAGTGTCCCGATTTGGATGCGAATTAATTGAGGAC\n+AATTGTGACTTTGTTTTGTAAAAAAACTATTTTTTTTACTGAAAATTACA\n+ATCAAGAATCTAAGGCCAAATCAGAATATTTTCACTGCGGTTTTTTGATC\n+GCAATTCTGCTAAATCGGGTTCCGTGCCAAAAAGCTGACTATTTTTTTTA\n+CTGAGAATTAGCATCAAGAATTTATTGCCAAAACAGAACGCAATTCTGCT\n+AAATCGGGTTGCCCTGCCAAAAGGCTGGCCGTTTTGCGCATTCAATAACA\n+CAAGCTAACGGTTTACAGCACATTCGGAAAGATCCAAAAGAATTTCTATT\n+TCGGCATTTTTTATGTATTATCGTCTAATTTTGGTATGTGTATTCATTCT\n+TTTGGCTGTCCGTTATTAAGCTGCTTTTCTTATTCACATATTCAATGGCG\n+CAGTACATAAAAAGAATGAACCGTGGTTTTCTTGCCCTCTCCATCTCCCT\n+CTACCACTTCCCCTCTCAACAACTATCTCACGCACTCTGTCCCTTCTCGT\n+CTCTGTCACCCTCTCTTTACCTACCTCACTCTGGCACACTCTCTCTACCT\n+ATCTCACTCTGTCACCTTCTTCTACCTAATTCTCTCTGTCGCGCTCGCTC\n+TCTCAACATGCCTTTCGCACCGTATCTCTTCGTTTCTCTGTATGCTTGCT\n+CTCTTAATTTAAGTTTCTCTTTCTTTGTGTTCAATATCTTTCGCGCTCGT\n+GACTCCTATTGACCGGACTCTGAGCGGTGCTCATTAAGAGTGGAGTTTTC\n+GATGATGGCGGGTGGCGCGAACGAGAATTTTTTACATAAAGGTAAGTTGC\n+CAATTCTTTTTTAAATGTGACATACAGCATGCATATTTTATTTATTGTAA\n+TTATATGTGAAAGAATAAAATTATATGTACTTTTATCTAATCTATTGCAT\n+CTATTTTTTCACAGGTAAACGAGTCACACGAGAAGTAAAACACAAACACA\n+AGGATCAAAATAAAATTCAGGTGAGTGAACGAACGTGTTGAAAGTAGTTA\n+ATAGTGCATGTCTATTTAAGTGTAAGAAACAAAAAAGACACAAATGGGCC\n+AATAATTCGTTTCTTTAATAGATAACTGCCTATATTATGTTCAAACTATG\n+CTAAAAAGACCCAAAAGGAAAACATAAAGTATATACCTTGCAAAATGAAT\n+AAAAAGAAATCATATATATTCATATACGTTTGACCGGTACCACCGGTCAT\n+ACATACATAAACATAAACACAAAAAGACTAGAATATAAATACCATATTTT\n+TGATTGGCTTAAAAATGGCACAAAAAAAAGATAAAAACTAGAGTGTCTAG\n+CTTTAAGTGACAATCGACTCGGAAAATGATCAAGAAATAAATGAAAAATT\n+TGTCTTGCGGCTTTTTGGTCGCAATTCTAAATCGGTTTGTATGTATGTCA\n+CTCTTCATGTATACAATTTGGTGGCTTTGTATTCCACAAAAGTCACAGTA\n+GTCACAAAAGTTTTTTTTACTGAAAATTACCATCAAGAGTCTATGGCCAA\n+ATCAGAATATTTTCACTGCGGTTTTTTATTTCAATTCTGCTAAATCGGGT\n+TTCCGTGCCAAAAAGCTTTTGCAGCCAACAACAATATTCAATTTTTTGGC\n+AAAAAATCGACAAAAAAATT\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/common/dbia3.sizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/common/dbia3.sizes Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ +contig1 45179 +contig2 45017 +contig3 40006 +contig4 55011 +contig5 50018 +contig6 40015 +contig7 50017 +contig8 35012 +contig9 60018 +contig10 43013 +contig11 35013 +contig12 56019 +contig13 45015 +contig14 45010 +contig15 50014 +contig16 45017 +contig17 40013 +contig18 40012 +contig19 45013 +contig20 50014 +contig21 50011 +contig22 60010 +contig23 50012 +contig24 40010 +contig25 75023 +contig26 40013 +contig27 50016 +contig28 50013 +contig29 50006 +contig30 70018 +contig31 40012 +contig32 40014 +contig33 40016 +contig34 50012 +contig35 48011 +contig36 45010 +contig37 50013 +contig38 50017 +contig39 45019 +contig40 60015 +contig41 60014 +contig42 70020 +contig43 50016 +contig44 50013 +contig45 50013 +contig46 50012 +contig47 35007 +contig48 65012 +contig49 30003 +contig50 40009 +contig51 50015 +contig52 40012 +contig53 50013 +contig54 35008 +contig55 40015 +contig56 55020 +contig57 60013 +contig58 50011 +contig59 40011 +contig60 50013 +contig61 40008 +contig62 50017 +contig63 55021 +contig64 40016 +contig65 45013 +contig66 45011 +contig67 44531 +contig68 25628 +contig69 44962 +contig70 55020 |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default_color/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_6.dat', u'long_label': u'', u'name': u'HISAT2_Accepted_Hits', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x7ff90b812650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/189/dataset_214_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_HISAT2_Accepted_Hits_bam (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/default_color_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default_color/default_color_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,73 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default_color/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default_color/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_HISAT2_Accepted_Hits_bam +longLabel HISAT2 Accepted Hits.bam +shortLabel HISAT2 Accepted H +bigDataUrl tracks/HISAT2_Accepted_Hits.bam +type bam +visibility pack +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam |
| b |
| Binary file test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai |
| b |
| Binary file test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default_color/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/default_color/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default_color/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_147.dat +DEBUG:root:data_value: {u'long_label': u'Augustus', u'name': u'Augustus_Gene_Predictions', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:Calling gff3ToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpzTV91Q.sorted.bigGenePred +DEBUG:root:chrom_sizes_file_name: /tmp/tmpfTKTZ_.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/168/dataset_194_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gff3.Gff3 object at 0x7f8d7b8a7710>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/168/dataset_194_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_Augustus_Gene_Predictions_bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/gff3_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/gff3_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/inputs/Augustus_Gene_Predictions --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/inputs/Augustus_Gene_Predictions Wed May 16 18:04:20 2018 -0400 |
| [ |
| b'@@ -0,0 +1,6937 @@\n+##gff-version 3\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/svc_galaxy/new/galaxy/tool_dependency/augustus/3.1/iuc/package_augustus_3_1/24009970003a/config/ ...\n+# fly version. Using default transition matrix.\n+# Looks like /home/svc_galaxy/new/galaxy/database/files/000/dataset_98.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 45179, name = contig1) -----\n+#\n+# Predicted genes for sequence number 1 on both strands\n+# start gene contig1.g1\n+contig1\tAUGUSTUS\tgene\t553\t34688\t0.03\t-\t.\tID=contig1.g1\n+contig1\tAUGUSTUS\ttranscript\t553\t34688\t0.03\t-\t.\tID=contig1.g1.t1;Parent=contig1.g1\n+contig1\tAUGUSTUS\tCDS\t553\t578\t0.41\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t652\t1047\t0.25\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t12541\t12968\t0.87\t-\t1\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t32202\t33826\t0.89\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t33880\t34044\t0.98\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t34107\t34619\t0.99\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t34674\t34688\t0.45\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tstart_codon\t34686\t34688\t.\t-\t0\tParent=contig1.g1.t1\n+# coding sequence = [atggcagcactctcgcaaaaggactttaatgacggaaaccagagaaatcgtcagaggaaaagtactgtcactgagcagc\n+# cctcatcaacatcaggaagcgtggcccaagtagaagcggacagcgcatcgtcacatttgtctgatcgctgttataacaacatagcaagtactaccaaa\n+# agtattgttggtgatgtgaaaacaagcagacgctgtgaagactttataagtagtggatcagcttcgactccattaaatgaatatgattgtgccaacgc\n+# tgatacgacggatattaaagatgaacctggagattttatagaaacaaattgtcattggcgaagttgttgtattgaatttaatacgcaagatgagcttg\n+# ttaaacatatcaataatgaccatatccaaaccaataagaaggcctttgtctgtcgatgggaaaattgtacccgtggtgaaaaacctttcaaagcgcag\n+# tatatgctagttgtgcatatgcgtcgtcataccggcgaaaagccacataaatgcacatttgaaggctgttttaaggcatattcacgcttggaaaacct\n+# aaaaacacatttacggtcacacacaggtgaaaaaccctatatgtgcgagtatccgggatgcagcaaggcgtttagtaatgcaagcgatcgtgcaaagc\n+# atcaaaatcgtactcacagtaatgagaaaccgtacatttgtaaagctcctggttgcacgaaacgttacaccgacccaagttctttgcgtaaacatgtt\n+# aaaacagttcatggtgctgagttttatgctaataaaaaacacaagggattgcccctaaatgatgcgaactctcgcctccaccgagacagtggccaagg\n+# tcggcataatcttcaagagcataatattgactctagcccttgcagcgaagaacttcaggtgggaaaacttataggcatgtctagtcccagtattaaat\n+# ctgaatctgatgaaagttcaccacatcatcagttgttaagtggagttcgagcttcagactgttttttaacatattcacaagatggtgccgccgaacat\n+# ataactttagatgacggctgggattgtgacgatgacgttgacgtggccgacttaccaattgtcttgcgtgctatggtaaatgttggcagcggaaattc\n+# gatggccccgaccattggagggggtgttgttgcgaggcagcgatttagaagtcgtttgcaaactaaaggaataaactctagtatggttatgcttggca\n+# acatccccgaaagcaatcgcaccattggaataagcgaacttaaccagcgtataacagaacttaagatggagcctggtaccgcttgtgatattacagtt\n+# ccattgaatacggggctggaaaggatttcagaagacttatcacaaaatcaatcaaatataacattaaataagcaaagcttctttaccgcttccggctc\n+# tctccaaggacattttcgtcgcgatagccagaactccactgcaagtacatattatggtagcatgcaaagtcgccgcagtagtcaatcatctcaggtgt\n+# cttctatatctacaatgcgtccaggcccatcgtacaacacaaccacagcttccctctatgatccaatttccccaggatgctctcgacgctctagccaa\n+# atgtctaatgtagtcaactcctacgcacttacatcaacatcaggattgactgcaattaacaaggacttaaatgcaaacagcagcccaaatgcttctat\n+# taataaaccgggtcttggtggtcagtactttggtttttacaataacagtcttcctccacctccatcgtctcatttaattgccaccaatttgaagcatc\n+# tgcaggacacagactctaggagttgttatcacaacacaactggcggtcgattttccattcccaattgtacgccatctctacatttagactacaatgga\n+# ccggctggagagcaggaaattgataaagaaatcccgaataacatattacgacgtcaatctgagccaatgccaaac'..b'ttcgtgttggacgaatattgcgctcgctatggtgtgcggggatgctaccgacatttatgctacctttctgatttactggatcgtgcagaaaagcaac\n+# acatgatagatccaacactaattcactattcatttgcgttttgcgcaagccacgttcacggaaatcgacctgatggggtaggaagcattacgcatgag\n+# gaaaaggaaaaattttctgaaatcaaagaacgcctacgtcagttactggagtttcaaataaccaattttagatactgttttcctttcggtcgccccga\n+# aggcgctcttaaagcgacattatctttactagagagagtgctaatgaaagacattgttacccctgttccacctgaagaagttcgtcaaatgattaaaa\n+# aaagtttagagacggcagcgcttgtaaattacacccgtctctccaataaagctaagattgaaggcacttttccgttcaagggacacgtgccagggaaa\n+# tcctatcggaatttcaaaatttttccaagcactttcctgtacacgggaaacgtcccagggaaagcctatcggaaaggtcccagggaaatcccgtcgga\n+# tattcaggatttgcgaggagaggttattgttccgcccccaaaaaaactagaggacctaattcacttagcagaactttgtgttgatctgttgcaacaaa\n+# atgaagagcactatggagaactgcgcaaacatgacaaaatggataaaattaaaatgcgtaaggaagatgatgatgtaccaaaaggccacaatgaaagc\n+# gatattgatttaaccgccaatactggactcagtagcacatcagacctggcttctgcagcatcaactaatggatcgtcatttcgttattataatttgag\n+# gaatgggcgttttcatcagcacctgcgagacacattcgcaccattagtcgtgcggtacgtggatctgatggaatcttcaatagctcagtcgattcata\n+# agggatttgaaaaagaacgctgggaaagtaaagggaacggatgtgccacctctgaagacttattttggaaactagatgctctacagtcgtttataaga\n+# gacctgcactggccagacgcagagtttcgacaacatttagaacagcgtcttaaaatgatggccgtcgatatgatagagcaatgtatacaacgaactga\n+# ttcgtcttttcagtcgtggctaaaaaaaaacattgccttcatatcaactgattatattttaccttcagaaatgtgcgctatggtcaatgtgatattag\n+# atgctaaaaatcaaagctttaaattgactactattgacggcattgatttgtataaatttcatgcaaaaattgacgaccaaatcgacaaagcgaatgta\n+# gctatgacacaaggtctaactggtaaacttatgtcagtgctagagtcgactttgtcaaaattagcacgatacgacgaaggtagcctaatcggctcgat\n+# tcttagttttacaaatgtatcgagctcgggaaaggatctcgggcaaggatatgtaaatttctttagaaataatatggatcaagtacgaggaaaaattg\n+# gcgacgatttatggaccctgaatttctttgagcagtggtactcgcagcagattaacatgctatgtaattggctttcggaacgtttggaccacgctctg\n+# cactacgctcaagtttcatctatttctcacattatcaagaaaatatattcagacttcgaattacaaggtgtattagaagataaattaaactctaaagc\n+# atatcaagcagtcgcacagcgaatggcgacagaggaagcgacatgtgctttgacaatgcctgatgttagcgaagatgaaccctgtgacgacattcgag\n+# aaggggaagaagaagatactggcgacgaatctacctctaacataccaaggggcttaccaaaaccaaaaattgctgccgctcaagctgctgctgttacc\n+# aacgttgttgccggccgtgtgggtaatttactcggcaaaggcattggcggccttagttcaaagttgggaagtggaagttggttttaa]\n+# protein sequence = [MIDPSSSEEEGEDDPIANVSSKGRLTHAPKGTNTVSILGGVSGPGVGSNMAISGSNGDLAGNQRQSNISSISNRNDAG\n+# NVAGVGGSSNKNEQIHGSRVDGGNLEVPNSCIPSGVSQETLNQSIGSSRANSLPRPLSPSPSLTSEKPDTGDPHAFLKGETQIMADEAFQNAVQSYHD\n+# VFLKSERVLKMVQSGASSQHDFREVFRNNIEKRVRSLPEIDGLSKETVLTSWMAKFDIILKGTGEEDSKRPSRMQQSLNSELILSKEQLYDMFQQILL\n+# VKKFEHQILYNALMLDSADEQAAAIRRELDGRMQRVGEMEKNRKLMPKFVLKEMESLYVEELKSSINLLMANLESLPVSKGNMDSKYGLQKLKRYNHR\n+# KLILRSHGSLSKLEGDSEDGSTQLTKLDVVLTFQLEVIVMEVKGLKSLAPNRIVYCTMEVENGEKLQTDQAEASKPMWDTQGDFTTTHPLPVVKVKLY\n+# TENPGMLALEDKELGKVILKPTPLSSKSPEWHRMVIPKNLPDQDIRIKIACRLDKPLNMKHCGYKEKKSEPSEMMQLDGYTVDYIEAASANLMFGIDL\n+# NGGRFFFNAVREGDSISFACDDENECSLWVMAMYRATGQSHKPTPPITQDKNSAMSKIQGARVAPDGSIFLWASFFVAAATRNSSSYHWFRVGGRLNP\n+# MVVSAAARMEWDMCAQSPLASTWRGIGWWSSSERGQPYDLVDVEVPKSGATHYHVSCRGEVNQPETVVRDGLMEAESTDGGVKDAFATELCVEVPEDK\n+# LHVVVWGWFSPGQVFVLDEYCARYGVRGCYRHLCYLSDLLDRAEKQHMIDPTLIHYSFAFCASHVHGNRPDGVGSITHEEKEKFSEIKERLRQLLEFQ\n+# ITNFRYCFPFGRPEGALKATLSLLERVLMKDIVTPVPPEEVRQMIKKSLETAALVNYTRLSNKAKIEGTFPFKGHVPGKSYRNFKIFPSTFLYTGNVP\n+# GKAYRKGPREIPSDIQDLRGEVIVPPPKKLEDLIHLAELCVDLLQQNEEHYGELRKHDKMDKIKMRKEDDDVPKGHNESDIDLTANTGLSSTSDLASA\n+# ASTNGSSFRYYNLRNGRFHQHLRDTFAPLVVRYVDLMESSIAQSIHKGFEKERWESKGNGCATSEDLFWKLDALQSFIRDLHWPDAEFRQHLEQRLKM\n+# MAVDMIEQCIQRTDSSFQSWLKKNIAFISTDYILPSEMCAMVNVILDAKNQSFKLTTIDGIDLYKFHAKIDDQIDKANVAMTQGLTGKLMSVLESTLS\n+# KLARYDEGSLIGSILSFTNVSSSGKDLGQGYVNFFRNNMDQVRGKIGDDLWTLNFFEQWYSQQINMLCNWLSERLDHALHYAQVSSISHIIKKIYSDF\n+# ELQGVLEDKLNSKAYQAVAQRMATEEATCALTMPDVSEDEPCDDIREGEEEDTGDESTSNIPRGLPKPKIAAAQAAAVTNVVAGRVGNLLGKGIGGLS\n+# SKLGSGSWF]\n+# end gene contig70.g117\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /home/svc_galaxy/new/galaxy/database/files/000/dataset_98.dat --UTR=off --genemodel=complete --species=fly\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_Augustus_Gene_Predictions_bb +longLabel Augustus +shortLabel Augustus +bigDataUrl tracks/Augustus_Gene_Predictions.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb |
| b |
| Binary file test-data/gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1188.dat +DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Multi-Fasta_GlimmerHMM_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling gff3ToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpESpr1K.sorted.bigGenePred +DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpl9r8fF.chrom.sizes +DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/916/dataset_1284_files/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gff3.Gff3 object at 0x1e8acd0>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/916/dataset_1284_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/gff3_multi_fasta_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/gff3_multi_fasta_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb">Multi-Fasta_GlimmerHMM_Gene_Predictions.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,2081 @@\n+##gff-version 3\n+##sequence-region contig1 1 45179\n+contig1\tGlimmerHMM\tmRNA\t641\t20329\t.\t-\t.\tID=contig1.path1.gene1;Name=contig1.path1.gene1\n+contig1\tGlimmerHMM\tCDS\t641\t5409\t.\t-\t2\tID=contig1.cds1.1;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=final-exon\n+contig1\tGlimmerHMM\tCDS\t12541\t12968\t.\t-\t1\tID=contig1.cds1.2;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t14821\t14944\t.\t-\t2\tID=contig1.cds1.3;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t15123\t15424\t.\t-\t1\tID=contig1.cds1.4;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t17402\t17543\t.\t-\t2\tID=contig1.cds1.5;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t17886\t17986\t.\t-\t1\tID=contig1.cds1.6;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t20226\t20329\t.\t-\t0\tID=contig1.cds1.7;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=initial-exon\n+contig1\tGlimmerHMM\tmRNA\t22912\t26939\t.\t-\t.\tID=contig1.path1.gene2;Name=contig1.path1.gene2\n+contig1\tGlimmerHMM\tCDS\t22912\t23136\t.\t-\t0\tID=contig1.cds2.1;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=final-exon\n+contig1\tGlimmerHMM\tCDS\t23431\t23705\t.\t-\t2\tID=contig1.cds2.2;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t26810\t26939\t.\t-\t0\tID=contig1.cds2.3;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=initial-exon\n+contig1\tGlimmerHMM\tmRNA\t29101\t41509\t.\t-\t.\tID=contig1.path1.gene3;Name=contig1.path1.gene3\n+contig1\tGlimmerHMM\tCDS\t29101\t29152\t.\t-\t1\tID=contig1.cds3.1;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=final-exon\n+contig1\tGlimmerHMM\tCDS\t31365\t33826\t.\t-\t0\tID=contig1.cds3.2;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t33880\t34044\t.\t-\t0\tID=contig1.cds3.3;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t34107\t34619\t.\t-\t0\tID=contig1.cds3.4;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t34674\t35311\t.\t-\t2\tID=contig1.cds3.5;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t35384\t35766\t.\t-\t1\tID=contig1.cds3.6;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t41472\t41509\t.\t-\t0\tID=contig1.cds3.7;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=initial-exon\n+##sequence-region contig2 1 45017\n+contig2\tGlimmerHMM\tmRNA\t2231\t5162\t.\t-\t.\tID=contig2.path1.gene1;Name=contig2.path1.gene1\n+contig2\tGlimmerHMM\tCDS\t2231\t2376\t.\t-\t2\tID=contig2.cds1.1;Parent=contig2.path1.gene1;Name=contig2.path1.gene1;Note=final-exon\n+contig2\tGlimmerHMM\tCDS\t2719\t2819\t.\t-\t1\tID=contig2.cds1.2;Parent=contig2.path1.gene1;Name=contig2.path1.gene1;Note=internal-exon\n+contig2\tGlimmerHMM\tCDS\t5059\t5162\t.\t-\t0\tID=contig2.cds1.3;Parent=contig2.path1.gene1;Name=contig2.path1.gene1;Note=initial-exon\n+contig2\tGlimmerHMM\tmRNA\t7745\t11772\t.\t-\t.\tID=contig2.path1.gene2;Name=contig2.path1.gene2\n+contig2\tGlimmerHMM\tCDS\t7745\t7969\t.\t-\t0\tID=contig2.cds2.1;Parent=contig2.path1.gene2;Name=contig2.path1.gene2;Note=final-exon\n+contig2\tGlimmerHMM\tCDS\t8264\t8538\t.\t-\t2\tID=contig2.cds2.2;Parent=contig2.path1.gene2;Name=contig2.path1.gene2;Note=internal-exon\n+contig2\tGlimmerHMM\tCDS\t11643\t11772\t.\t-\t0\tID=contig2.cds2.3;Parent=contig2.path1.gene2;Name=contig2.path1.gene2;Note=initial-exon\n+contig2\tGlimmerHMM\tmRNA\t13934\t36373\t.\t-\t.\tID=contig2.path1.gene3;Name=contig2.path1.gene3\n+contig2\tGlimmerHMM\tCDS\t13934\t13985\t.\t-\t1\tID=contig2.cds3.1;Parent=contig2.path1.gene3;Name=contig2.path1.gene3;Note=final-exon\n+contig2\tGlimmerHMM\tCDS\t16198\t18659\t.\t-\t0\tID=contig2.cds3.2;Parent=contig2.path1.gene3;Name=contig2.path1.gene3;Note=internal-exon\n+contig2\tGlimmerHMM\tCDS\t18713\t18877\t.\t-\t0\tID=contig2.cds3.3;Parent=contig2.path1.gene3;Name=contig2.path1.gene3;N'..b'9\t12828\t.\t+\t1\tID=contig70.cds1.10;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t12886\t13092\t.\t+\t2\tID=contig70.cds1.11;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t15494\t15832\t.\t+\t2\tID=contig70.cds1.12;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t15998\t16096\t.\t+\t2\tID=contig70.cds1.13;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t16376\t16723\t.\t+\t2\tID=contig70.cds1.14;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t16861\t17074\t.\t+\t2\tID=contig70.cds1.15;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t17114\t17366\t.\t+\t1\tID=contig70.cds1.16;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t21277\t21354\t.\t+\t0\tID=contig70.cds1.17;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t21531\t21822\t.\t+\t0\tID=contig70.cds1.18;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t22845\t22924\t.\t+\t2\tID=contig70.cds1.19;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t24039\t24226\t.\t+\t0\tID=contig70.cds1.20;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t24288\t24577\t.\t+\t1\tID=contig70.cds1.21;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t27274\t27411\t.\t+\t2\tID=contig70.cds1.22;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t28524\t28636\t.\t+\t2\tID=contig70.cds1.23;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t31963\t32034\t.\t+\t0\tID=contig70.cds1.24;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t33015\t33225\t.\t+\t0\tID=contig70.cds1.25;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t36266\t36324\t.\t+\t2\tID=contig70.cds1.26;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t36995\t37151\t.\t+\t0\tID=contig70.cds1.27;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t38419\t38560\t.\t+\t2\tID=contig70.cds1.28;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t38856\t39023\t.\t+\t1\tID=contig70.cds1.29;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t45726\t46035\t.\t+\t1\tID=contig70.cds1.30;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t46098\t46478\t.\t+\t0\tID=contig70.cds1.31;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t46932\t47068\t.\t+\t0\tID=contig70.cds1.32;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t47124\t47317\t.\t+\t1\tID=contig70.cds1.33;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t50861\t51057\t.\t+\t2\tID=contig70.cds1.34;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t51487\t51513\t.\t+\t0\tID=contig70.cds1.35;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=final-exon\n+contig70\tGlimmerHMM\tmRNA\t54155\t54504\t.\t+\t.\tID=contig70.path1.gene2;Name=contig70.path1.gene2\n+contig70\tGlimmerHMM\tCDS\t54155\t54191\t.\t+\t0\tID=contig70.cds2.1;Parent=contig70.path1.gene2;Name=contig70.path1.gene2;Note=initial-exon\n+contig70\tGlimmerHMM\tCDS\t54315\t54370\t.\t+\t2\tID=contig70.cds2.2;Parent=contig70.path1.gene2;Name=contig70.path1.gene2;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t54472\t54504\t.\t+\t0\tID=contig70.cds2.3;Parent=contig70.path1.gene2;Name=contig70.path1.gene2;Note=final-exon\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb + longLabel Multi-Fasta GlimmerHMM Gene Predictions + shortLabel Multi-Fasta Gli + bigDataUrl tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb + type bigGenePred + visibility dense + thickDrawItem off + priority 10 + color 0,0,0 + group default_group + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb |
| b |
| Binary file test-data/gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gff3_multi_fasta/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3_multi_fasta/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email rmarenco@gwu.edu +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_158.dat +DEBUG:root:data_value: {u'long_label': u'StringTie transcripts', u'name': u'StringTie_Assembled_Transcripts', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpO0sxeA.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /tmp/tmp9W1pAA.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/169/dataset_195_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x7f8acc88c650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/169/dataset_195_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_StringTie_Assembled_Transcripts_bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/gtf_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/gtf_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/inputs/StringTie_Assembled_Transcripts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/inputs/StringTie_Assembled_Transcripts Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ +# stringtie /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat -o /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat -p 1 +# StringTie version 1.2.3 +contig16 StringTie transcript 1751 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "14.618678"; FPKM "322160.531250"; TPM "866155.937500"; +contig16 StringTie exon 1751 1897 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "6.787892"; +contig16 StringTie exon 11285 11463 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "19.860081"; +contig16 StringTie exon 11518 11705 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "23.926477"; +contig16 StringTie exon 11759 11858 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "17.452721"; +contig16 StringTie exon 11922 11975 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "11.461867"; +contig16 StringTie exon 12601 12811 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "11.876496"; +contig16 StringTie exon 17222 17337 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "15.915709"; +contig16 StringTie exon 17406 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "8"; cov "11.738873"; |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_StringTie_Assembled_Transcripts_bb +longLabel StringTie transcripts +shortLabel StringTie transcr +bigDataUrl tracks/StringTie_Assembled_Transcripts.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb |
| b |
| Binary file test-data/gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf_gff/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,60 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1184.dat +DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling gff3ToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp7sqcWp.sorted.bigGenePred +DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpp6ZdZ_.chrom.sizes +DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat +DEBUG:root:data_value: {u'order_index': u'11', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp66b4It.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpp6ZdZ_.chrom.sizes +DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x1ecae10>, <Gff3.Gff3 object at 0x1ecad10>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group) +DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/gtf_gff_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf_gff/gtf_gff_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,73 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf_gff/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf_gff/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,22 @@ + track StringTie_Assembled_Transcripts.bb + longLabel StringTie Assembled Transcripts + shortLabel StringTie Assem + bigDataUrl tracks/StringTie_Assembled_Transcripts.bb + type bigGenePred + visibility dense + thickDrawItem off + priority 11 + color 0,0,0 + group default_group + + track Augustus_Gene_Predictions.bb + longLabel Augustus Gene Predictions + shortLabel Augustus Gene P + bigDataUrl tracks/Augustus_Gene_Predictions.bb + type bigGenePred + visibility dense + thickDrawItem off + priority 10 + color 0,0,0 + group default_group + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb |
| b |
| Binary file test-data/gtf_gff/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb |
| b |
| Binary file test-data/gtf_gff/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf_gff/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/gtf_gff/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf_gff/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email rmarenco@gwu.edu +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/Hub_Archive_Creator_on_data_15,_data_19,_and_data_1_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one_group_two_tracks/Hub_Archive_Creator_on_data_15,_data_19,_and_data_1_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,76 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam">HISAT2_on_data_1,_data_3,_and_data_2.bam</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/StringTie_on_data_15:_Assembled_transcripts.bb">StringTie_on_data_15:_Assembled_transcripts.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam.bai">HISAT2_on_data_1,_data_3,_and_data_2.bam.bai</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one_group_two_tracks/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,42 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_5.dat', u'long_label': u'HISAT sequence alignment', u'name': u'HISAT2_on_data_1,_data_3,_and_data_2', u'database': u'', u'track_color': u'#c0504d', u'group_name': u'RNA-Seq', u'order_index': u'11'} +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_158.dat +DEBUG:root:data_value: {u'long_label': u'StringTie transcripts ', u'name': u'StringTie_on_data_15:_Assembled_transcripts', u'database': u'', u'track_color': u'#c0504d', u'group_name': u'RNA-Seq', u'order_index': u'10'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpp_i4_J.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /tmp/tmpTsX28d.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/150/dataset_177_files/myHub/Dbia3/tracks/StringTie_on_data_15:_Assembled_transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x7f11363da650>, <Gtf.Gtf object at 0x7f11363da6d0>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/150/dataset_177_files/myHub/Dbia3/groups.txt the group RNA-Seq +DEBUG:root:We just added track gonramp_HISAT2_on_data_1__data_3__and_data_2_bam (in group rna-seq) +DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/150/dataset_177_files/myHub/Dbia3/groups.txt the group RNA-Seq +DEBUG:root:We just added track gonramp_StringTie_on_data_15__Assembled_transcripts_bb (in group rna-seq) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one_group_two_tracks/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name rna-seq +label RNA-Seq +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one_group_two_tracks/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,24 @@ + +track gonramp_HISAT2_on_data_1__data_3__and_data_2_bam +longLabel HISAT sequence alignment +shortLabel HISAT sequence al +bigDataUrl tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam +type bam +visibility pack +thickDrawItem off +priority 11 +color 192,80,77 +group rna-seq +searchIndex name + +track gonramp_StringTie_on_data_15__Assembled_transcripts_bb +longLabel StringTie transcripts +shortLabel StringTie transcr +bigDataUrl tracks/StringTie_on_data_15:_Assembled_transcripts.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 10 +color 192,80,77 +group rna-seq +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam |
| b |
| Binary file test-data/one_group_two_tracks/myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam.bai |
| b |
| Binary file test-data/one_group_two_tracks/myHub/Dbia3/tracks/HISAT2_on_data_1,_data_3,_and_data_2.bam.bai has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/Dbia3/tracks/StringTie_on_data_15:_Assembled_transcripts.bb |
| b |
| Binary file test-data/one_group_two_tracks/myHub/Dbia3/tracks/StringTie_on_data_15:_Assembled_transcripts.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one_group_two_tracks/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/one_group_two_tracks/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one_group_two_tracks/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/only_genome/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/only_genome/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,16 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/only_genome/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/only_genome/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/only_genome/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/only_genome/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/only_genome/only_genome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/only_genome/only_genome.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,54 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,36 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_191.dat +DEBUG:root:data_value: {u'long_label': u'BLAST Alignment', u'name': u'blastXmlToPsl', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:Calling pslToBigPsl: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Hello +DEBUG:root:sorted_bed_file_name: /tmp/tmp2i4e0Tpsl +DEBUG:root:chrom_sizes_file_name: /tmp/tmp1BIsqk.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/166/dataset_192_files/myHub/Dbia3/tracks/blastXmlToPsl.bb +DEBUG:root:typeOption: bed12+12 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigPsl.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Psl.Psl object at 0x7fc17d9d0690>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/166/dataset_192_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_blastXmlToPsl_bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/inputs/blastXmlToPsl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/inputs/blastXmlToPsl Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,20 @@ +276 357 36 0 4 12 1 9 +- FBpp0070070 1623 153 834 contig14 45010 32918 33596 6 126,45,18,324,57,99, 153,282,327,348,675,735, 11414,11540,11594,11612,11936,11993, +129 276 0 0 0 0 3 21 +- FBpp0070070 1623 822 1227 contig14 45010 31613 32039 4 39,156,69,141, 822,861,1017,1086, 12971,13022,13181,13256, +276 357 36 0 4 12 1 9 +- FBpp0070070 1623 153 834 contig15 50014 2911 3589 6 126,45,18,324,57,99, 153,282,327,348,675,735, 46425,46551,46605,46623,46947,47004, +129 276 0 0 0 0 3 21 +- FBpp0070070 1623 822 1227 contig15 50014 1606 2032 4 39,156,69,141, 822,861,1017,1086, 47982,48033,48192,48267, +204 177 0 0 2 132 1 63 ++ FBpp0070566 2046 873 1386 contig36 45010 41724 42168 4 102,87,30,162, 873,975,1116,1224, 41724,41889,41976,42006, +135 102 0 0 1 3 0 0 ++ FBpp0070566 2046 165 405 contig36 45010 38740 38977 2 213,24, 165,381, 38740,38953, +99 156 0 0 0 0 0 0 ++ FBpp0070566 2046 606 861 contig36 45010 40303 40558 1 255, 606, 40303, +96 93 0 0 0 0 1 3 ++ FBpp0070566 2046 1476 1665 contig36 45010 42322 42514 2 39,150, 1476,1515, 42322,42364, +204 177 0 0 2 132 1 63 ++ FBpp0070566 2046 873 1386 contig37 50013 11717 12161 4 102,87,30,162, 873,975,1116,1224, 11717,11882,11969,11999, +135 102 0 0 1 3 0 0 ++ FBpp0070566 2046 165 405 contig37 50013 8733 8970 2 213,24, 165,381, 8733,8946, +99 156 0 0 0 0 0 0 ++ FBpp0070566 2046 606 861 contig37 50013 10296 10551 1 255, 606, 10296, +96 93 0 0 0 0 1 3 ++ FBpp0070566 2046 1476 1665 contig37 50013 12315 12507 2 39,150, 1476,1515, 12315,12357, +207 174 0 0 3 72 1 63 ++ FBpp0070567 1986 873 1326 contig36 45010 41724 42168 5 102,93,9,15,162, 873,975,1086,1131,1164, 41724,41889,41982,41991,42006, +135 102 0 0 1 3 0 0 ++ FBpp0070567 1986 165 405 contig36 45010 38740 38977 2 213,24, 165,381, 38740,38953, +99 156 0 0 0 0 0 0 ++ FBpp0070567 1986 606 861 contig36 45010 40303 40558 1 255, 606, 40303, +96 93 0 0 0 0 1 3 ++ FBpp0070567 1986 1416 1605 contig36 45010 42322 42514 2 39,150, 1416,1455, 42322,42364, +207 174 0 0 3 72 1 63 ++ FBpp0070567 1986 873 1326 contig37 50013 11717 12161 5 102,93,9,15,162, 873,975,1086,1131,1164, 11717,11882,11975,11984,11999, +135 102 0 0 1 3 0 0 ++ FBpp0070567 1986 165 405 contig37 50013 8733 8970 2 213,24, 165,381, 8733,8946, +99 156 0 0 0 0 0 0 ++ FBpp0070567 1986 606 861 contig37 50013 10296 10551 1 255, 606, 10296, +96 93 0 0 0 0 1 3 ++ FBpp0070567 1986 1416 1605 contig37 50013 12315 12507 2 39,150, 1416,1455, 12315,12357, |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +track gonramp_blastXmlToPsl_bb +longLabel BLAST Alignment +shortLabel BLAST Alignment +bigDataUrl tracks/blastXmlToPsl.bb +type bigPsl +visibility dense +thickDrawItem off +priority 10 +color 0,0,0 +group default_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/myHub/Dbia3/tracks/blastXmlToPsl.bb |
| b |
| Binary file test-data/psl/myHub/Dbia3/tracks/blastXmlToPsl.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/psl/psl_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psl/psl_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/blastXmlToPsl.bb">blastXmlToPsl.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1329.dat +DEBUG:root:data_value: {u'order_index': u'10', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmptjLL_6.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp5N24Cj.chrom.sizes +DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/964/dataset_1331_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x179fd10>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/964/dataset_1331_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/inputs/stringtie_assembled_transcripts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/inputs/stringtie_assembled_transcripts Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ +# stringtie /home/svc_galaxy/new/galaxy/database/files/001/dataset_1102.dat -o /home/svc_galaxy/new/galaxy/database/files/001/dataset_1103.dat -p 1 +# StringTie version 1.1.0 +contig16 StringTie transcript 1751 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "14.618678"; FPKM "322160.531250"; TPM "880020.875000"; +contig16 StringTie exon 1751 1897 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "6.787892"; +contig16 StringTie exon 11285 11463 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "19.860081"; +contig16 StringTie exon 11518 11705 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "23.926477"; +contig16 StringTie exon 11759 11858 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "17.452721"; +contig16 StringTie exon 11922 11975 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "11.461867"; +contig16 StringTie exon 12601 12811 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "11.876496"; +contig16 StringTie exon 17222 17337 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "15.915709"; +contig16 StringTie exon 17406 45020 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "8"; cov "11.738873"; |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/Dbia3.2bit |
| b |
| Binary file test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/Dbia3.2bit has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + track StringTie_Assembled_Transcripts.bb + longLabel StringTie Assembled Transcripts + shortLabel StringTie Assem + bigDataUrl tracks/StringTie_Assembled_Transcripts.bb + type bigGenePred + visibility dense + thickDrawItem off + priority 10 + color 0,0,0 + group default_group + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb |
| b |
| Binary file test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email rmarenco@gwu.edu +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/bigbed_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/bigbed_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,83 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed">BLAT_alignment_bigbed.bigbed</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + trix + </li> + <ul> + + <li> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx">BLAT_alignment_bigbed.bigbed.ixx</a> + </li> + <li> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix">BLAT_alignment_bigbed.bigbed.ix</a> + </li> + + </ul> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/blast_alignment_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/blast_alignment_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,83 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb">BLAST_alignment_bigpsl.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + trix + </li> + <ul> + + <li> + <a href="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx">BLAST_alignment_bigpsl.bb.ixx</a> + </li> + <li> + <a href="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix">BLAST_alignment_bigpsl.bb.ix</a> + </li> + + </ul> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/blast_out.ix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/blast_out.ix Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,5922 @@\n+100 FBpp0305833,33\n+10004032..10004101 FBpp0076082,6 FBpp0303926,6 FBpp0304911,6 FBpp0304912,6 FBpp0311219,6\n+1002 FBpp0110195,43\n+10033183..10033424 FBpp0076082,7 FBpp0303926,7 FBpp0304911,7 FBpp0304912,7 FBpp0311219,7\n+10036646..10036856 FBpp0076082,8 FBpp0303926,8 FBpp0304911,8 FBpp0304912,8 FBpp0311219,8\n+10037344..10037471 FBpp0076082,9 FBpp0303926,9 FBpp0304911,9 FBpp0304912,9 FBpp0311219,9\n+10040856..10041024 FBpp0303926,10 FBpp0304911,10 FBpp0304912,10 FBpp0311219,10\n+10040856..10041056 FBpp0076082,10\n+1004158..1004373 FBpp0308592,11\n+1004158..1004412 FBpp0088249,11\n+1004470..1004618 FBpp0088249,12 FBpp0308592,12\n+1005 FBpp0290500,46\n+1005807..1006009 FBpp0088249,13 FBpp0308592,13\n+1006066..1006160 FBpp0088249,14 FBpp0308592,14\n+10071644..10072014 FBpp0311219,11\n+10071662..10072014 FBpp0303926,11\n+1010 FBpp0088293,43 FBpp0088297,39 FBpp0302771,37\n+10113188..10113228 FBpp0304911,11\n+10138856..10138887 FBpp0304912,11\n+1014359..1014526 FBpp0088287,14 FBpp0088288,13 FBpp0088289,13 FBpp0301599,14\n+1014583..1014728 FBpp0088287,13 FBpp0088288,12 FBpp0088289,12 FBpp0301599,13\n+1014778..1014908 FBpp0088287,12 FBpp0088288,11 FBpp0088289,11 FBpp0301599,12\n+10149341..10149669 FBpp0076037,13 FBpp0076038,13 FBpp0076039,13\n+1014966..1015301 FBpp0301599,11\n+1014966..1015352 FBpp0088287,11 FBpp0088288,10 FBpp0088289,10\n+10150333..10150501 FBpp0076037,12 FBpp0076038,12 FBpp0076039,12\n+10150976..10151103 FBpp0076037,11 FBpp0076038,11 FBpp0076039,11\n+10153613..10153750 FBpp0076037,10 FBpp0076038,10 FBpp0076039,10\n+1015425..1015620 FBpp0088287,10 FBpp0088288,9 FBpp0088289,9 FBpp0301599,10\n+10154762..10154972 FBpp0076037,9 FBpp0076038,9 FBpp0076039,9\n+10156353..10156564 FBpp0076037,8 FBpp0076038,8 FBpp0076039,8\n+1016376..1018709 FBpp0088287,9 FBpp0088288,8 FBpp0088289,8 FBpp0301599,9\n+10182243..10182282 FBpp0076037,7 FBpp0076038,7 FBpp0076039,7\n+1018770..1019925 FBpp0088288,7 FBpp0088289,7\n+1018770..1020015 FBpp0088287,8 FBpp0301599,8\n+1022242..1023471 FBpp0088287,7 FBpp0301599,7\n+1031890..1031953 FBpp0088250,6 FBpp0305828,6 FBpp0311086,6\n+1032889..1033218 FBpp0305828,7\n+1032907..1033218 FBpp0088250,7 FBpp0311086,7\n+1033272..1034413 FBpp0088250,8 FBpp0305828,8 FBpp0311086,8\n+1037278..1037422 FBpp0088281,19 FBpp0088282,19 FBpp0088283,20 FBpp0099496,21 FBpp0099497,20 FBpp0099498,20 FBpp0289606,19 FBpp0289607,21 FBpp0289608,21 FBpp0305829,19 FBpp0305830,21 FBpp0305831,20\n+1037476..1037569 FBpp0305829,18 FBpp0305830,20 FBpp0305831,19\n+1037476..1037590 FBpp0088281,18 FBpp0088282,18 FBpp0088283,19 FBpp0099496,20 FBpp0099497,19 FBpp0099498,19 FBpp0289606,18 FBpp0289607,20 FBpp0289608,20\n+1037646..1037740 FBpp0088281,17 FBpp0088282,17 FBpp0088283,18 FBpp0099496,19 FBpp0099497,18 FBpp0099498,18 FBpp0289606,17 FBpp0289607,19 FBpp0289608,19 FBpp0305829,17 FBpp0305830,19 FBpp0305831,18\n+1038359..1038434 FBpp0099496,18 FBpp0289607,18 FBpp0305829,16 FBpp0305830,18 FBpp0305831,17\n+1038359..1038437 FBpp0088281,16 FBpp0088282,16 FBpp0088283,17 FBpp0099497,17 FBpp0289606,16 FBpp0289608,18\n+1038359..1038458 FBpp0099498,17\n+1040013..1040078 FBpp0099496,17 FBpp0289607,17 FBpp0289608,17 FBpp0305830,17 FBpp0305831,16\n+104083..104413 FBpp0300839,16\n+1043468..1043521 FBpp0305830,16\n+1043468..1043524 FBpp0088283,16 FBpp0099496,16 FBpp0099497,16 FBpp0099498,16 FBpp0289607,16 FBpp0289608,16\n+1045156..1045248 FBpp0088281,15 FBpp0088282,15 FBpp0088283,15 FBpp0099496,15 FBpp0099497,15 FBpp0099498,15 FBpp0289606,15 FBpp0289607,15 FBpp0289608,15 FBpp0305829,15 FBpp0305830,15 FBpp0305831,15\n+1047 FBpp0088152,49\n+1047264..1047390 FBpp0088281,14 FBpp0088282,14 FBpp0088283,14 FBpp0099496,14 FBpp0099497,14 FBpp0099498,14 FBpp0289606,14 FBpp0289607,14 FBpp0289608,14 FBpp0305829,14 FBpp0305830,14 FBpp0305831,14\n+1047453..1047575 FBpp0088281,13 FBpp0088282,13 FBpp0088283,13 FBpp0099496,13 FBpp0099497,13 FBpp0099498,13 FBpp0289606,13 FBpp0289607,13 FBpp0289608,13 FBpp0305829,13 FBpp0305830,13 FBpp0305831,13\n+1047635..1047729 FBpp0088281,12 FBpp0088282,12 FBpp00'..b' FBpp0300963,45 FBpp0301556,33 FBpp0301599,31 FBpp0301616,29 FBpp0302583,34 FBpp0302584,26 FBpp0302585,34 FBpp0302673,27 FBpp0302674,27 FBpp0302676,24 FBpp0302677,24 FBpp0302678,24 FBpp0302730,27 FBpp0302758,30 FBpp0302759,30 FBpp0302760,30 FBpp0302771,31 FBpp0302942,27 FBpp0302965,30 FBpp0303037,30 FBpp0303372,38 FBpp0303458,41 FBpp0303843,27 FBpp0303844,27 FBpp0303926,28 FBpp0304310,24 FBpp0304364,27 FBpp0304397,29 FBpp0304911,28 FBpp0304912,28 FBpp0304920,63 FBpp0304921,61 FBpp0304922,60 FBpp0304923,60 FBpp0304924,57 FBpp0304925,60 FBpp0304926,56 FBpp0304928,60 FBpp0304929,53 FBpp0305080,30 FBpp0305081,26 FBpp0305124,32 FBpp0305125,36 FBpp0305126,37 FBpp0305127,35 FBpp0305128,34 FBpp0305133,31 FBpp0305364,29 FBpp0305826,30 FBpp0305827,33 FBpp0305828,25 FBpp0305829,36 FBpp0305830,38 FBpp0305831,37 FBpp0305832,29 FBpp0305833,27 FBpp0305834,31 FBpp0305835,27 FBpp0305836,24 FBpp0305837,25 FBpp0305852,26 FBpp0305853,34 FBpp0305854,36 FBpp0305856,28 FBpp0306185,41 FBpp0306186,32 FBpp0306187,28 FBpp0306251,23 FBpp0306415,35 FBpp0306510,34 FBpp0306511,30 FBpp0306512,30 FBpp0306552,57 FBpp0306553,65 FBpp0306555,47 FBpp0306556,25 FBpp0306557,25 FBpp0306615,23 FBpp0306687,27 FBpp0306688,31 FBpp0306689,29 FBpp0306723,32 FBpp0306805,40 FBpp0306958,29 FBpp0307023,35 FBpp0307024,35 FBpp0307131,27 FBpp0307154,30 FBpp0307155,30 FBpp0307156,30 FBpp0307251,30 FBpp0307252,29 FBpp0307433,27 FBpp0307559,30 FBpp0307567,32 FBpp0307596,26 FBpp0307597,26 FBpp0307627,30 FBpp0307631,30 FBpp0307867,27 FBpp0307912,33 FBpp0308592,31 FBpp0308779,26 FBpp0308780,26 FBpp0308953,28 FBpp0309009,26 FBpp0309069,28 FBpp0309247,30 FBpp0309354,25 FBpp0309437,26 FBpp0309503,26 FBpp0309504,26 FBpp0309974,30 FBpp0310041,26 FBpp0310042,26 FBpp0310043,26 FBpp0310122,28 FBpp0310184,30 FBpp0310241,31 FBpp0310326,24 FBpp0310409,23 FBpp0310410,23 FBpp0310439,31 FBpp0310504,28 FBpp0310628,41 FBpp0310629,40 FBpp0310630,40 FBpp0310922,28 FBpp0311086,25 FBpp0311183,34 FBpp0311184,36 FBpp0311188,36 FBpp0311190,30 FBpp0311208,24 FBpp0311219,28 FBpp0311224,45 FBpp0311232,29 FBpp0311242,63 FBpp0311294,25 FBpp0311295,25 FBpp0311372,25 FBpp0311373,25 FBpp0311392,34 FBpp0311396,28 FBpp0311450,26 FBpp0311451,34 FBpp0311463,29 FBpp0311464,29 FBpp0311465,30 FBpp0311493,29 FBpp0311495,28 FBpp0311705,25\n+vha55-pa FBpp0082140,13\n+vha55-pb FBpp0082139,13\n+vha55-pc FBpp0290875,13\n+vha68-2-pa FBpp0079999,13\n+vha68-2-pb FBpp0080000,13\n+vha68-2-pc FBpp0080001,13\n+vha68-2-pd FBpp0294002,13\n+vha68-2-pe FBpp0307596,13\n+vha68-2-pf FBpp0307597,13\n+vha68-3-pa FBpp0080002,11\n+x FBpp0070070,4 FBpp0070566,4 FBpp0070567,4 FBpp0070723,4 FBpp0070763,4 FBpp0070802,4 FBpp0070804,4 FBpp0071086,4 FBpp0071229,4 FBpp0073476,4 FBpp0073513,4 FBpp0073515,4 FBpp0073730,4 FBpp0074564,4 FBpp0089045,4 FBpp0112979,4 FBpp0289609,4 FBpp0292066,4 FBpp0292091,4 FBpp0298271,4 FBpp0300801,4 FBpp0307154,4 FBpp0307155,4 FBpp0307156,4 FBpp0309354,4 FBpp0310122,4 FBpp0310184,4 FBpp0310241,4 FBpp0310504,4 FBpp0311372,4 FBpp0311373,4\n+x2j708 FBpp0310042,28\n+x2j8x8 FBpp0311219,30\n+x2j9e1 FBpp0311224,47\n+x2jbi2 FBpp0311208,26\n+x2jc49 FBpp0310629,42\n+x2jcm1 FBpp0310630,42\n+x2jcs2 FBpp0311294,27\n+x2jd84 FBpp0311295,27\n+x2jd86 FBpp0310043,28\n+x2jd89 FBpp0311242,65\n+x2jej4 FBpp0310184,32\n+x2jgd3 FBpp0310628,43\n+y-pa FBpp0070070,11\n+yellow-b-pa FBpp0080451,11\n+yellow-b-pb FBpp0310326,11\n+yellow-c-pa FBpp0080260,12\n+yellow-c-pb FBpp0311705,12\n+yellow-d-pa FBpp0071920,12\n+yellow-d2-pa FBpp0071921,11\n+yellow-e-pa FBpp0082225,12\n+yellow-e2-pb FBpp0291732,13\n+yellow-e3-pa FBpp0082227,13\n+yellow-f-pa FBpp0082191,14\n+yellow-f-pb FBpp0303843,14\n+yellow-f-pc FBpp0303844,14\n+yellow-f2-pa FBpp0082190,14\n+yellow-g2-pa FBpp0072761,11\n+yellow-h-pa FBpp0088184,12\n+zfh2-pa FBpp0088139,19\n+zfh2-pb FBpp0297996,19\n+zfh2-pc FBpp0305133,18\n+zip102b-pb FBpp0088201,12\n+zip102b-pd FBpp0305837,12\n+zip102b-pe FBpp0309503,13\n+zip102b-pf FBpp0309504,13\n+zyx-pa FBpp0088274,17\n+zyx-pb FBpp0088275,17\n+zyx-pg FBpp0088278,17\n+zyx-ph FBpp0301616,16\n+zyx-pl FBpp0311465,17\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/blast_out.ixx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/blast_out.ixx Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +100 0000000000 +404 0000010A45 +cdk2-0000020A52 +fbpp0000002CEC4 +gluri00000409E8 +np_65000005085C +type 00000620E7 |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/blat_alignment_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/blat_alignment_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,83 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb">BLAT_alignment_bigpsl.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + trix + </li> + <ul> + + <li> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix">BLAT_alignment_bigpsl.bb.ix</a> + </li> + <li> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx">BLAT_alignment_bigpsl.bb.ixx</a> + </li> + + </ul> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/blat_out.ix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/blat_out.ix Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,209 @@\n+102a NM_001038713,8 NM_001258487,8 NM_001272121,8 NM_143657,8\n+102b NM_001144383,8 NM_001297784,8 NM_143662,8 NM_205872,8\n+102c NM_143694,5\n+102f NM_001272158,7 NM_079892,7\n+2 NM_001258496,6 NM_001272130,6 NM_079884,6\n+26 NM_143679,6 NM_166791,6\n+3 NM_001038721,7 NM_001038723,7 NM_001038725,7\n+3c NM_143682,6\n+4 NM_001258479,6 NM_001272118,6 NM_143648,6\n+4-kinase NM_001038716,5 NM_001038717,5\n+49 NM_001272135,6 NM_143669,6\n+4e-t NM_001272149,4 NM_166796,4 NM_166797,4 NM_166798,4\n+4g NM_001103382,7 NM_001144385,7 NM_079901,7\n+5-phosphate NM_001038716,4 NM_001038717,4\n+7 NM_001103380,7 NM_001103381,7 NM_001258488,4 NM_166748,4 NM_166749,4 NM_166751,4 NM_205871,4\n+a NM_001014703,6 NM_001031860,9 NM_001038717,8 NM_001038719,6 NM_001038721,11 NM_001258499,4 NM_079877,7 NM_079878,8 NM_079879,8 NM_079882,8 NM_079884,10 NM_079889,7 NM_079891,7 NM_079892,11 NM_079893,7 NM_079894,7 NM_079895,7 NM_079898,4 NM_079898,7 NM_079899,9 NM_079900,8 NM_079901,11 NM_080103,6 NM_143648,10 NM_143649,6 NM_143651,8 NM_143661,6 NM_143668,6 NM_143669,12 NM_143671,6 NM_143673,8 NM_143674,9 NM_143676,6 NM_143677,6 NM_143679,9 NM_143684,6 NM_143692,6 NM_166718,7 NM_166730,6 NM_166735,6 NM_166742,6 NM_166745,6 NM_166748,7 NM_166753,6 NM_166759,11 NM_166767,9 NM_166770,6 NM_166775,10 NM_166780,7 NM_166786,7 NM_166792,6 NM_166804,4 NM_166805,4 NM_166807,6 NM_166808,10 NM_166810,11 NM_166816,6 NM_205874,7\n+actbeta NM_143685,4\n+activating NM_001038713,5 NM_001258487,5 NM_001272121,5 NM_143657,5\n+activator NM_001031858,5 NM_001031859,5 NM_001031860,5 NM_001258510,5 NM_001258511,5\n+activin-beta NM_143685,3\n+adp NM_001258479,3 NM_001272118,3 NM_001272158,3 NM_079892,3 NM_143648,3\n+ank NM_001169348,7 NM_175926,7 NM_175927,7 NM_175928,7\n+ankyrin NM_001169348,3 NM_175926,3 NM_175927,3 NM_175928,3\n+apolipophorin NM_001272156,3 NM_001297791,3 NM_001297792,3 NM_079895,3\n+apolpp NM_001272156,4 NM_001297791,4 NM_001297792,4 NM_079895,4\n+arf102f NM_001272158,8 NM_079892,8\n+arl4 NM_001258479,7 NM_001272118,7 NM_143648,7\n+asator NM_001272125,3 NM_001272125,7 NM_001272126,3 NM_001272126,7 NM_001272127,3 NM_001272127,7 NM_001272128,3 NM_001272128,7 NM_001272129,3 NM_001272129,7 NM_001297785,3 NM_001297785,7 NM_143667,3 NM_143667,7 NM_166765,3 NM_166765,7 NM_166766,3 NM_166766,7\n+at NM_001038713,7 NM_001258487,7 NM_001272121,7 NM_001272158,6 NM_079892,6 NM_143657,7\n+atp NM_001272152,3 NM_001297790,3 NM_166808,3\n+atpase NM_001014687,6 NM_001014688,6 NM_001014689,6 NM_001038714,6 NM_001201585,6 NM_001201586,6 NM_001201587,6 NM_001201588,6 NM_001201589,6 NM_166754,6 NM_166755,6\n+atpsynbeta NM_001272152,7 NM_001297790,7 NM_166808,7\n+b NM_001014695,6 NM_001031859,9 NM_001038716,8 NM_001038718,6 NM_001042785,9 NM_001103382,11 NM_001169358,7 NM_001258471,4 NM_001258471,7 NM_001258473,8 NM_001258479,10 NM_001258481,6 NM_001258496,10 NM_001272124,6 NM_001272131,6 NM_001272135,12 NM_001272136,6 NM_001272137,6 NM_001272147,8 NM_001272156,7 NM_001272158,11 NM_001297780,6 NM_079877,4 NM_079880,7 NM_079885,9 NM_143656,6 NM_143670,6 NM_143758,6 NM_166714,8 NM_166732,6 NM_166736,6 NM_166744,8 NM_166749,7 NM_166752,6 NM_166756,8 NM_166758,7 NM_166760,11 NM_166773,6 NM_166777,10 NM_166779,8 NM_166781,7 NM_166789,7 NM_166791,9 NM_166794,6 NM_166797,7 NM_166804,7 NM_166811,11 NM_166823,7 NM_166824,6 NM_166826,6 NM_166827,7 NM_175926,6 NM_205870,8 NM_205872,12\n+bent NM_001169354,3 NM_001272142,3 NM_001272143,3 NM_001297787,3 NM_205876,3\n+beta NM_001272152,5 NM_001297790,5 NM_166808,5\n+binding NM_001272132,4 NM_001272133,4 NM_001272134,4 NM_079885,4 NM_166767,4 NM_166768,4 NM_166769,4\n+bip2 NM_143666,3 NM_143666,4\n+bt NM_001169354,4 NM_001272142,4 NM_001272143,4 NM_001297787,4 NM_205876,4\n+c NM_001014694,7 NM_001014705,6 NM_001038713,12 NM_001038723,11 NM_001144385,11 NM_001169359,7 NM_001169364,6 NM_001258472,8 NM_001258478,6 NM_001258492,7 NM_001258507,6 NM_001272118,10 NM_001272122,8 NM_001272123,6 NM_001272130,10 NM_001272138,6 NM_001272139,6 NM_001272144,6 NM_001272148,8 NM_'..b'1031860,8 NM_001038709,6 NM_001038712,5 NM_001038713,11 NM_001038714,9 NM_001038716,7 NM_001038717,7 NM_001038718,5 NM_001038719,5 NM_001038721,10 NM_001038723,10 NM_001038725,10 NM_001042785,8 NM_001042786,8 NM_001103379,5 NM_001103380,10 NM_001103381,10 NM_001103382,10 NM_001144383,11 NM_001144385,10 NM_001169348,5 NM_001169350,5 NM_001169351,5 NM_001169352,5 NM_001169353,9 NM_001169354,6 NM_001169356,5 NM_001169357,5 NM_001169358,6 NM_001169359,6 NM_001169360,10 NM_001169361,10 NM_001169362,10 NM_001169363,6 NM_001169364,5 NM_001201585,9 NM_001201586,9 NM_001201587,9 NM_001201588,9 NM_001201589,9 NM_001258471,6 NM_001258472,7 NM_001258473,7 NM_001258475,7 NM_001258476,6 NM_001258477,6 NM_001258478,5 NM_001258479,9 NM_001258480,5 NM_001258481,5 NM_001258482,7 NM_001258483,7 NM_001258484,5 NM_001258485,5 NM_001258487,11 NM_001258488,6 NM_001258491,7 NM_001258492,6 NM_001258493,6 NM_001258496,9 NM_001258497,5 NM_001258498,5 NM_001258499,6 NM_001258500,5 NM_001258501,5 NM_001258506,5 NM_001258507,5 NM_001258508,5 NM_001258510,8 NM_001258511,8 NM_001272114,5 NM_001272115,5 NM_001272116,5 NM_001272117,5 NM_001272118,9 NM_001272120,5 NM_001272121,11 NM_001272122,7 NM_001272123,5 NM_001272124,5 NM_001272125,5 NM_001272126,5 NM_001272127,5 NM_001272128,5 NM_001272129,5 NM_001272130,9 NM_001272131,5 NM_001272132,8 NM_001272133,8 NM_001272134,8 NM_001272135,11 NM_001272136,5 NM_001272137,5 NM_001272138,5 NM_001272139,5 NM_001272140,5 NM_001272141,5 NM_001272142,6 NM_001272143,6 NM_001272144,5 NM_001272145,5 NM_001272146,5 NM_001272147,7 NM_001272148,7 NM_001272149,6 NM_001272150,6 NM_001272151,8 NM_001272152,9 NM_001272153,10 NM_001272154,10 NM_001272155,10 NM_001272156,6 NM_001272157,6 NM_001272158,10 NM_001297780,5 NM_001297781,7 NM_001297782,7 NM_001297783,5 NM_001297784,11 NM_001297785,5 NM_001297786,5 NM_001297787,6 NM_001297788,5 NM_001297789,7 NM_001297790,9 NM_001297791,6 NM_001297792,6 NM_001297793,6 NM_001297794,5 NM_079877,6 NM_079878,7 NM_079879,7 NM_079880,6 NM_079882,7 NM_079883,10 NM_079884,9 NM_079885,8 NM_079886,9 NM_079889,6 NM_079891,6 NM_079892,10 NM_079893,6 NM_079894,6 NM_079895,6 NM_079896,10 NM_079898,6 NM_079899,8 NM_079900,7 NM_079901,10 NM_080103,5 NM_143648,9 NM_143649,5 NM_143651,7 NM_143656,5 NM_143657,11 NM_143661,5 NM_143662,11 NM_143667,5 NM_143668,5 NM_143669,11 NM_143670,5 NM_143671,5 NM_143673,7 NM_143674,8 NM_143676,5 NM_143677,5 NM_143679,8 NM_143684,5 NM_143686,5 NM_143692,5 NM_143693,5 NM_143758,5 NM_166714,7 NM_166718,6 NM_166720,6 NM_166723,6 NM_166724,6 NM_166728,5 NM_166729,5 NM_166730,5 NM_166731,5 NM_166732,5 NM_166733,5 NM_166735,5 NM_166736,5 NM_166737,5 NM_166738,5 NM_166740,5 NM_166742,5 NM_166743,7 NM_166744,7 NM_166745,5 NM_166746,5 NM_166747,5 NM_166748,6 NM_166749,6 NM_166751,6 NM_166752,5 NM_166753,5 NM_166754,9 NM_166755,9 NM_166756,7 NM_166757,7 NM_166758,6 NM_166759,10 NM_166760,10 NM_166761,10 NM_166764,10 NM_166765,5 NM_166766,5 NM_166767,8 NM_166768,8 NM_166769,8 NM_166770,5 NM_166771,5 NM_166773,5 NM_166774,9 NM_166775,9 NM_166776,9 NM_166777,9 NM_166779,7 NM_166780,6 NM_166781,6 NM_166783,6 NM_166784,6 NM_166785,6 NM_166786,6 NM_166787,6 NM_166788,6 NM_166789,6 NM_166791,8 NM_166792,5 NM_166793,5 NM_166794,5 NM_166796,6 NM_166797,6 NM_166798,6 NM_166804,6 NM_166805,6 NM_166807,5 NM_166808,9 NM_166810,10 NM_166811,10 NM_166812,10 NM_166813,10 NM_166815,5 NM_166816,5 NM_166819,5 NM_166822,6 NM_166823,6 NM_166824,5 NM_166825,5 NM_166826,5 NM_166827,6 NM_175926,5 NM_175927,5 NM_175928,5 NM_205865,5 NM_205866,5 NM_205870,7 NM_205871,6 NM_205872,11 NM_205873,7 NM_205874,6 NM_205876,6 NM_205878,5\n+yellow-h NM_143655,3 NM_143655,4\n+zfh2 NM_001258496,7 NM_001272130,7 NM_079884,7\n+zinc NM_001144383,3 NM_001297784,3 NM_143662,3 NM_205872,3\n+zip102b NM_001144383,9 NM_001297784,9 NM_143662,9 NM_205872,9\n+zn NM_001258496,3 NM_001272130,3 NM_079884,3\n+zyx NM_001258501,7 NM_143758,7 NM_166815,7 NM_166816,7 NM_166819,7\n+zyxin NM_001258501,3 NM_143758,3 NM_166815,3 NM_166816,3 NM_166819,3\n' |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/trix_index_files/blat_out.ixx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trix_index_files/blat_out.ixx Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +102a 0000000000 |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_multiple_tracks/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,68 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_154.dat +DEBUG:root:data_value: {u'index': u'/home/galaxy/galaxy/database/datasets/_metadata_files/000/metadata_6.dat', u'long_label': u'', u'name': u'HISAT2_Accepted_Hits', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'11'} +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_157.dat +DEBUG:root:data_value: {u'long_label': u'', u'name': u'RNA-Seq_Alignment_Coverage', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_150.dat +DEBUG:root:data_value: {u'long_label': u'', u'name': u'Multi-Fasta_GlimmerHMM_Gene_Predictions', u'database': u'', u'track_color': u'#000000', u'group_name': u'Other group', u'order_index': u'21'} +DEBUG:root:Calling gff3ToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpCO1Rvj.sorted.bigGenePred +DEBUG:root:chrom_sizes_file_name: /tmp/tmpa23XII.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/188/dataset_213_files/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_158.dat +DEBUG:root:data_value: {u'long_label': u'', u'name': u'StringTie_Assembled_Transcripts', u'database': u'', u'track_color': u'#000000', u'group_name': u'Other group', u'order_index': u'20'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpq6ZNag.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /tmp/tmpa23XII.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/188/dataset_213_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x7efc7727b690>, <BigWig.BigWig object at 0x7efc7727b750>, <Gtf.Gtf object at 0x7efc7727b850>, <Gff3.Gff3 object at 0x7efc7727b810>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/188/dataset_213_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_HISAT2_Accepted_Hits_bam (in group default_group) +DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/188/dataset_213_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_RNA_Seq_Alignment_Coverage_bigwig (in group default_group) +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/188/dataset_213_files/myHub/Dbia3/groups.txt the group Other group +DEBUG:root:We just added track gonramp_StringTie_Assembled_Transcripts_bb (in group other_group) +DEBUG:root:We DON'T add in /home/galaxy/galaxy/database/jobs/000/188/dataset_213_files/myHub/Dbia3/groups.txt the group Other group +DEBUG:root:We just added track gonramp_Multi_Fasta_GlimmerHMM_Gene_Predictions_bb (in group other_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + +name other_group +label Other group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,50 @@ + +track gonramp_HISAT2_Accepted_Hits_bam +longLabel HISAT2 Accepted Hits.bam +shortLabel HISAT2 Accepted H +bigDataUrl tracks/HISAT2_Accepted_Hits.bam +type bam +visibility pack +thickDrawItem off +priority 11 +color 0,0,0 +group default_group +searchIndex name + +track gonramp_RNA_Seq_Alignment_Coverage_bigwig +longLabel RNA-Seq Alignment Coverage +shortLabel RNA-Seq Alignment +bigDataUrl tracks/RNA-Seq_Alignment_Coverage.bigwig +visibility full +priority 10 +color 0,0,0 +group default_group +type bigWig 1.000000 39.000000 +autoScale on +maxHeightPixels 100:32:8 +windowingFunction mean+whiskers + + +track gonramp_StringTie_Assembled_Transcripts_bb +longLabel StringTie Assembled Transcripts +shortLabel StringTie Assembl +bigDataUrl tracks/StringTie_Assembled_Transcripts.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 20 +color 0,0,0 +group other_group +searchIndex name + +track gonramp_Multi_Fasta_GlimmerHMM_Gene_Predictions_bb +longLabel Multi-Fasta GlimmerHMM Gene Predictions +shortLabel Multi-Fasta Glimm +bigDataUrl tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 21 +color 0,0,0 +group other_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam |
| b |
| Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai |
| b |
| Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb |
| b |
| Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig |
| b |
| Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb |
| b |
| Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_multiple_tracks/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_multiple_tracks/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,82 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig">RNA-Seq_Alignment_Coverage.bigwig</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb">Multi-Fasta_GlimmerHMM_Gene_Predictions.bb</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_no_track/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_no_track/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,16 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_no_track/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_no_track/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_no_track/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_no_track/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_no_track/two_groups_no_track_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_no_track/two_groups_no_track_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,54 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_both/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,42 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_157.dat +DEBUG:root:data_value: {u'long_label': u'', u'name': u'RNA-Seq_Alignment_Coverage', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_158.dat +DEBUG:root:data_value: {u'long_label': u'', u'name': u'StringTie_Assembled_Transcripts', u'database': u'', u'track_color': u'#000000', u'group_name': u'Other group', u'order_index': u'20'} +DEBUG:root:Calling gtfToGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling genePredToBigGenePred: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:sorted_bed_file_name: /tmp/tmpnPwD96.sortedBed.bigGenePred +DEBUG:root:chrom_sizes_file_name: /tmp/tmp1csS9Z.chrom.sizes +DEBUG:root:big_bed_file_name: /home/galaxy/galaxy/database/jobs/000/186/dataset_211_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb +DEBUG:root:typeOption: bed12+8 +DEBUG:root:autoSql: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/6aa28a85cc38/hubarchivecreator/bigGenePred.as +DEBUG:root:tab option: True +DEBUG:root:Calling bedToBigBed: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigWig.BigWig object at 0x7f12dc4d7650>, <Gtf.Gtf object at 0x7f12dc4d7750>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/186/dataset_211_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_RNA_Seq_Alignment_Coverage_bigwig (in group default_group) +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/186/dataset_211_files/myHub/Dbia3/groups.txt the group Other group +DEBUG:root:We just added track gonramp_StringTie_Assembled_Transcripts_bb (in group other_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + +name other_group +label Other group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,26 @@ + +track gonramp_RNA_Seq_Alignment_Coverage_bigwig +longLabel RNA-Seq Alignment Coverage +shortLabel RNA-Seq Alignment +bigDataUrl tracks/RNA-Seq_Alignment_Coverage.bigwig +visibility full +priority 10 +color 0,0,0 +group default_group +type bigWig 1.000000 39.000000 +autoScale on +maxHeightPixels 100:32:8 +windowingFunction mean+whiskers + + +track gonramp_StringTie_Assembled_Transcripts_bb +longLabel StringTie Assembled Transcripts +shortLabel StringTie Assembl +bigDataUrl tracks/StringTie_Assembled_Transcripts.bb +type bigGenePred +visibility dense +thickDrawItem off +priority 20 +color 0,0,0 +group other_group +searchIndex name |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig |
| b |
| Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb |
| b |
| Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_both/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_both/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,73 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig">RNA-Seq_Alignment_Coverage.bigwig</a> + </li> + <li> + <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/__main__.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/__main__.log Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,20 @@ +DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### + +DEBUG:root:Calling faToTwoBit: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling twoBitInfo: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:Calling sort: +DEBUG:root:--------- +DEBUG:root: +DEBUG:root:input_false_path: /home/galaxy/galaxy/database/datasets/000/dataset_157.dat +DEBUG:root:data_value: {u'long_label': u'', u'name': u'RNA-Seq_Alignment_Coverage', u'database': u'', u'track_color': u'#000000', u'group_name': u'Default group', u'order_index': u'10'} +DEBUG:root:----- End of all_datatype_dictionary processing ----- +DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigWig.BigWig object at 0x7f9036ad9650>] +DEBUG:root:----- Beginning of Track adding processing ----- +DEBUG:root:We just added in /home/galaxy/galaxy/database/jobs/000/184/dataset_209_files/myHub/Dbia3/groups.txt the group Default group +DEBUG:root:We just added track gonramp_RNA_Seq_Alignment_Coverage_bigwig (in group default_group) +DEBUG:root:----- End of Track adding processing ----- +DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +name default_group +label Default group +priority 2 +defaultIsClosed 0 + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ + +track gonramp_RNA_Seq_Alignment_Coverage_bigwig +longLabel RNA-Seq Alignment Coverage +shortLabel RNA-Seq Alignment +bigDataUrl tracks/RNA-Seq_Alignment_Coverage.bigwig +visibility full +priority 10 +color 0,0,0 +group default_group +type bigWig 1.000000 39.000000 +autoScale on +maxHeightPixels 100:32:8 +windowingFunction mean+whiskers + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig |
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| Binary file test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/myHub/genomes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/genomes.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,10 @@ +genome Dbia3 +trackDb Dbia3/trackDb.txt +groups Dbia3/groups.txt +description Dbia3 +twoBitPath Dbia3/Dbia3.2bit +organism Dbia3 +defaultPos contig25 +orderKey 4500 +scientificName Dbia3 +htmlPath Dbia3/description.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/myHub/hub.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/myHub/hub.txt Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +hub gonrampDbia3 +shortLabel Dbia3 +longLabel Dbia3 +genomesFile genomes.txt +email gonramp@temporary.domain +descriptionUrl Dbia3.html |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -0,0 +1,70 @@ + +<html> + <body> + <p> + The following has been generated by Hub Archive Creator: + </p> + <ul> + + <li> + myHub + </li> + <ul> + + <li> + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 + </li> + <ul> + + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> + </li> + <li> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> + </li> + <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + tracks + </li> + <ul> + + <li> + <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig">RNA-Seq_Alignment_Coverage.bigwig</a> + </li> + + </ul> + <li> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + + </ul> + + </ul> + <li> + . + </li> + <ul> + + <li> + <a href="./__main__.log">__main__.log</a> + </li> + + </ul> + + </ul> + </body> +</html> + + + |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Wed May 16 18:04:20 2018 -0400 |
| b |
| b'@@ -0,0 +1,925 @@\n+ #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"\n+ #set database = str($f.formatChoice.bedChoice.database)\n+ #silent $extra_data_dict.update({"database": $database})\n+ #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"\n+ #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index\n+ #if $i.element_identifier.endswith("ix")\n+ #$extra_data_dict.update({"index_ix": str($i)})\n+ #elif $i.element_identifier.endswith("ixx")\n+ #$extra_data_dict.update({"index_ixx": str($i)})\n+ #end if\n+ #end for\n+ ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)\n+ ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)\n+ ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})\n+ #end if\n+ #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,\n+ $extra_data_dict)\n+ #end if\n+ #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"\n+ #set database = str($f.formatChoice.bedChoice.database)\n+ #silent $extra_data_dict.update({"database": $database})\n+ #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"\n+ #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index\n+ #if $i.element_identifier.endswith("ix")\n+ #$extra_data_dict.update({"index_ix": str($i)})\n+ #elif $i.element_identifier.endswith("ixx")\n+ #$extra_data_dict.update({"index_ixx": str($i)})\n+ #end if\n+ #end for\n+ ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)\n+ ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)\n+ ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})\n+ #end if\n+ #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,\n+ $extra_data_dict)\n+ #end if \n+ \n+ #if $f.formatChoice.format_select == "bigbed"\n+ #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"\n+ ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)\n+ ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)\n+ #for i in $f.formatChoice.add_trix_index.trix_index\n+ #if $i.element_identifier.endswith("ix")\n+ #$extra_data_dict.update({"index_ix": str($i)})\n+ #elif $i.element_identifier.endswith("ixx")\n+ #$extra_data_dict.update({"index_ixx": str($i)})\n+ #end if\n+ #end for\n+ #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})\n+ ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)\n+ ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})\n+ #end if\n+ #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,\n+ $extra_data_dict)\n+ #end if \n+ <!-- Test with only the fasta file -->\n+ <test>\n+ <param name="genome_name" value="Dbia3"/>\n+ '..b' <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="gtf"/>\n+ <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>\n+ <param name="track_color" value="#000000"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">\n+ <extra_files type="file"\n+ name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"\n+ value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"\n+ compare="sim_size"\n+ />\n+ <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />\n+\n+ <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->\n+ </output>\n+ </test>\n+\n+ <!-- Test default label in a track -->\n+ <test>\n+ <param name="genome_name" value="Dbia3"/>\n+ <param name="fasta_file" value="common/dbia3.fa"/>\n+ <repeat name="group">\n+ <param name="group_name" value="Default group"/>\n+ <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="bam"/>\n+ <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>\n+ <param name="track_color" value="#000000"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <output name="output" file="default_color/default_color_trackhub.html">\n+ <expand macro="verify_hub_structure" test="default_color" />\n+ <!-- Verify trackDb.txt contains default label -->\n+ <extra_files type="file" name="myHub/Dbia3/trackDb.txt">\n+ <assert_contents>\n+ <has_text text="longLabel HISAT2 Accepted Hits.bam"/>\n+ </assert_contents>\n+ </extra_files>\n+\n+ <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->\n+ </output>\n+ </test>\n+\n+ <!-- Test customized label in a track -->\n+ <test>\n+ <param name="genome_name" value="Dbia3"/>\n+ <param name="fasta_file" value="common/dbia3.fa"/>\n+ <repeat name="group">\n+ <param name="group_name" value="Default group"/>\n+ <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="bam"/>\n+ <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>\n+ <param name="longLabel" value="HISAT sequence alignment" />\n+ <param name="track_color" value="#000000"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <output name="output" file="changed_label/changed_label_trackhub.html">\n+ <expand macro="verify_hub_structure" test="changed_label" />\n+ <!-- Verify trackDb.txt contains the customized label -->\n+ <extra_files type="file" name="myHub/Dbia3/trackDb.txt">\n+ <assert_contents>\n+ <has_text text="longLabel HISAT sequence alignment"/>\n+ </assert_contents>\n+ </extra_files>\n+\n+ <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->\n+ </output>\n+ </test>\n' |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jul 10 17:08:38 2017 -0400 +++ b/tool_dependencies.xml Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -16,7 +16,7 @@ <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_hac" version="340"> - <repository changeset_revision="a819439b6d76" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1a15120c22c8" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_bigbed" version="340"> <repository changeset_revision="e3faf2af4e59" name="package_ucsc_bigbed_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| b |
| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Fasta.py --- a/util/Fasta.py Mon Jul 10 17:08:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,16 +0,0 @@ -#!/usr/bin/python -# -*- coding: utf8 -*- - -""" -Class describing the Fasta format -(As of the 07/20/2016, only used with the reference genome) -""" - -class Fasta(object): - def __init__(self, false_path, name, assembly_id): - self.false_path = false_path - self.name = name - - if not assembly_id: - assembly_id = "unknown" - self.assembly_id = assembly_id \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Fasta.pyc |
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| Binary file util/Fasta.pyc has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Filters.py --- a/util/Filters.py Mon Jul 10 17:08:38 2017 -0400 +++ b/util/Filters.py Wed May 16 18:04:20 2018 -0400 |
| b |
| @@ -7,3 +7,5 @@ if record.exc_text or record.exc_info: s = record.message return s + + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Filters.pyc |
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| Binary file util/Filters.pyc has changed |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Logger.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util/Logger.py Wed May 16 18:04:20 2018 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +import os +import sys +import json +import logging +import logging.config + +#from util.Filters import TraceBackFormatter + +class Logger(object): + def __init__(self, tool_directory, debug="False", extra_files_path=None): + self.tool_directory = tool_directory + self.default_level = logging.INFO + self.debug = debug + self.extra_files_path = extra_files_path + + def setup_logging(self): + """Setup logging configuration + reference: https://fangpenlin.com/posts/2012/08/26/good-logging-practice-in-python/ + """ + config_path = os.path.join(self.tool_directory, 'logging.json') + default_level=logging.INFO + if self.debug.lower() == "true": + default_level=logging.DEBUG + if os.path.exists(config_path): + with open(config_path, 'rt') as f: + config = json.load(f) + config["handlers"]["console"]["level"] = default_level + if self.extra_files_path: + for i in config["handlers"]: + if "filename" in config["handlers"][i]: + config["handlers"][i]["filename"] = os.path.join(self.extra_files_path, config["handlers"][i]["filename"]) + logging.config.dictConfig(config) + else: + logging.warn("Extra files path is not set. The log files will exist at current working directory instead of final output folder") + else: + logging.basicConfig(level=default_level) + logging.warn("Cannot find logging configuration file!\n") + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Logger.pyc |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/Reader.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util/Reader.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,117 @@ +import json +import logging +import codecs + + +# Internal dependencies +from datatypes.binary.Bam import Bam +from datatypes.binary.BigWig import BigWig +from datatypes.binary.BigBed import BigBed +from datatypes.interval.Bed import Bed +from datatypes.interval.BedSimpleRepeats import BedSimpleRepeats +from datatypes.interval.BedSpliceJunctions import BedSpliceJunctions +from datatypes.interval.CytoBand import CytoBand +from datatypes.interval.BedBlatAlignments import BedBlatAlignments +from datatypes.interval.BedBlastAlignments import BedBlastAlignments +from datatypes.interval.Gff3 import Gff3 +from datatypes.interval.Gtf import Gtf +from datatypes.interval.Psl import Psl +from datatypes.sequence.Fasta import Fasta +from util import santitizer + +class Reader(object): + + DATATYPE_CLASS = [Bam, BigWig, BigBed, Bed, BedSimpleRepeats, BedSpliceJunctions, CytoBand, BedBlatAlignments, BedBlastAlignments, Gff3, Gtf, Psl, Fasta] + + def __init__(self, input_json_file): + self.inputFile = input_json_file + self.args = self.loadJson() + + + def loadJson(self): + try: + data_file = codecs.open(self.inputFile, 'r', 'utf-8') + return json.load(data_file) + except IOError: + print "Cannot find JSON file\n" + exit(1) + + def getToolDir(self): + try: + return self.args["tool_directory"] + except KeyError: + print ("tool_directory is not defined in the input file!") + exit(1) + + def getExtFilesPath(self): + try: + return self.args["extra_files_path"] + except KeyError: + print ("extra_files_path is not defined in the input file!") + exit(1) + + def getUserEmail(self): + try: + return self.args["user_email"] + except KeyError: + print ("user_email is not defined in the input file!") + exit(1) + + def getDebugMode(self): + try: + return self.args["debug_mode"] + except KeyError: + print ("debug_mode is not defined in the input file!") + exit(1) + + + def getRefGenome(self): + array_inputs_reference_genome = self.args["fasta"] + # TODO: Replace these with the object Fasta + input_fasta_file = array_inputs_reference_genome["false_path"] + input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"]) + genome_name = santitizer.sanitize_name_input(self.args["genome_name"]) + reference_genome = Fasta(input_fasta_file, + input_fasta_file_name, genome_name) + return reference_genome + + + def getTracksData(self): + self.logger = logging.getLogger(__name__) + all_datatype_dictionary = dict() + for datatype in self.DATATYPE_CLASS: + class_name = datatype.__name__ + array_inputs = self.args.get(str(class_name)) + if array_inputs: + self.logger.debug("Create %s objects\n", class_name) + self.logger.debug("array_inputs: %s", array_inputs) + all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs)) + + return all_datatype_dictionary + + def create_ordered_datatype_objects(self, ExtensionClass, array_inputs): + """ + Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub + and update the dictionary of datatype + + :param ExtensionClass: + :param array_inputs: + :type ExtensionClass: Datatype + :type array_inputs: list[string] + """ + + datatype_dictionary = {} + + # TODO: Optimize this double loop + for input_data in array_inputs: + input_false_path = input_data["false_path"] + input_data["name"] = santitizer.sanitize_name_input(input_data["name"]) + extensionObject = ExtensionClass(input_false_path, input_data) + extensionObject.generateCustomTrack() + datatype_dictionary.update({input_data["order_index"]: extensionObject}) + return datatype_dictionary + + + + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/index/DatabaseIndex.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util/index/DatabaseIndex.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,44 @@ +#!/usr/bin/python + +import collections +from ExternIndex import ExternIndex + +class DatabaseIndex(ExternIndex): + def __init__(self, database, **args): + self.database = database + self.seqType=args.get("seqType") + self.useIframe=args.get("useIframe") + self.iframeHeight=args.get("iframeHeight") + self.iframeWidth=args.get("iframeWidth") + + def setExtLink(self): + return self.setDatabaseLink(self.database, self.seqType, self.useIframe, self.iframeHeight, self.iframeWidth) + + + def setDatabaseLink(self, database, seqType=None, useIframe=None, iframeHeight=None, iframeWidth=None): + database_settings = collections.OrderedDict() + if "NCBI" in database: + if not seqType: + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$" + elif seqType == 2: + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$" + elif seqType == 1: + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$" + else: + raise Exception("Sequence Type {0} is not valid, should be either protein (seqType==2) or nucleotide (seqType==1). Stopping the application".format(seqType)) + elif "UniProt" in database: + database_settings["url"] = "http://www.uniprot.org/uniprot/$$" + elif "FlyBase" in database: + database_settings["url"] = "http://flybase.org/reports/$$" + else: + database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$" + database_settings["urlLabel"] = database + " Details:" + if useIframe or useIframe is None: + database_settings["iframeUrl"] = database_settings["url"] + if not iframeHeight: + iframeHeight = "600" + if not iframeWidth: + iframeWidth = "800" + database_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth) + return database_settings + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/index/ExternIndex.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util/index/ExternIndex.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,16 @@ +#!/usr/bin/python +import collections +import abc +from abc import ABCMeta + +class ExternIndex(object): + __metaclass__ = ABCMeta + + @abc.abstractmethod + def __init__(self): + """init""" + + @abc.abstractmethod + def setExtLink(self): + """set external link""" + \ No newline at end of file |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/index/TrixIndex.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util/index/TrixIndex.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,45 @@ +#!/usr/bin/python + +import os +import collections +import shutil +import logging +from ExternIndex import ExternIndex + +class TrixIndex(ExternIndex): + def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args): + self.logger = logging.getLogger(__name__) + self.indexIx = indexIx + self.indexIxx = indexIxx + self.trackName = trackName + self.mySpecieFolderPath = mySpecieFolderPath + self.index_settings = collections.OrderedDict() + self.trixId = trixId.rstrip() + + + def setExtLink(self): + self.setSearchIndex() + self.moveIndexFile() + self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName + return self.index_settings + + def moveIndexFile(self): + indexFolder = os.path.join(self.mySpecieFolderPath, 'trix') + self.indexIxName = "".join( ( self.trackName, ".ix") ) + self.indexIxxName = "".join( ( self.trackName, ".ixx") ) + if not os.path.exists(indexFolder): + os.makedirs(indexFolder) + + # Move index files to the index folder + self.indexIxPath = os.path.join(indexFolder, self.indexIxName) + shutil.copyfile(self.indexIx, self.indexIxPath) + self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName) + shutil.copyfile(self.indexIxx, self.indexIxxPath) + + def setSearchIndex(self): + if not self.trixId: + self.logger.error("Didn't specify Trix Id") + self.logger.debug("trixId= %s, searchIndex= %s", self.trixId, self.trixId) + self.index_settings["searchIndex"] = self.trixId + + |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/santitizer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util/santitizer.py Wed May 16 18:04:20 2018 -0400 |
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| @@ -0,0 +1,61 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +""" +This class handles the subprocess calls of the different tools used +in HubArchiveCreator +""" + +import logging +import os +import subprocess +import sys +import string +import tempfile + + +def prefixTrackName(filename): + """ + santitize trackName. Because track name must begin with a letter and + contain only the following chars: [a-zA-Z0-9_]. + See the "track" Common settings at: + https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments + skip the santitization for cytoBandIdeo track + """ + if filename == 'cytoBandIdeo': + return filename + valid_chars = "_%s%s" % (string.ascii_letters, string.digits) + sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename]) + sanitize_name = "gonramp_" + sanitize_name + return sanitize_name + +def sanitize_name_input(string_to_sanitize): + """ + Sanitize the string passed in parameter by replacing '/' and ' ' by '_' + + :param string_to_sanitize: + :return : + + :Example: + + >>> sanitize_name_input('this/is an//example') + this_is_an__example + """ + return string_to_sanitize \ + .replace("/", "_") \ + .replace(" ", "_") + +def sanitize_name_inputs(inputs_data): + """ + Sanitize value of the keys "name" of the dictionary passed in parameter. + + Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces. + Also, it can contain '/' character and could break the use of os.path function. + + :param inputs_data: dict[string, dict[string, string]] + """ + for key in inputs_data: + inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"]) + +def sanitize_group_name(group_name): + return group_name.lower().replace(' ', '_') |
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| diff -r 6aa28a85cc38 -r 7e8a8b732db3 util/subtools.py --- a/util/subtools.py Mon Jul 10 17:08:38 2017 -0400 +++ b/util/subtools.py Wed May 16 18:04:20 2018 -0400 |
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| b'@@ -13,6 +13,7 @@\n import string\n import tempfile\n \n+\n class PopenError(Exception):\n def __init__(self, cmd, error, return_code):\n self.cmd = cmd\n@@ -20,10 +21,13 @@\n self.return_code = return_code\n \n def __str__(self):\n- message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)\n- message = \',\'.join((message, "Its error message is: {0}".format(self.error)))\n+ message = "The subprocess {0} has returned the error: {1}.".format(\n+ self.cmd, self.return_code)\n+ message = \',\'.join(\n+ (message, "Its error message is: {0}".format(self.error)))\n return repr(message)\n \n+\n def _handleExceptionAndCheckCall(array_call, **kwargs):\n """\n This class handle exceptions and call the tool.\n@@ -41,12 +45,13 @@\n \n # TODO: Check the value of array_call and <=[0]\n logging.debug("Calling {0}:".format(cmd))\n-\n+ logging.debug("%s", array_call)\n logging.debug("---------")\n \n # TODO: Use universal_newlines option from Popen?\n try:\n- p = subprocess.Popen(array_call, stdout=stdout, stderr=stderr, shell=shell)\n+ p = subprocess.Popen(array_call, stdout=stdout,\n+ stderr=stderr, shell=shell)\n \n # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate\n \n@@ -64,29 +69,35 @@\n raise PopenError(cmd, error, p.returncode)\n else:\n # TODO: To Handle properly with a design behind, if we received a option as a file for the error\n- raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\\\n+ raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\n .format(cmd, stderr.name, p.returncode))\n \n except OSError as e:\n- message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)\n+ message = "The subprocess {0} has encountered an OSError: {1}".format(\n+ cmd, e.strerror)\n if e.filename:\n- message = \'\\n\'.join((message, ", against this file: {0}".format(e.filename)))\n+ message = \'\\n\'.join(\n+ (message, ", against this file: {0}".format(e.filename)))\n logging.error(message)\n sys.exit(-1)\n except PopenError as p:\n- message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)\n- message = \'\\n\'.join((message, "Its error message is: {0}".format(p.error)))\n+ message = "The subprocess {0} has returned the error: {1}.".format(\n+ p.cmd, p.return_code)\n+ message = \'\\n\'.join(\n+ (message, "Its error message is: {0}".format(p.error)))\n \n logging.exception(message)\n \n sys.exit(p.return_code)\n except Exception as e:\n- message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)\n+ message = "The subprocess {0} has encountered an unknown error: {1}".format(\n+ cmd, e)\n logging.exception(message)\n \n sys.exit(-1)\n return p\n \n+\n def twoBitInfo(two_bit_file_name, two_bit_info_file):\n """\n Call twoBitInfo and write the result into twoBit_info_file\n@@ -98,6 +109,7 @@\n p = _handleExceptionAndCheckCall(array_call)\n return p\n \n+\n def faToTwoBit(fasta_file_name, twoBitFile):\n """\n This function call faToTwoBit UCSC tool, and return the twoBitFile\n@@ -111,6 +123,7 @@\n \n return twoBitFile\n \n+\n def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):\n """\n Call gtfToGenePred and write the result into gene_pred_file_name\n@@ -122,6 +135,7 @@\n p = _handleExceptionAndCheckCall(array_call)\n return p\n \n+\n def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):\n """\n Call gff3ToGenePred and write the result into gene_pred'..b's:\n+ typeOption = options.get("typeOption")\n+ autoSql = options.get("autoSql")\n+ tab = options.get("tab")\n+ extraIndex = options.get("extraIndex")\n+ if typeOption:\n+ typeOption = \'\'.join([\'-type=\', typeOption])\n+ array_call.append(typeOption)\n+ if autoSql:\n+ autoSql = \'\'.join([\'-as=\', autoSql])\n+ array_call.append(autoSql)\n+ if tab:\n+ array_call.append(\'-tab\')\n+ if extraIndex:\n+ index = \'\'.join([\'-extraIndex=\', extraIndex])\n+ array_call.append(index)\n p = _handleExceptionAndCheckCall(array_call)\n return p\n \n@@ -223,10 +237,12 @@\n :param output_sorted_bam_name:\n :return:\n """\n- array_call = [\'samtools\', \'sort\', input_bam_file_name, \'-o\', output_sorted_bam_name]\n+ array_call = [\'samtools\', \'sort\',\n+ input_bam_file_name, \'-o\', output_sorted_bam_name]\n p = _handleExceptionAndCheckCall(array_call)\n return p\n \n+\n def createBamIndex(input_sorted_bam_file_name, output_name_index_name):\n """\n Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name\n@@ -234,10 +250,12 @@\n :param output_name_index_name:\n :return:\n """\n- array_call = [\'samtools\', \'index\', input_sorted_bam_file_name, output_name_index_name]\n+ array_call = [\'samtools\', \'index\',\n+ input_sorted_bam_file_name, output_name_index_name]\n p = _handleExceptionAndCheckCall(array_call)\n return p\n \n+\n def pslToBigPsl(input_psl_file_name, output_bed12_file_name):\n """\n Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name\n@@ -251,30 +269,44 @@\n p = _handleExceptionAndCheckCall(array_call)\n return p\n \n-#santitize trackName. Because track name must begin with a letter and\n+# santitize trackName. Because track name must begin with a letter and\n # contain only the following chars: [a-zA-Z0-9_].\n # See the "track" Common settings at:\n-#https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments\n-def fixName(filename):\n- if filename == \'cytoBandIdeo\':\n- return filename\n- valid_chars = "_%s%s" % (string.ascii_letters, string.digits)\n- sanitize_name = \'\'.join([c if c in valid_chars else \'_\' for c in filename])\n- sanitize_name = "gonramp_" + sanitize_name\n- return sanitize_name\n+# https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments\n \n-def validateGff(orig_gff3, valid_gff3):\n+def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):\n+ """\n+ Call validateFiles on input_file, using chrom_sizes_file_name and file_type\n+ :param input_file:\n+ :param chrom_sizes_file_name:\n+ :param file_type:\n+ :return:\n """\n- Remove extra meta line: ##gff-version 3\n+ \n+ array_call = [\'validateFiles\', \'-chromInfo=\' + chrom_sizes_file_name, \'-type=\'+ file_type, input_file]\n+ if options:\n+ tab = options.get("tab")\n+ autoSql = options.get("autoSql")\n+ logging.debug("tab: {0}".format(tab))\n+ logging.debug("autoSql: {0}".format(autoSql))\n+ if autoSql:\n+ autoSql = \'\'.join([\'-as=\', autoSql])\n+ array_call.append(autoSql)\n+ if tab:\n+ array_call.append(\'-tab\')\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def pslCheck(input_file, options=None):\n """\n- valid = open(valid_gff3, \'w\')\n- num = 0\n- with open(orig_gff3, \'r\') as f:\n- for line in f:\n- if \'##gff-version 3\' in line:\n- if num == 0:\n- num += 1\n- else:\n- continue\n- valid.write(line)\n- \n+ Call pslCheck on input_file\n+ :param input_file:\n+ :return:\n+ """\n+\n+ array_call = [\'pslCheck\', input_file]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+ \n+\n' |
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