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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306 |
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modified:
flaimapper.xml |
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added:
test-data/filter-parameters.duck.15.txt test-data/snord81.bam test-data/snord81.fa test-data/snord81.flaimapper.duck-15.gtf test-data/snord81.flaimapper.gtf test-data/snord81.flaimapper.no-seq.txt test-data/snord81.flaimapper.offsets_5_5.gtf test-data/snord81.flaimapper.txt test-data/test_genomic_SE_reads.fastqsanger test-data/test_genomic_alignment.bam test-data/test_genomic_all_chromosomes.fa test-data/test_genomic_flaimapper_output.gtf test-data/test_genomic_flaimapper_output.no-seq.txt test-data/test_genomic_flaimapper_output.txt test-data/test_genomic_genes.gtf |
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removed:
README.rst flaimapper-gtf-from-fasta.xml test-data/test1/ncrnadb09.fa test-data/test1/ncrnadb09.v2.gtf test-data/test1/snord81.bam test-data/test1/snord81.flaimapper.txt test-data/test2/test_genomic_SE_reads.fastqsanger test-data/test2/test_genomic_alignment.bam test-data/test2/test_genomic_all_chromosomes.fa test-data/test2/test_genomic_flaimapper_output.txt test-data/test2/test_genomic_genes.gtf test-data/test3/ncrnadb09.fa test-data/test3/reference.gtf tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf README.rst --- a/README.rst Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,41 +0,0 @@ -FlaiMapper wrapper for Galaxy -============================= - -https://github.com/yhoogstrate/flaimapper -http://www.ncbi.nlm.nih.gov/pubmed/25338717 -http://dx.doi.org/10.1093/bioinformatics/btu696 - -Fragment Location Annotation Identification Mapper - -FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. - -Development ------------ - -* Repository-Maintainer: Youri Hoogstrate -* Repository-Developers: Youri Hoogstrate - -* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands). - -License -------- - -**flaimapper** and **wrapper**: - -GPL (>=3) - -**pysam**: - -The MIT License - -References ----------- -**FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.** - -*Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673 - -- http://www.ncbi.nlm.nih.gov/pubmed/25338717 -- http://dx.doi.org/10.1093/bioinformatics/btu696 \ No newline at end of file |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf flaimapper-gtf-from-fasta.xml --- a/flaimapper-gtf-from-fasta.xml Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,111 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w2"> - <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description> - <requirements> - <requirement type="package" version="1.2.1">flaimapper</requirement> - </requirements> - - <stdio> - <regex - match="[fai_load] build FASTA index." - source="stderr" - level="log" - description="The FASTA file is being indexed." /> - </stdio> - - <version_command>flaimapper --version</version_command> - - <command><![CDATA[ - gtf-from-fasta -o $output $fasta - ]]></command> - - <inputs> - <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="This is the FASTA file that fits the used reference genome (e.g. hg19 or a ncRNA database)." /> - </inputs> - - <outputs> - <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" /> - </outputs> - - <tests> - <test> - <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" /> - - <output name="output" file="test3/reference.gtf" /> - </test> - </tests> - - <help><![CDATA[ -FlaiMapper wrapper for Galaxy -============================= - -https://github.com/yhoogstrate/flaimapper -http://www.ncbi.nlm.nih.gov/pubmed/25338717 -http://dx.doi.org/10.1093/bioinformatics/btu696 - -Fragment Location Annotation Identification Mapper - -FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. - -Input formats -------------- -To make FlaiMapper compatible with both an entire reference genome as a -separate ncRNA database, it requires an additional GTF file *(mask file)*. -The major difference between an entire reference and a ncRNA database -is that an entire reference usually contains multiple ncRNAs per sequence -entry (chromosome). While for the ncRNA database, each entry should -represent one single mature ncRNA. - -Therefore the mask file that represents to the FASTA file of a ncRNA -database will only contain the start- and end positions of each entry. -To generate this in an automated fashion, you can make use of this tool -*as long as the FASTA file doesn't contain entire chromosomes* but -mature ncRNA. - -An example input file is **ncRNAdb09**, available at the following URLs: -https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* - -It should generate a GTF/GFF file (mask file) similar to the following URL: -https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* - -Installation ------------- - -The wrapper makes use of easy_install to install a python egg. Please -ensure you have easy_install installed. - -License -------- - -**flaimapper** and **wrapper**: - -GPL (>=3) - -**pysam**: - -The MIT License - -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands). - - -Development ------------ - -* Repository-Maintainer: Youri Hoogstrate -* Repository-Developers: Youri Hoogstrate - -* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands). - - ]]></help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btu696</citation> - </citations> -</tool> |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf flaimapper.xml --- a/flaimapper.xml Fri Jul 31 05:31:02 2015 -0400 +++ b/flaimapper.xml Mon Jan 23 03:13:40 2017 -0500 |
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| b'@@ -1,65 +1,133 @@\n <?xml version="1.0" encoding="UTF-8"?>\n-<tool id="flaimapper" name="FlaiMapper" version="1.2.1.w2">\n- <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>\n+<tool id="flaimapper" name="FlaiMapper" version="2.3.4-0">\n+ <description>detects small ncRNA derived fragments in small RNA-Seq data</description>\n <requirements>\n- <requirement type="package" version="1.2.1">flaimapper</requirement>\n+ <requirement type="package" version="2.3.4">flaimapper</requirement>\n </requirements>\n \n- <stdio>\n- <regex match="in parse_gff.*?ValueError: invalid literal for int\\(\\) with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\\n" />\n- <regex match="[fai_load] build FASTA index." source="stderr" level="log" />\n- </stdio>\n+ <version_command>flaimapper --version 2>&1 | head -n 1</version_command>\n \n- <version_command>flaimapper --version</version_command>\n- \n- <command><![CDATA[\n+ <command detect_errors="exit_code"><![CDATA[\n flaimapper\n- -v\n- -f $output_format\n- -o $output\n- -m $mask\n- -r $fasta\n- \n- #for $alignment in $alignments\n- $alignment\n- #end for\n+ -v\n+ -f \'${output_select.output_format}\'\n+ -o \'${output}\'\n+\n+ #if $output_select.output_format == \'1\':\n+ #if $output_select.fasta:\n+ -r \'${output_select.fasta}\'\n+ #end if\n+ #else\n+ --offset5p ${output_select.offset5p}\n+ --offset3p ${output_select.offset3p}\n+ #end if\n+\n+ #if $parameters:\n+ -p \'${parameters}\'\n+ #end if\n+\n+ \'${alignment}\'\n ]]></command>\n \n <inputs>\n- <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />\n- \n- <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />\n- \n- <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />\n+ <param name="alignment" type="data" format="bam" multiple="false"\n+ label="Alignment file"\n+ help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />\n \n- <param name="output_format" type="select" label="Output format">\n- <option value="1">Tabular (1 fragment per column)</option>\n- <option value="2">Tabular (1 precursor per column)</option>\n- <option value="3">GenBank</option>\n- <!-- option value="gtf">GTF/GFF</option -->\n- </param>\n+ <conditional name="output_select">\n+ <param name="output_format" type="select" label="Output format" argument="-f">\n+ <option value="1">Tabular</option>\n+ <option value="2">GTF</option>\n+ </param>\n+ \n+ <when value="1">\n+ <param name="fasta" type="data" format="fasta" optional="true"\n+ label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database" help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />\n+ </when>\n+ \n+ <when value="2">\n+ <param name="offset5p" type="integer" value="4"\n+ label="5\' offset added to the exon-type GTF entry"\n+ hel'..b'" />\n+ <param name="parameters" value="filter-parameters.duck.15.txt"/>\n+ \n+ <output name="output" file="snord81.flaimapper.duck-15.gtf" />\n </test>\n </tests>\n \n@@ -67,10 +135,6 @@\n FlaiMapper wrapper for Galaxy\n =============================\n \n-https://github.com/yhoogstrate/flaimapper\n-http://www.ncbi.nlm.nih.gov/pubmed/25338717\n-http://dx.doi.org/10.1093/bioinformatics/btu696\n-\n Fragment Location Annotation Identification Mapper\n \n FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.\n@@ -79,90 +143,35 @@\n Input\n -----\n \n-Alignments\n-**********\n-\n-Aligned reads from small RNA-Seq experiments have to be provided in the BAM format.\n-In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments.\n-\n-Mask File\n+Alignment\n *********\n \n-There are two strategies to analyze using FlaiMapper:\n+This file has to contain aligned single end reads from a small RNA-Seq experiment, provided in the BAM format.\n \n-- Relative to mature ncRNA sequences\n-- Relative to chromosomes\n-\n-Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (MASK) regions should be provided in the GFF/GTF format:\n+Prior to running FlaiMapper, it is common to align sequencing reads to either:\n \n-- http://genome.ucsc.edu/FAQ/FAQformat.html#format3\n-- http://www.ensembl.org/info/website/upload/gff.html\n-\n-If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one.\n-\n+- mature ncRNA sequences\n+- all chromosomes\n \n-You can access **ncRNAdb09** GTF file at the following URL:\n-https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*\n-\n-Fasta sequence\n-**************\n+Example- and reference data\n+***************************\n \n The reference sequence should be provided in FASTA format.\n \n You can access **ncRNAdb09** FASTA file at the following URL:\n https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*\n \n-Example- and reference data\n-***************************\n-\n-To align reads to ncRNA you need aligner specific indexed version of the reference. We have made\n-the following available for ncRNAdb09:\n-\n- - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz\n- - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz\n-\n If you want to test FlaiMapper with example data you can obtain several\n alignment files from the following directory tree:\n \n https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments\n \n-Installation\n-------------\n-\n-The wrapper makes use of easy_install to install a python egg. Please\n-ensure you have easy_install installed.\n-\n-License\n--------\n-\n-**flaimapper** and **wrapper**:\n-\n-GPL (>=3)\n-\n-**pysam**:\n-\n-The MIT License\n+More details are given in the manual at the following website:\n \n-Contact\n--------\n-\n-The tool wrapper has been written by Youri Hoogstrate from the Erasmus\n-Medical Center (Rotterdam, Netherlands).\n-\n-\n-Development\n------------\n-\n-* Repository-Maintainer: Youri Hoogstrate\n-* Repository-Developers: Youri Hoogstrate\n-\n-* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools\n-\n-The tool wrapper has been written by Youri Hoogstrate from the Erasmus\n-Medical Center (Rotterdam, Netherlands).\n+https://github.com/yhoogstrate/flaimapper\n ]]></help>\n \n <citations>\n <citation type="doi">10.1093/bioinformatics/btu696</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/filter-parameters.duck.15.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filter-parameters.duck.15.txt Mon Jan 23 03:13:40 2017 -0500 |
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| @@ -0,0 +1,30 @@ +-15 100.0 +-14 100.0 +-13 100.0 +-12 100.0 +-11 100.0 +-10 100.0 +-9 100.0 +-8 100.0 +-7 100.0 +-6 100.0 +-5 100.0 +-4 100.0 +-3 100.0 +-2 100.0 +-1 100.0 +1 100.0 +2 100.0 +3 100.0 +4 100.0 +5 100.0 +6 100.0 +7 100.0 +8 100.0 +9 100.0 +10 100.0 +11 100.0 +12 100.0 +13 100.0 +14 100.0 +15 100.0 |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.bam |
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| Binary file test-data/snord81.bam has changed |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.fa Mon Jan 23 03:13:40 2017 -0500 |
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| @@ -0,0 +1,2 @@ +>HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 +ATTATAATTGCAGAATACATGATGATCTCAATCCAACTTGAACTCTCTCACTGATTACTTGATGACAATAAAATATCTGATATTCTGCATTCCCATG |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.flaimapper.duck-15.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.flaimapper.duck-15.gtf Mon Jan 23 03:13:40 2017 -0500 |
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| @@ -0,0 +1,4 @@ +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 43 72 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 11 41 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.flaimapper.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.flaimapper.gtf Mon Jan 23 03:13:40 2017 -0500 |
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| @@ -0,0 +1,6 @@ +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 43 72 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 11 41 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 55 80 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 51 84 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.flaimapper.no-seq.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.flaimapper.no-seq.txt Mon Jan 23 03:13:40 2017 -0500 |
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| @@ -0,0 +1,4 @@ +Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) +FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001 22 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 97 74 171 +FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002 23 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 70 29 99 +FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003 26 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 54 28 82 |
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| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.flaimapper.offsets_5_5.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.flaimapper.offsets_5_5.gtf Mon Jan 23 03:13:40 2017 -0500 |
| [ |
| @@ -0,0 +1,6 @@ +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 42 73 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 10 42 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 sncdRNA 55 80 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.3.4 exon 50 85 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/snord81.flaimapper.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.flaimapper.txt Mon Jan 23 03:13:40 2017 -0500 |
| [ |
| @@ -0,0 +1,4 @@ +Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence (no fasta file given) Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) +FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001 22 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 CTCACTGATTACTTGATGACAA 97 74 171 +FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002 23 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 ATACATGATGATCTCAATCCAAC 70 29 99 +FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003 26 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 TTACTTGATGACAATAAAATATCTGA 54 28 82 |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test1/ncrnadb09.fa --- a/test-data/test1/ncrnadb09.fa Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,4538 +0,0 @@\n->HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\n-GCGCTGCCCCGTGAGCAGTCTCCACCACCTCCCCTGCAAACGTCCAGTGGTGCAGAGGTAATGGACGTTGGCTCTGGTGGTGATGGACAGTCCGAACTCCCTGCT\n->HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\n-TTGATGCTAGACAGGTAGTGTCCCTCAGGGCTGTAGAACAGGGCTGGGATTACTAAAGCCCTGTTCTATGCCCTGAGGGACACTGAGCATGTCATTTCACTTCT\n->HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\n-ATGGTGGGCTGCCACCAAGAAGGTGAAGGGAGGGTCAGTCCCAATCTGAATCCCACCAAAATAGGTGGTAGAGGGTTGCCCTCCTTTCTTCCCTCACCTCTGACCCCGCTCTTCG\n->HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\n-TGCCACCTCATGGTACTCGGAGGGAGGTTGTCCGTGGTGAGTTCGCATTATTTAATGATGCCCAATACACGGTCGACCTCTTTTCGGTATCAGATCTCACCA\n->HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\n-AACCCCAATATGCCAATGCCTATCACATATCTGCCTGTCCTATGACAAACATGGCAGGTAGATATTTGATAGGCATTGGCACACTGGCAAA\n->HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\n-CTGGCCTAAAATATATGAAATGTAGAGATTGATCAAAATAGTTTCTATCAAAATAGTTTTGATCAATCTCTGCAATTTTATATATGAGGAAACTG\n->HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\n-TTTTTGCTGATTTTTTTTTAGTATTTTTCCATCAGTGTTCATAAGGAATGTTGCTCTGTAGTTTTCTTATAGTGTGGCTTTCTTAGAGCAAAGATGGTTCCCTATTACTTTCTA\n->HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\n-AAATGGGCTTTCAGAAGAAAAAACAGGAGATAAAGTTTGTGATAATGTTTGTCTATATAGTTATGAATGTTTTTTCCTGTTTCCTTCAGGGCCATAATACTCCC\n->HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\n-GTCCTGGGTTGGGTCGATGATGAGAACCTTATATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n->HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\n-CCATCACTTGCCCCAGCTAGGTAAAGAGCCCTGTGGAGACACCTGGATTCAGAGAACATGTCTCCACTGAGCACTTGGGCCTTGATGGCGGCTCTTGTTCCAA\n->HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\n-TGTGTCGGGGGTCCAGGCAGGAGCCGGACTGGACCTCAGGGAAGAGGCTGACCCGGCCCCTCTTGCGGCAGGCTTCACC\n->HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\n-AAAATTGAATAGTGAGCAACCCAGTGGGCTATGGAAATGTGTGGAAGATGGCATTTCTATTTCTCAGTGGGGCTCTTACCTATTACTCAT\n->HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\n-TATGTCAAGTATAGCCAATCATTAGTATTCTGAGCTGTAGGAATCAAAGATTTTGATTAGATTCTGTAACTCAGAGGTTTATTAGAAAAAA\n->HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\n-CCGCTCCAGCCCTGCCGGGGCTAAAGTGCTGACAGTGCAGATAGTGGTCCTCTCCGTGCTACCGCACTGTGGGTACTTGCTGCTCCAGCAGGGCACGCACAG\n->HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\n-GTCCTAGGTTGGGTCAATGATGAGAACCTTATAATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n->HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]'..b'ME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\n-GGTTCCATAGTGTAGCGGTtATCACGTCTGCTTTACACGCAGAAGGtCCTGGGTTCGAGCCCCAGTGGAACCAcca\n->NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\n-GTCTCTGTGGCGCAATCGGCtAGCGCGTTTGGCTGTTAACTAAAAAGtTGGTGGTTCGAACACACCCAGAGGCGcca\n->NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\n-GTCTCTGTGGCGCAATCGGTtAGCGCATTCGGCTGTTAACCGAAAGGtTGGTGGTTCGAGCCCACCCAGGGACGcca\n->NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\n-GGCAGTAAAGTAGGGTGGTtAAGACAAGGGGCTCTGGAGCAAGACTGCCCAAGATCAAATCCTGGTGCTGCCAcca\n->NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\n-CCTTCGATAGCTCAGTTGGTAGAGCGGAGGACTGTAGATCCTTAGGtCGCTGGTTCGATTCCGGCTCGAAGGAcca\n->NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\n-GGTTCCATAGTGTAGTGGTtATCACATCTGCTTTACACGCAGAAGGtCCTGGGTTCAAGCCCCAGTGGAACCAcca\n->NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\n-GCAGCGATGGCCGAGTGGTtAAGGCGTTGGACTTGAAATCCAATGGGGTCTCCCCGCGCAGGTTCGAACCCTGCTCGCTGCGcca\n->NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\n-GCCCAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGtCATGGGTTTGAGCCCCACGTTTGGTGcca\n->NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\n-GGCAGAATGGTGCAGCGGTtcAGCACCCAGGCTCTGCAGCCAGCTGTTGCCTGGGCTCAAATCCCAGCTCTGCCAcca\n->HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene 1&LOCI=[chr22:42471953-42472275:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008259&GENOME=hg19\n-ATTGTTGAACTATAGGGTATGAACTATAGGGTGTCCAGTGTACAGCATTTTATGGCTACTTGGTGTCACTCTAGAGCCACATAGCAAGTGGCTTCAAGAGGTAATTCTTGATCCTTTTGTAGTTCATGAGCGTGATGATTGGGTGTTCACATGCATGTGTGAGCTGTGCCACCCTCGAACCTTGTTACCATGTAGGCACATTACCGATCTGACATGAAGAAAAGAAAAGAAAAAAAAAGAAAAAGAGATAATTCTTTAGCTCAAGGGAGGAGTAAGACTTGACAGCTGTTGCGTTTCAGTATGTCTGGGCCTGATTATTTAAA\n->HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\n-ATACGTGGCTGGGTTGCCATGCTCCATCTGCTGAGAGGCGTATTGTGAGTGGCAGGTGTTATGGATCACAGCCTCTGCATATGTGCCAGCAGAAAAAGTAATTGTAACCAGCAAAGCATTTTACTACATAAACGTTTTAGCCCCTATAAAAACATCCGGAGATCCTTTTGTTGTTCATGAGCATGACAATTGGGTGTTTTCATGCAGCGAGTGAGATGTGCCACCCTGGAACCTTGTTACGACGTCGCATGTTACCTGTCTGACCTGAAAAATAATTAATAAGTAAAACATACGGAAGCCAGTTTCTCATGGCTATTTCCAACTAGTCACTTGAAGAATATGGAATTAGTTATACAATTAGTTATACGTTGTATAACCATCATAAAATTAGTTACAGATTGATGTGACATTATCTTGAAATTAAT\n->HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\n-GAGGGTTCTCAGCTTGAAGTTCCTTGTGCCTCTTTTAGGGAAGACACTCAGATGGTATATCGAGTATAAAATGACTTAGCGATTCTTCTCCTCAAAATGTGTCATTTATGATCCTTTTGTAGTTCATGAGTGTGATGATTGTGTGTTCATACGCTTGTGTGAGATGTGCCACCCTTGAACCTTGTTACGACATTGGCACATTACCCGTCTGATCTGAAAAAAAAAGTATCATTTATTTACTTACCTAAAATCTATGGAGTGCTTACTATGTGCCAAGTGCTTTTTAAAGCACTTGGAATACCTGACTGCATGAACAGAAACA\n->HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\n-TGTATGTGGGAATGAATGATGACAAAATGTTTCAGTCCCAAATGATACATACTGATTATACCATTATATTTATCCTGACATTCCTCTAAGGCTTT\n->HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\n-TGCCTCTAGGGGCTGGCTTTAGCTCAGCGGTTACTTCGACAATGCTTTCCATGGTTAGGAAACCAACCTCTCTGGGTGGTTTGAGACCCGTGGGCCCTCTCCAGTCCTTTTGTGGTCGCCA\n' |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test1/ncrnadb09.v2.gtf --- a/test-data/test1/ncrnadb09.v2.gtf Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,2269 +0,0 @@\n-HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\tflaimapper\tncRNA\t1\t106\t.\t+\t.\n-HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\tflaimapper\tncRNA\t1\t105\t.\t-\t.\n-HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\tflaimapper\tncRNA\t1\t116\t.\t-\t.\n-HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t+\t.\n-HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\tflaimapper\tncRNA\t1\t92\t.\t-\t.\n-HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\tflaimapper\tncRNA\t1\t96\t.\t+\t.\n-HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\tflaimapper\tncRNA\t1\t115\t.\t+\t.\n-HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\tflaimapper\tncRNA\t1\t105\t.\t+\t.\n-HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t+\t.\n-HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\tflaimapper\tncRNA\t1\t104\t.\t-\t.\n-HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\tflaimapper\tncRNA\t1\t80\t.\t-\t.\n-HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t-\t.\n-HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\tflaimapper\tncRNA\t1\t92\t.\t+\t.\n-HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t-\t.\n-HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t+\t.\n-HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\tflaimapper\tncRNA\t1\t92\t.\t+\t.\n-HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\tflaimapper\tncRNA\t1\t106\t.\t-\t.\n-HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\tflaimapper\tncRNA\t1\t153\t.\t-\t.\n-HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\tflaimapper\tncRNA\t1\t153\t.\t-\t.\n-HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\tflaimapper\tncRNA\t1\t123\t.\t-\t.\n-HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t-\t.\n-H'..b'.tRNA59-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t+\t.\n-NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n-NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t+\t.\n-NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t-\t.\n-NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n-NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t79\t.\t-\t.\n-NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n-NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t-\t.\n-NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n-NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n-NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t+\t.\n-NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\tflaimapper\tncRNA\t1\t86\t.\t-\t.\n-NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n-NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n-NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n-NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t+\t.\n-NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t+\t.\n-NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n-NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\tflaimapper\tncRNA\t1\t86\t.\t+\t.\n-NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n-NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t79\t.\t-\t.\n-HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\tflaimapper\tncRNA\t1\t324\t.\t-\t.\n-HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\tflaimapper\tncRNA\t1\t426\t.\t+\t.\n-HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\tflaimapper\tncRNA\t1\t323\t.\t-\t.\n-HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\tflaimapper\tncRNA\t1\t96\t.\t+\t.\n-HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\tflaimapper\tncRNA\t1\t122\t.\t+\t.\n' |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test1/snord81.bam |
| b |
| Binary file test-data/test1/snord81.bam has changed |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test1/snord81.flaimapper.txt --- a/test-data/test1/snord81.flaimapper.txt Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,4 +0,0 @@ -Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_1 23 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 ATACATGATGATCTCAATCCAAC 70 29 99 -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_2 22 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 CTCACTGATTACTTGATGACAA 97 74 171 -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_3 26 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 TTACTTGATGACAATAAAATATCTGA 54 28 82 |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test2/test_genomic_SE_reads.fastqsanger --- a/test-data/test2/test_genomic_SE_reads.fastqsanger Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,240 +0,0 @@ -@read_001_fragment_1_chr1:120-148 (len=29) -GGATAGTGCCAAAGCTCACTCACCACTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_002_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_003_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_004_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_005_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_006_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_007_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_008_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_009_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_010_fragment_1_chr1:120-149 (len=30) -GGATAGTGCCAAAGCTCACTCACCACTGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_011_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_012_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_013_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_014_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_015_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_016_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_017_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_018_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_019_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_020_fragment_2_chr1:260-289 (len=30) -GCTTACCTCTAGAATAAGTGTCAGCCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_021_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_022_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_023_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_024_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_025_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_026_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_027_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_028_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_029_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_030_fragment_3_chr1:400-429 (len=30) -atacgtggcatttcaggaggcggccggagg -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_031_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_032_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_033_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_034_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_035_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_036_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_037_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_038_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_039_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_040_fragment_4_chr22:100-149 (len=50) -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_041_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_042_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_043_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_044_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_045_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_046_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_047_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_048_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_049_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_050_fragment_5_chr22:370-399 (len=30) -TCTTGAGTGTTAAAATGTTGACCCCTGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_051_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_052_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_053_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_054_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_055_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_056_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_057_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_058_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_059_fragment_6_chrY:0-29 (len=30) -TTGGGATGCGGGTAGTAGATGACTGCAGGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@read_060_fragment_6_chrY:0-30 (len=31) -TTGGGATGCGGGTAGTAGATGACTGCAGGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test2/test_genomic_alignment.bam |
| b |
| Binary file test-data/test2/test_genomic_alignment.bam has changed |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test2/test_genomic_all_chromosomes.fa --- a/test-data/test2/test_genomic_all_chromosomes.fa Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,27 +0,0 @@ ->chr1 -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -TCTAGTGGTATGGTGGTATAGTAAGCTCGTACTGTGATACATGCGACAGG -GGTAAGACCATCAGTAGTAGGGATAGTGCCAAAGCTCACTCACCACTGCC -TATAAGGGGTGCTTACCTCTAGAATAAGTGTCAGCCAGTATAACCCCATG -aagccgcgacacgacggctcacagccggtaagagtaaccccggagtgaac -acctatggggctggataaaactgccctggtgaccgccatcaacaacccga -atacgtggcatttcaggaggcggccggaggggggatgttttctactattc -gaggccgttcgttataacttgttgcgttcctagccgctatatttgtctct -GAGGCCGTTCGTTATAACTTGTTGCGTTCCTAGCCGCTATATTTGTCTCT -TTGCCGACTAATGAGAACAACCACACCATAGCGATTTGACGCAGCGCCTC -GGAATACCGTATCAGCAGGCGCCTCGTAAGGCCATTGCGAATACCAGGTA -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa ->chr22 -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -CTGGCTATGCACGAAGCAACTCTTGAGTGTTAAAATGTTGACCCCTGTAT ->chrY -TTGGGATGCGGGTAGTAGATGACTGCAGGGACTCCGACGTCAAGTACATT -ACCCTCTCATAGGCGGCGTTCTAGATCACGTTACCGCCATATCATCCGAG \ No newline at end of file |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test2/test_genomic_flaimapper_output.txt --- a/test-data/test2/test_genomic_flaimapper_output.txt Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) -ncRNA_1_chr1_Fragment_1 30 chr1 220 249 ncRNA_1 120 149 GGATAGTGCCAAAGCTCACTCACCACTGCC 10 9 19 -ncRNA_2_chr1_Fragment_1 30 chr1 220 249 ncRNA_2 20 49 GGATAGTGCCAAAGCTCACTCACCACTGCC 10 9 19 -ncRNA_2_chr1_Fragment_2 30 chr1 260 289 ncRNA_2 60 89 GCTTACCTCTAGAATAAGTGTCAGCCAGTA 10 10 20 -ncRNA_3_chr1_Fragment_1 30 chr1 400 429 ncRNA_3 50 79 atacgtggcatttcaggaggcggccggagg 10 10 20 -ncRNA_4_chr22_Fragment_1 50 chr22 100 149 ncRNA_4 0 49 AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA 10 10 20 -ncRNA_5_chr22_Fragment_1 30 chr22 370 399 ncRNA_5 170 199 TCTTGAGTGTTAAAATGTTGACCCCTGTAT 10 10 20 -ncRNA_6_chrY_Fragment_1 30 chrY 0 29 ncRNA_6 0 29 TTGGGATGCGGGTAGTAGATGACTGCAGGG 10 9 19 |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test2/test_genomic_genes.gtf --- a/test-data/test2/test_genomic_genes.gtf Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -chr1 flaimapper testing ncRNA 101 250 . + . gene_id="ncRNA_1" -chr1 flaimapper testing ncRNA 201 400 . + . gene_id="ncRNA_2" -chr1 flaimapper testing ncRNA 351 500 . + . gene_id="ncRNA_3" -chr22 flaimapper testing ncRNA 101 200 . + . gene_id="ncRNA_4" -chr22 flaimapper testing ncRNA 201 400 . + . gene_id="ncRNA_5" -chrY flaimapper testing ncRNA 1 100 . + . gene_id="ncRNA_6" \ No newline at end of file |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test3/ncrnadb09.fa --- a/test-data/test3/ncrnadb09.fa Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,4538 +0,0 @@\n->HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\n-GCGCTGCCCCGTGAGCAGTCTCCACCACCTCCCCTGCAAACGTCCAGTGGTGCAGAGGTAATGGACGTTGGCTCTGGTGGTGATGGACAGTCCGAACTCCCTGCT\n->HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\n-TTGATGCTAGACAGGTAGTGTCCCTCAGGGCTGTAGAACAGGGCTGGGATTACTAAAGCCCTGTTCTATGCCCTGAGGGACACTGAGCATGTCATTTCACTTCT\n->HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\n-ATGGTGGGCTGCCACCAAGAAGGTGAAGGGAGGGTCAGTCCCAATCTGAATCCCACCAAAATAGGTGGTAGAGGGTTGCCCTCCTTTCTTCCCTCACCTCTGACCCCGCTCTTCG\n->HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\n-TGCCACCTCATGGTACTCGGAGGGAGGTTGTCCGTGGTGAGTTCGCATTATTTAATGATGCCCAATACACGGTCGACCTCTTTTCGGTATCAGATCTCACCA\n->HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\n-AACCCCAATATGCCAATGCCTATCACATATCTGCCTGTCCTATGACAAACATGGCAGGTAGATATTTGATAGGCATTGGCACACTGGCAAA\n->HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\n-CTGGCCTAAAATATATGAAATGTAGAGATTGATCAAAATAGTTTCTATCAAAATAGTTTTGATCAATCTCTGCAATTTTATATATGAGGAAACTG\n->HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\n-TTTTTGCTGATTTTTTTTTAGTATTTTTCCATCAGTGTTCATAAGGAATGTTGCTCTGTAGTTTTCTTATAGTGTGGCTTTCTTAGAGCAAAGATGGTTCCCTATTACTTTCTA\n->HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\n-AAATGGGCTTTCAGAAGAAAAAACAGGAGATAAAGTTTGTGATAATGTTTGTCTATATAGTTATGAATGTTTTTTCCTGTTTCCTTCAGGGCCATAATACTCCC\n->HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\n-GTCCTGGGTTGGGTCGATGATGAGAACCTTATATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n->HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\n-CCATCACTTGCCCCAGCTAGGTAAAGAGCCCTGTGGAGACACCTGGATTCAGAGAACATGTCTCCACTGAGCACTTGGGCCTTGATGGCGGCTCTTGTTCCAA\n->HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\n-TGTGTCGGGGGTCCAGGCAGGAGCCGGACTGGACCTCAGGGAAGAGGCTGACCCGGCCCCTCTTGCGGCAGGCTTCACC\n->HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\n-AAAATTGAATAGTGAGCAACCCAGTGGGCTATGGAAATGTGTGGAAGATGGCATTTCTATTTCTCAGTGGGGCTCTTACCTATTACTCAT\n->HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\n-TATGTCAAGTATAGCCAATCATTAGTATTCTGAGCTGTAGGAATCAAAGATTTTGATTAGATTCTGTAACTCAGAGGTTTATTAGAAAAAA\n->HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\n-CCGCTCCAGCCCTGCCGGGGCTAAAGTGCTGACAGTGCAGATAGTGGTCCTCTCCGTGCTACCGCACTGTGGGTACTTGCTGCTCCAGCAGGGCACGCACAG\n->HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\n-GTCCTAGGTTGGGTCAATGATGAGAACCTTATAATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n->HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]'..b'ME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\n-GGTTCCATAGTGTAGCGGTtATCACGTCTGCTTTACACGCAGAAGGtCCTGGGTTCGAGCCCCAGTGGAACCAcca\n->NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\n-GTCTCTGTGGCGCAATCGGCtAGCGCGTTTGGCTGTTAACTAAAAAGtTGGTGGTTCGAACACACCCAGAGGCGcca\n->NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\n-GTCTCTGTGGCGCAATCGGTtAGCGCATTCGGCTGTTAACCGAAAGGtTGGTGGTTCGAGCCCACCCAGGGACGcca\n->NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\n-GGCAGTAAAGTAGGGTGGTtAAGACAAGGGGCTCTGGAGCAAGACTGCCCAAGATCAAATCCTGGTGCTGCCAcca\n->NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\n-CCTTCGATAGCTCAGTTGGTAGAGCGGAGGACTGTAGATCCTTAGGtCGCTGGTTCGATTCCGGCTCGAAGGAcca\n->NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\n-GGTTCCATAGTGTAGTGGTtATCACATCTGCTTTACACGCAGAAGGtCCTGGGTTCAAGCCCCAGTGGAACCAcca\n->NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\n-GCAGCGATGGCCGAGTGGTtAAGGCGTTGGACTTGAAATCCAATGGGGTCTCCCCGCGCAGGTTCGAACCCTGCTCGCTGCGcca\n->NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\n-GCCCAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGtCATGGGTTTGAGCCCCACGTTTGGTGcca\n->NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\n-GGCAGAATGGTGCAGCGGTtcAGCACCCAGGCTCTGCAGCCAGCTGTTGCCTGGGCTCAAATCCCAGCTCTGCCAcca\n->HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene 1&LOCI=[chr22:42471953-42472275:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008259&GENOME=hg19\n-ATTGTTGAACTATAGGGTATGAACTATAGGGTGTCCAGTGTACAGCATTTTATGGCTACTTGGTGTCACTCTAGAGCCACATAGCAAGTGGCTTCAAGAGGTAATTCTTGATCCTTTTGTAGTTCATGAGCGTGATGATTGGGTGTTCACATGCATGTGTGAGCTGTGCCACCCTCGAACCTTGTTACCATGTAGGCACATTACCGATCTGACATGAAGAAAAGAAAAGAAAAAAAAAGAAAAAGAGATAATTCTTTAGCTCAAGGGAGGAGTAAGACTTGACAGCTGTTGCGTTTCAGTATGTCTGGGCCTGATTATTTAAA\n->HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\n-ATACGTGGCTGGGTTGCCATGCTCCATCTGCTGAGAGGCGTATTGTGAGTGGCAGGTGTTATGGATCACAGCCTCTGCATATGTGCCAGCAGAAAAAGTAATTGTAACCAGCAAAGCATTTTACTACATAAACGTTTTAGCCCCTATAAAAACATCCGGAGATCCTTTTGTTGTTCATGAGCATGACAATTGGGTGTTTTCATGCAGCGAGTGAGATGTGCCACCCTGGAACCTTGTTACGACGTCGCATGTTACCTGTCTGACCTGAAAAATAATTAATAAGTAAAACATACGGAAGCCAGTTTCTCATGGCTATTTCCAACTAGTCACTTGAAGAATATGGAATTAGTTATACAATTAGTTATACGTTGTATAACCATCATAAAATTAGTTACAGATTGATGTGACATTATCTTGAAATTAAT\n->HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\n-GAGGGTTCTCAGCTTGAAGTTCCTTGTGCCTCTTTTAGGGAAGACACTCAGATGGTATATCGAGTATAAAATGACTTAGCGATTCTTCTCCTCAAAATGTGTCATTTATGATCCTTTTGTAGTTCATGAGTGTGATGATTGTGTGTTCATACGCTTGTGTGAGATGTGCCACCCTTGAACCTTGTTACGACATTGGCACATTACCCGTCTGATCTGAAAAAAAAAGTATCATTTATTTACTTACCTAAAATCTATGGAGTGCTTACTATGTGCCAAGTGCTTTTTAAAGCACTTGGAATACCTGACTGCATGAACAGAAACA\n->HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\n-TGTATGTGGGAATGAATGATGACAAAATGTTTCAGTCCCAAATGATACATACTGATTATACCATTATATTTATCCTGACATTCCTCTAAGGCTTT\n->HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\n-TGCCTCTAGGGGCTGGCTTTAGCTCAGCGGTTACTTCGACAATGCTTTCCATGGTTAGGAAACCAACCTCTCTGGGTGGTTTGAGACCCGTGGGCCCTCTCCAGTCCTTTTGTGGTCGCCA\n' |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test3/reference.gtf --- a/test-data/test3/reference.gtf Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,2269 +0,0 @@\n-HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\tflaimapper\tncRNA\t1\t105\t.\t.\t.\n-HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\tflaimapper\tncRNA\t1\t104\t.\t.\t.\n-HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\tflaimapper\tncRNA\t1\t115\t.\t.\t.\n-HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n-HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t.\t.\n-HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\tflaimapper\tncRNA\t1\t95\t.\t.\t.\n-HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\tflaimapper\tncRNA\t1\t114\t.\t.\t.\n-HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\tflaimapper\tncRNA\t1\t104\t.\t.\t.\n-HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\tflaimapper\tncRNA\t1\t101\t.\t.\t.\n-HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t.\t.\n-HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\tflaimapper\tncRNA\t1\t79\t.\t.\t.\n-HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\tflaimapper\tncRNA\t1\t90\t.\t.\t.\n-HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t.\t.\n-HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n-HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n-HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t.\t.\n-HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\tflaimapper\tncRNA\t1\t105\t.\t.\t.\n-HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\tflaimapper\tncRNA\t1\t152\t.\t.\t.\n-HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\tflaimapper\tncRNA\t1\t152\t.\t.\t.\n-HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\tflaimapper\tncRNA\t1\t122\t.\t.\t.\n-HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n-H'..b'.tRNA59-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n-NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n-NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n-NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n-NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t.\t.\n-NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n-NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n-NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n-NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\tflaimapper\tncRNA\t1\t74\t.\t.\t.\n-NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\tflaimapper\tncRNA\t1\t85\t.\t.\t.\n-NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n-NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n-NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\tflaimapper\tncRNA\t1\t85\t.\t.\t.\n-NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n-NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t.\t.\n-HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\tflaimapper\tncRNA\t1\t323\t.\t.\t.\n-HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\tflaimapper\tncRNA\t1\t425\t.\t.\t.\n-HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\tflaimapper\tncRNA\t1\t322\t.\t.\t.\n-HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\tflaimapper\tncRNA\t1\t95\t.\t.\t.\n-HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\tflaimapper\tncRNA\t1\t121\t.\t.\t.\n' |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_SE_reads.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_genomic_SE_reads.fastqsanger Mon Jan 23 03:13:40 2017 -0500 |
| b |
| @@ -0,0 +1,240 @@ +@read_001_fragment_1_chr1:120-148 (len=29) +GGATAGTGCCAAAGCTCACTCACCACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_002_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_003_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_004_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_005_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_006_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_007_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_008_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_009_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_010_fragment_1_chr1:120-149 (len=30) +GGATAGTGCCAAAGCTCACTCACCACTGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_011_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_012_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_013_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_014_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_015_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_016_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_017_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_018_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_019_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_020_fragment_2_chr1:260-289 (len=30) +GCTTACCTCTAGAATAAGTGTCAGCCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_021_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_022_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_023_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_024_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_025_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_026_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_027_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_028_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_029_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_030_fragment_3_chr1:400-429 (len=30) +atacgtggcatttcaggaggcggccggagg ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_031_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_032_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_033_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_034_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_035_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_036_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_037_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_038_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_039_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_040_fragment_4_chr22:100-149 (len=50) +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_041_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_042_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_043_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_044_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_045_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_046_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_047_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_048_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_049_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_050_fragment_5_chr22:370-399 (len=30) +TCTTGAGTGTTAAAATGTTGACCCCTGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_051_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_052_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_053_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_054_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_055_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_056_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_057_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_058_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_059_fragment_6_chrY:0-29 (len=30) +TTGGGATGCGGGTAGTAGATGACTGCAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@read_060_fragment_6_chrY:0-30 (len=31) +TTGGGATGCGGGTAGTAGATGACTGCAGGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_alignment.bam |
| b |
| Binary file test-data/test_genomic_alignment.bam has changed |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_all_chromosomes.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_genomic_all_chromosomes.fa Mon Jan 23 03:13:40 2017 -0500 |
| b |
| @@ -0,0 +1,27 @@ +>chr1 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +TCTAGTGGTATGGTGGTATAGTAAGCTCGTACTGTGATACATGCGACAGG +GGTAAGACCATCAGTAGTAGGGATAGTGCCAAAGCTCACTCACCACTGCC +TATAAGGGGTGCTTACCTCTAGAATAAGTGTCAGCCAGTATAACCCCATG +aagccgcgacacgacggctcacagccggtaagagtaaccccggagtgaac +acctatggggctggataaaactgccctggtgaccgccatcaacaacccga +atacgtggcatttcaggaggcggccggaggggggatgttttctactattc +gaggccgttcgttataacttgttgcgttcctagccgctatatttgtctct +GAGGCCGTTCGTTATAACTTGTTGCGTTCCTAGCCGCTATATTTGTCTCT +TTGCCGACTAATGAGAACAACCACACCATAGCGATTTGACGCAGCGCCTC +GGAATACCGTATCAGCAGGCGCCTCGTAAGGCCATTGCGAATACCAGGTA +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +>chr22 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +CTGGCTATGCACGAAGCAACTCTTGAGTGTTAAAATGTTGACCCCTGTAT +>chrY +TTGGGATGCGGGTAGTAGATGACTGCAGGGACTCCGACGTCAAGTACATT +ACCCTCTCATAGGCGGCGTTCTAGATCACGTTACCGCCATATCATCCGAG \ No newline at end of file |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_flaimapper_output.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_genomic_flaimapper_output.gtf Mon Jan 23 03:13:40 2017 -0500 |
| b |
| @@ -0,0 +1,12 @@ +chr1 flaimapper-v2.3.4 sncdRNA 261 290 20 . . gene_id "FM_chr1_000000000001" +chr1 flaimapper-v2.3.4 exon 257 294 20 . . gene_id "FM_chr1_000000000001" +chr1 flaimapper-v2.3.4 sncdRNA 221 250 19 . . gene_id "FM_chr1_000000000002" +chr1 flaimapper-v2.3.4 exon 217 254 19 . . gene_id "FM_chr1_000000000002" +chr1 flaimapper-v2.3.4 sncdRNA 401 430 20 . . gene_id "FM_chr1_000000000001" +chr1 flaimapper-v2.3.4 exon 397 434 20 . . gene_id "FM_chr1_000000000001" +chr22 flaimapper-v2.3.4 sncdRNA 101 150 20 . . gene_id "FM_chr22_000000000001" +chr22 flaimapper-v2.3.4 exon 97 154 20 . . gene_id "FM_chr22_000000000001" +chr22 flaimapper-v2.3.4 sncdRNA 371 400 20 . . gene_id "FM_chr22_000000000001" +chr22 flaimapper-v2.3.4 exon 367 404 20 . . gene_id "FM_chr22_000000000001" +chrY flaimapper-v2.3.4 sncdRNA 1 30 19 . . gene_id "FM_chrY_000000000001" +chrY flaimapper-v2.3.4 exon 1 34 19 . . gene_id "FM_chrY_000000000001" |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_flaimapper_output.no-seq.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_genomic_flaimapper_output.no-seq.txt Mon Jan 23 03:13:40 2017 -0500 |
| b |
| @@ -0,0 +1,7 @@ +Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) +FM_chr1_000000000001 30 chr1 260 289 chr1 56 85 10 10 20 +FM_chr1_000000000002 30 chr1 220 249 chr1 16 45 10 9 19 +FM_chr1_000000000001 30 chr1 400 429 chr1 16 45 10 10 20 +FM_chr22_000000000001 50 chr22 100 149 chr22 16 65 10 10 20 +FM_chr22_000000000001 30 chr22 370 399 chr22 16 45 10 10 20 +FM_chrY_000000000001 30 chrY 0 29 chrY 0 29 10 9 19 |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_flaimapper_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_genomic_flaimapper_output.txt Mon Jan 23 03:13:40 2017 -0500 |
| b |
| @@ -0,0 +1,7 @@ +Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence (no fasta file given) Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) +FM_chr1_000000000001 30 chr1 260 289 chr1 56 85 GCTTACCTCTAGAATAAGTGTCAGCCAGTA 10 10 20 +FM_chr1_000000000002 30 chr1 220 249 chr1 16 45 GGATAGTGCCAAAGCTCACTCACCACTGCC 10 9 19 +FM_chr1_000000000001 30 chr1 400 429 chr1 16 45 atacgtggcatttcaggaggcggccggagg 10 10 20 +FM_chr22_000000000001 50 chr22 100 149 chr22 16 65 AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA 10 10 20 +FM_chr22_000000000001 30 chr22 370 399 chr22 16 45 TCTTGAGTGTTAAAATGTTGACCCCTGTAT 10 10 20 +FM_chrY_000000000001 30 chrY 0 29 chrY 0 29 TTGGGATGCGGGTAGTAGATGACTGCAGGG 10 9 19 |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf test-data/test_genomic_genes.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_genomic_genes.gtf Mon Jan 23 03:13:40 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +chr1 flaimapper testing ncRNA 101 250 . + . gene_id="ncRNA_1" +chr1 flaimapper testing ncRNA 201 400 . + . gene_id="ncRNA_2" +chr1 flaimapper testing ncRNA 351 500 . + . gene_id="ncRNA_3" +chr22 flaimapper testing ncRNA 101 200 . + . gene_id="ncRNA_4" +chr22 flaimapper testing ncRNA 201 400 . + . gene_id="ncRNA_5" +chrY flaimapper testing ncRNA 1 100 . + . gene_id="ncRNA_6" \ No newline at end of file |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> -<!-- Location of all GFF/GTF files --> -<table name="gene_sets" comment_char="#"> -<columns>name, dbkey, value, provider, reference</columns> -<file path="tool-data/gene_sets.loc" /> -</table> -</tables> \ No newline at end of file |
| b |
| diff -r 79dcb1e0be6b -r c143e7e1fdbf tool_dependencies.xml --- a/tool_dependencies.xml Fri Jul 31 05:31:02 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="flaimapper" version="1.2.1"> - <repository changeset_revision="13df148b30ef" name="package_flaimapper_1_2_1" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |