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Commit message:
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c |
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added:
cpt-macros.xml cpt_convert_glimmer_to_gff3.py cpt_convert_glimmer_to_gff3.xml macros.xml test-data/ConvGlim_In.fasta test-data/ConvGlim_In.out test-data/ConvGlim_Out.gff3 |
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removed:
cpt_convert_glimmer/cpt-macros.xml cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.py cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml cpt_convert_glimmer/macros.xml cpt_convert_glimmer/test-data/ConvGlim_In.fasta cpt_convert_glimmer/test-data/ConvGlim_In.out cpt_convert_glimmer/test-data/ConvGlim_Out.gff3 |
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| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt-macros.xml Mon Jun 05 02:40:30 2023 +0000 |
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| @@ -0,0 +1,115 @@ +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <requirement type="package" version="1.2.2">cpt_gffparser</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd '$__tool_directory__' && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros> |
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| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/cpt-macros.xml --- a/cpt_convert_glimmer/cpt-macros.xml Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,115 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="gff_requirements"> - <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.65">biopython</requirement> - <requirement type="package" version="2.12.1">requests</requirement> - <yield/> - </requirements> - <version_command> - <![CDATA[ - cd $__tool_directory__ && git rev-parse HEAD - ]]> - </version_command> - </xml> - <xml name="citation/mijalisrasche"> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex">@unpublished{galaxyTools, - author = {E. Mijalis, H. Rasche}, - title = {CPT Galaxy Tools}, - year = {2013-2017}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - </xml> - <xml name="citations"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {E. Mijalis, H. Rasche}, - title = {CPT Galaxy Tools}, - year = {2013-2017}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-crr"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {C. Ross}, - title = {CPT Galaxy Tools}, - year = {2020-}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-2020"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {E. Mijalis, H. Rasche}, - title = {CPT Galaxy Tools}, - year = {2013-2017}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {A. Criscione}, - title = {CPT Galaxy Tools}, - year = {2019-2021}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-2020-AJC-solo"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {A. Criscione}, - title = {CPT Galaxy Tools}, - year = {2019-2021}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-clm"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {C. Maughmer}, - title = {CPT Galaxy Tools}, - year = {2017-2020}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="sl-citations-clm"> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {C. Maughmer}, - title = {CPT Galaxy Tools}, - year = {2017-2020}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </xml> -</macros> |
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| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.py --- a/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.py Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,91 +0,0 @@ -#!/usr/bin/env python -import sys -import argparse -from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature -from Bio import SeqIO -from Bio.SeqFeature import SeqFeature -from Bio.SeqFeature import FeatureLocation -import logging - -logging.basicConfig(level=logging.INFO) - - -def glimmer3_to_gff3(glimmer, genome): - seq_dict = SeqIO.to_dict(SeqIO.parse(genome, "fasta")) - - current_record = None - for line in glimmer: - if line.startswith(">"): - chromId = line.strip().replace(">", "") - if chromId in seq_dict: - if current_record is not None: - yield current_record - current_record = seq_dict[chromId] - else: - raise Exception( - "Found results for sequence %s which was not in fasta file sequences (%s)" - % (chromId, ", ".join(seq_dict.keys())) - ) - - if not line.startswith(">"): - (gene_id, gstart, gend, phase, score) = line.strip().split() - gstart = int(gstart) - gend = int(gend) - - if "+" in phase: - strand = 1 - start = gstart - end = gend - else: - strand = -1 - start = gend - end = gstart - - # Correct for gff3 - start -= 1 - - if start > end: - #gene found on boundary (ex [4000, 200]) from glimmer assuming circular genome - #-------------start<=======|sequence end|========>end------ - if strand > 0: - end = len(current_record) - else: - start = 0 - gene_id+="_truncated" - - cds_feat = gffSeqFeature( - FeatureLocation(start, end), - type="CDS", - strand=strand, - id="%s.%s" % (current_record.id, gene_id), - qualifiers={ - "source": "Glimmer3", - "ID": "%s.cds_%s" % (current_record.id, gene_id), - }, - source="Glimmer3" - ) - - gene = gffSeqFeature( - FeatureLocation(start, end), - type="gene", - strand=strand, - id="%s.%s" % (current_record.id, gene_id), - qualifiers={ - "source": "Glimmer3", - "ID": "%s.%s" % (current_record.id, gene_id), - }, - source="Glimmer3" - ) - gene.sub_features = [cds_feat] - current_record.features.append(gene) - yield current_record - - -if __name__ == "__main__": - parser = argparse.ArgumentParser(description="Convert Glimmer to GFF3") - parser.add_argument("glimmer", type=argparse.FileType("r"), help="Glimmer3 Output") - parser.add_argument("genome", type=argparse.FileType("r"), help="Fasta Genome") - args = parser.parse_args() - - for result in glimmer3_to_gff3(**vars(args)): - gffWrite([result], sys.stdout) |
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| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml --- a/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,41 +0,0 @@ -<?xml version="1.0"?> -<tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0"> - <description>convert formats</description> - <macros> - <import>cpt-macros.xml</import> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="aggressive"> -@GENOME_SELECTOR_PRE@ - -python $__tool_directory__/cpt_convert_glimmer_to_gff3.py -$glimmer -@GENOME_SELECTOR@ -> $data -</command> - <inputs> - <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/> - <expand macro="genome_selector" /> - </inputs> - <outputs> - <data format="gff3" name="data"> - </data> - </outputs> - <tests> - <test> - <param name="reference_genome_source" value="history" /> - <param name="genome_fasta" value="ConvGlim_In.fasta" /> - <param name="glimmer" value="ConvGlim_In.out" /> - <output name="data" file="ConvGlim_Out.gff3" /> - </test> - </tests> - <help> - **What it does** - - Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping - around over the sequence boundary (as if circular) then it will only convert the upstream fragment and - label it as "_truncated" in the resulting GFF. - </help> - <expand macro="citations" /> -</tool> |
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| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/macros.xml --- a/cpt_convert_glimmer/macros.xml Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,43 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="3.8.13">python</requirement> - <requirement type="package" version="1.79">biopython</requirement> - <requirement type="package" version="1.2.2">cpt_gffparser</requirement> - <yield/> - </requirements> - </xml> - <xml name="genome_selector"> - <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> - </xml> - <xml name="gff3_input"> - <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> - </xml> - <xml name="input/gff3+fasta"> - <expand macro="gff3_input" /> - <expand macro="genome_selector" /> - </xml> - <token name="@INPUT_GFF@"> - "$gff3_data" - </token> - <token name="@INPUT_FASTA@"> - genomeref.fa - </token> - <token name="@GENOME_SELECTOR_PRE@"> - ln -s $genome_fasta genomeref.fa; - </token> - <token name="@GENOME_SELECTOR@"> - genomeref.fa - </token> - <xml name="input/fasta"> - <param label="Fasta file" name="sequences" type="data" format="fasta"/> - </xml> - - <token name="@SEQUENCE@"> - "$sequences" - </token> - <xml name="input/fasta/protein"> - <param label="Protein fasta file" name="sequences" type="data" format="fasta"/> - </xml> -</macros> |
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| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/test-data/ConvGlim_In.fasta --- a/cpt_convert_glimmer/test-data/ConvGlim_In.fasta Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,2936 +0,0 @@\n->Miro\n-TTAGTAATGGCTAAAACCATATGTAACATCAATCATGACTTTATAACGGCATACACGCAT\n-TTTTGCGTTATTGTAATCCACTGGGATCGCTACCACGTCAGCAGGATCCACCTTTACCTG\n-AATGACTCTACCAACACCGCCCCCGTAGTGTGGAAGGTATGATTTAGCCGCAACGTGTAG\n-GCCAGTAGAACAGGTGCGCGTTTTATCTTCGTCTACCATGTTTCGAGGCATGGAGACAGT\n-CACACCAGGACTATTATCAAATTTGCCAGTAGCGAGATCTTTATAGTTATCGCGCACACG\n-TTTCCAGGCAAGGAAACAACCATCATCGGTCAGTTCAATGTCATTATGTACAAGGAACCC\n-ATAAAGCTGGTATACAGCATCGCGTGAAGGGTTTCGCATCAACCGTTCAAAGAAGTTCAC\n-CAGATGTTCATACGGACGATCGTTATACATTTCGCGAATGATTCGTTGAGTGATATCAGA\n-ATCAAACACTACATCTTTATATAGAAGCTGATGACCAATGATTTTAATGTTGCCTTTGCT\n-ATAGGTTCGGATCGCTTCTTGAGTATCCAAACAAGTTACAGCACCTTTGACATCACCAGC\n-TTTCAGCATTTCATGCGCTTTCTTAAAGTTCGGATGTGTTTCACCCGCCATGAAAACGCG\n-CCCTTCGTATACAACCGTAATGAACGATTCAGATCCGATCATACGCGGTACAGTGTCTGA\n-TACTTTAGGCTTTTGTTTTACATCCCTTTTCTTAGGGAATTCCGCTAACTTGCGGTTGAT\n-AACGCGCCCAATGGTTCGGGCGCTTACGTTGAACTGTTGGGCCAGTGCTGTTTTACTTGC\n-CCCCGTCAACCATCCATTATAGATAGCTTTCTGTTGTACTTCGTCGAGAATTTTGACCAT\n-TATTTCCACCGTATTAATTTCTTAAACTCACTGAGATTCTTTTCGTTGTTGTAAATCGGA\n-CGAATTGAATAAGAATCGCTATGTTCAACAAGTGAAGCCAGTAACGGGTTTAGTGATTTA\n-AAGATTTCCCATGCCTGATCAACACGTTTTTTCATATTGCTGCGTTTAACGCGCATTGAT\n-GCTACGGACTCACGCAGAATCGGACAACGCACCCTGGAAAGATTTTTACCATCTTTCTCA\n-TACCCTTCCAGACACACTATACGTTCGAGGGTATCAACAATCTTATACAGTTTTTCATTA\n-TATCGGTTTTTCACAATCCGATCAAGCGATACACCGAAACGGCTATGCAATGCGTCTGTT\n-TCTGTTGAGTGATCCTTCCCAATCCATCCAGGCAAGCAATTATCTTTCAATGCCTTTTCA\n-GATTTAACATACTGCTTGCACAGCATATCATCAAAGCATACCAGATTTGAATCCGGGATC\n-CACTTCCAGAGGCTGTTACGTATAGCAAACACAACAGGGATCCCAGTATGGCGCATGATA\n-CGCGATAAAGTAGATTCTTTCATTGCTGAATCCATAGACAACCCGGAATTTTCACCATCT\n-AAGCGGCTATATTCATCAATACCATACAACCGAACACCTGGGGCTTTATCCAGTGATAAA\n-AACTCTGATTTTGTCATAAACAGAGAAGTTTTTGCCAGATTGCCGTTACTATCCAACTCA\n-TAACGATATACGGTCGGGGTTTTTGGGCGCGGTTCTGAATTTTTCGGTGCATATAGCGCT\n-TTTGATTTTTCGCGATCTGCATCATAGATCTCTTTTTCTTTTGTCATTTCACTGGTACGG\n-AGATACACAATTTCCGATTCATCAAAATGACCTTTCCGAACGATATCATTAACAATCTCA\n-CGCTTTGAATCACTATCGTAATATGCAACAAAGCTAACACGGCTTAGGTTATGCATTTTA\n-GCATACCCGACGATATACGGTTTAACCGTGTTGGTATCCACTTTTAACAGAATGAGTTTC\n-TTCTGTTTCCACGGATAATAAATGCGTGTGATGTCCTGGCGTTTGGTTGTTTCTGGCTTA\n-TACTTGCTCCAGCGGCCTCCGCTACCAGTTACCTGATACCATGCATCTTTACCGTCGTAT\n-TCGTTCGCCCAATACCCAGCAACATAATCATCATTATATTTGTTTGGTTTGACTAGTTCG\n-CTATGGATCCAGCCAATAGAATCACCATTGATGCGAAAATTAGCATCTTTACCAACAAAG\n-TTTTGTACCATTGAAGGCAGAGAATGGAACCACGTCAGTTTATCACGCACGGTTTGTAAC\n-TTATCGAATTCTGATTTAACTCGATTGAAATATACCCGGCTGATTTGTTTCAGACGTTCT\n-TTAACAATCCCTACTGTCATTTTATCCATACTCAACTCTTCGCGAGAAGGCATGAAATCA\n-AGTTCACCGATCGGGAAGTCAATAATATACGTATACTGGCTTTCTGTATAGCAATAGAAC\n-ATCGAGGTATCATACAAATCTTTATCCAGAGGATAAATGATGTTACCCATGCGAGCATAT\n-ACACCGCTAGTGTATGCTGATTTATGACGGATCACCCCGCTATCGTTGGTTGCTTCTTTC\n-GGCTGATAGTTGATTTTGAGAATAGAAGCACCAACAAAGTTAGGACGAATATCAGTAAAT\n-GATTCGTATACCCTTGCTGCTTCGTTTTCCCATTCTTTGATATCTTCAACCTTAACCGGA\n-ACAGTGATAGTAACCCCGTTAGGTTCATCGCTTTCAATCTCATACAGAGGATCGCAGAAA\n-GGTTCCCCATCATCCATATAGATTGTGTAACCGCATTTGATACCGTCTTTTACGGATTCC\n-ACCGTGAAAGCATCGGAATAGCAAAGCGGAGATTTGCAACCCAGACCCATAGAACCGATC\n-AGGTCGTTTGAATCATTTTTAGTTGATTCGAAGTAAACGGTAAACGCATCACTAACGAAA\n-TCAGGAGACATACCGATCCCGTAGTCACGAATAACAAAACGAGGATCAACAGCAGTTGGC\n-AACTGGACATCAAACGGGTTCTGATTTCCCGCTTCTTTGTGTCCATCAATCGCATTACAA\n-GACAGTTCGCGAATGATTGCGCGGATCTTGTATTTGTATACTGTCGAAGAAAGGATCTTA\n-TACGCTTTCTTGTTTGCGCGTAGAGATAGTTTGTTTCGTCCCTTGCTGGTATCTGTACCA\n-ACACGGTAGATGGTTTGCGGTGTATCTTCGCGTAATTTCATTGTTTATTTCTCACTTAAC\n-ATTAAAAATAACTTGGTCACAAGAGTACTTCGTTGGCTTTTTGTTCAGACCATATTCTAC\n-TACTTCACAATAGGTGTCAAGGAATTTTACCAATTTTTCTTCCTCGACCTGCTGTTTCTT\n-CATATCAAGGATACCCCACACGATAGCCCCGATAATGACAGAAAAGAACGCACAAAATCC\n-GAATATGGTCAGATATTTTCCCAACTTAGGCGCATTATAACGTGTCATACCTTACCCCTC\n-TTTGCGAATGTATGCAAGTTCTTCATGGGTTACTGGACGGATATACAGACGGCCTTTTGT\n-ATATGCCTTGCGCCCGCTGATCCAAATGTTTTTCATATCCTTAACACCGTTCATCACATC\n-GTTGTAAAACTTCTTATCAGCTTTAGCCTGATAGACTTCACGGCCTTGATAATCTTTCAT\n-GAACAAACAATAAAGGATCTCATTCTTATCAACTAGATTAGCATCCTTTGTAGTTGTTTT\n-ACTTGGTGAAGGTTTCGCACCCAGGCGCAAGGCCATAGCTTGCCACACTTTACCATGTTC\n-ATAACCGCGCCCGACAAGAGCATGAGCGATTTCGTGTAAAAGAGTGTCTAAAATATCCTC\n-GTAGATATCTTCCGCAACATGACGACCAGACAGTTCGATCAGTTTTTTGGTATAACTGCA\n-ACGG'..b'TCGGGTAATATCG\n-TTTGTGATGGGTGTGAAAACATGGAAACAATTGCTGATAAAAATAATTCTAATAATGGTT\n-ATGTTTCTTATGGTAGTAACTTGGTACAAATGGACTGATATATTCCCGATGATAAAAGGT\n-GCCCTTGTAGTCGATACAAGGGCTATCGAAATGGAAAGAACAGAAAAGTTTAATCAATCC\n-GCGTTGGAACAGTTGAGCATAGTTCATCTTACTTCCAACGCGGATTTTTCGGCGGTACTG\n-GCATTCAGACCAAAGAACATAAACTATTTTGTTGACATTGTAGAATATCAGGGAAAATTA\n-CCATCCCAAATCGATCCTAAAAACCTCGGTGGTTATCCGATCGATAAAACATCCGAAGAA\n-TACACGAATCATATAAATGGCTTGTACTATTCATCAACTACAGCAAGTTCCTACCTACCG\n-ACACGTGATTTTGTGCCAGTAGCTTATACTTTTAGTTGCCCTTATTTCAATCTTGATAAC\n-TACTATTCTGGATCGGTTTTGATGGAATGGTATGCAAAGCGGCCTGATATACCAGATATG\n-AAGATAAACATCATATGTGGACAGGCCGCGCGCATTTTAGGTCGAGCGAGGTGATTAACG\n-TAATGCTGGTGTTAAATTGTGTGATCTTCCAATAGCCCGTTTGATTGCTTTAAAGAAGTT\n-CATCACCGGGCTATTTTTCTCGTAAATATCCCAAACTTTCAATTTGTCCCACGGATCCGG\n-AACATAATCTTCATTCCTTGCCGAAACCCCCAACGTAACCCTCCTGTATCCAGCGCTGTC\n-GTGATAATACACGAAGAATGGCCTACCTATTGGCGCAACCTTACAACCTCTCTTAGCGGC\n-TCTCATAGCCTCATCGAACGTCATGGATTCCCCCAAAAATTTCTATGCATGAATGGTCGA\n-ATTCCGATAGTTTCACTCAAAATGAATATCGGATGATCTAGCTCATCGTGGTTTTCTTCG\n-TCAATGACGATATCCCAATCAGTAGCCTTTTGTTCTTCTACCGTGGCAATGAATACCTGG\n-TTTACTTCACACTTGCGGTGTGTACGTCTGATGATTGTATCCCCCTCACGAAACACAATC\n-ATATCAGGATTGGTAGTGCGGTACGCGGTTTTACCCGCGCACACTTCATTAAGCATATCT\n-TCGTATGTCATTATAAAACCTTTACACGTTGAACGATGGTTTGTTTAACGTCTTTGTATT\n-CTCCGTGCTCTTTAACGGTTGCTTTGAAAGTGATTTCATCACCTTCGTTTGCAATGTTAT\n-TACCGAAGTAAACAACAACATTACCATCAACATTAATTTTGGTCATGAATCTTTCTACAG\n-AAGTGTAGTAAGAAACTTGAGTATATCCCAGTGAAATCACTTTCTCAACGGTTCCGGTCA\n-TTTCCAGACGTTGTTTGATTTCACCGATGTGGTTAGCTTTAGAAATGCGTTCCTGGCGCT\n-CTTGTTCCCACTGTTCGCGGATTTCTTCGCGTTTGGCGATATAATCCTTTTCCAGTGCAA\n-CACCCATGCAGTAAGCGCACACAGCATCGAATACAGGGCTGTTTTTGTTGTCTTCTTTAG\n-ACTGGTCAGCCCACCAAAGAACAGTAAACATTGGCATTTCTGCAATTACTTCGCCTTTAC\n-GCTTGCCAATCGGCATGATCCCTTTTTCCAGCAGTTCCAGTTTTTCAGTATCGAACACTG\n-ACAGTTTACCGCGACGTTCGAACAGATCGAAATCTGCAAAGCCCTGGAATATCATTTTGA\n-AAGTATCAGTTTCAGTTAAACGGGCTGAAACACGGTCGAAATACTCACGCGCTTTCGCTT\n-CCGCTTTCTCCGGATCGGTAGATAAGTTGCAGATATAGTTATCAGAAGTATAACCGCCGC\n-CTCTACGCTCAACACGCAAGGTATACATTGCATTTTTACGACCAGAAGAAATGAAGTAAG\n-TGGTAGTAACTACGGTTGCGTTAGTCATGGTATTTCTCCTTAAAGGGTATCTCGTTTCGA\n-TATGGCTAATATAGCAAAAGCCCCTGACCGAAGTCAAGGGCTTTTTCATCATTCATTCGA\n-ATCTTTCATTGTTTTATGAAGATGAATATCAAAAATTTTCCAGTACGCCTTTCCGCGAGG\n-ATAAATTTTTGCTTTGTCAATATCGTTGTTGCTTCCCCATGTGTTGTTTGGGCCACGACA\n-TCGATTTTTTATATAATCTGTATGCCAGAATAAGCGCTGAACCGATGATTCCGTACCTAA\n-TGGATCTTCTTTACTGAACAGAATTTGTATACTCATAAGAAGAACCCAGTGCGAACAATC\n-AGATCGATTTTCTTTTCTGGTTCAAACGGTGATTTGCTATCGATGTTACACTGATAGAAC\n-ATACCAACATACTTTTCAGGAATGTTGGATTCACGCGCCCATTTCAGGTTATCATCGGTA\n-TTCGGCCCCAGCATGAGGTTAACAACATCAACAGCATAATCCTGTTCTTTGGTGTTGCCG\n-GAACCGTTTACATAATGCCCGTGGGCGGTTTTGAGGATCTCAATTACTTCGCTATCGTCA\n-GTTTCGACTTTGTAAAGCGTTGTATTTTCAGGAATTTCTTCAAGAATGATCAAAGCGGTT\n-TTCATCACACTTACCTTTGTGTTTCTGTTTACGTTTTGCTTCTTTAAATGCTCGCTTGCG\n-ATCGCGGTGAGTAGAAGCGCGGTTGAAATCATGTTTCGCTACCAAATTATTCATATAAGC\n-CCCTTAAAGAAAAATATTTAGGGGCTTTCGCCCCTGTATTAATCCAGCAATTTGCGGATC\n-TTGTCTGCGATACGTCCGGCGCGGGTTGCACTTGCAGTATGATCGCTTTCTTTTGAAGCC\n-AGTTCCGCCAGCTTACGCTGATGTTCTTCTTCTGCTGCTTGACGATCTGCTGCAACCTGT\n-GCAACCTGCTCATTATCGTGAGCAATACGCGCTTCCAGTTCAGACAGGGTTTTGTCGAAA\n-GTTGCTACGATTTCATCTACAGAACGAATTTTATTAAACAGTTTCATAATTTATCTCAAT\n-TGGTTAGTTTTAATCAGTATACATCAATATGGTTGAAATTCAAAATCATAAATGTCATTC\n-AGTGCGCGGTTCCACTCGGTGTAGTTTTCACCAGCACCATAACGCATTTGAATAGCACTT\n-TCGAACGTTGATCCGTTGAGGTTCGGGAAACCGAACAGGTTTTTGATTTTGTCATGTGCT\n-ACATAATACAGAGAAGCACTTTCCAGCATCGCAACCATCGCAGACGGTTCGTGTTCGCGG\n-CGCTTGATACGTAACAGAGTACGACTAGCACCAGTTTTACGGCGTTGATTTGGTGCTACG\n-TAGAAACGGAATACTACGCGCCCTGTTTTATCATCAACTACCAGGTAAAACCCGTTTTCT\n-TTCAGATCCACGCCTTCGAATTTCTTGAAGGTTCCGCGTTTCATGTCACCAATTTTAATT\n-GCATATTTGTGAATGTCAAGTCTTGTCAGAATTCTTTTCATATTTTTTAGATACCAGTTT\n-GCCTAATTTTGTAATTTCGCCTGTTTTTACGTTAACAAACAAGGCGATGCTCAGAAATGG\n-GATGCTAATCACTACGCTGATCAATGTAAACAGAAAACGTATCACAAAAAGAACAGCACG\n-TTCAAGATATCGTTGCATCCACGCGATTCCTAAACAACTATACCCTACTATAAAGGTGGT\n-TGCAACATAAAATGCACCAAATCCTTTACGAAATACGTAACCTTTCCCGGATTCTATCCG\n-GTCGTCGGCCCACATTTCACGGGCAGTTTTCAGAATAGATTCACCACTAGCGCGAGTTTC\n-GTTAGCCGAAGGCATGTTTTTAAATTTCATGATAGTCTCCTATGCGCCCAGAACTCTCCA\n-GGCGCGGTTGTTTAG\n' |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/test-data/ConvGlim_In.out --- a/cpt_convert_glimmer/test-data/ConvGlim_In.out Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,259 +0,0 @@\n->Miro\n-orf00001 900 1 -1 9.03\n-orf00002 3161 900 -3 8.16\n-orf00003 3408 3172 -1 2.33\n-orf00004 4020 3412 -1 6.61\n-orf00005 5324 4038 -3 7.54\n-orf00007 7222 5324 -2 8.91\n-orf00009 7403 7290 -3 11.40\n-orf00010 7894 7454 -2 6.54\n-orf00011 8384 7917 -3 8.53\n-orf00012 8733 8488 -1 3.78\n-orf00013 9359 8763 -3 5.35\n-orf00015 9728 9399 -3 10.83\n-orf00016 10012 9788 -2 10.71\n-orf00017 10349 10086 -3 12.41\n-orf00018 10707 10438 -1 7.65\n-orf00020 10961 10737 -3 2.85\n-orf00021 11441 11178 -3 10.54\n-orf00022 11701 11456 -2 2.48\n-orf00023 12117 11728 -1 9.11\n-orf00025 12707 12399 -3 6.00\n-orf00026 14003 12732 -3 11.58\n-orf00027 14347 14057 -2 3.72\n-orf00028 15065 14529 -3 13.22\n-orf00029 16098 15073 -1 7.69\n-orf00030 16362 16102 -1 2.28\n-orf00031 16564 16418 -2 4.66\n-orf00032 17121 16633 -1 10.98\n-orf00033 17813 17127 -3 3.24\n-orf00034 18201 17839 -1 5.40\n-orf00035 18464 18228 -3 5.21\n-orf00037 18810 18556 -1 12.10\n-orf00039 19014 18889 -1 5.45\n-orf00040 20638 19202 -2 11.95\n-orf00042 20968 20648 -2 9.61\n-orf00044 22163 21006 -3 12.67\n-orf00045 24937 22238 -2 10.44\n-orf00046 25298 24984 -3 4.08\n-orf00047 25597 25310 -2 3.41\n-orf00048 26028 25666 -1 8.33\n-orf00049 26595 26032 -1 9.85\n-orf00050 27596 26598 -3 10.29\n-orf00051 28320 27655 -1 13.49\n-orf00052 28616 28347 -3 9.40\n-orf00053 29643 28672 -1 15.00\n-orf00055 30270 29659 -1 4.93\n-orf00056 30560 30315 -3 8.17\n-orf00057 30827 30564 -3 14.14\n-orf00058 31754 30837 -3 10.56\n-orf00059 32076 32603 +3 9.83\n-orf00060 32693 32815 +2 5.52\n-orf00061 32841 33134 +3 5.04\n-orf00062 33186 34217 +3 9.85\n-orf00063 34267 34491 +1 1.56\n-orf00064 34514 36172 +2 8.89\n-orf00065 36172 36363 +1 4.57\n-orf00066 36437 38146 +2 12.99\n-orf00067 38230 38496 +1 2.01\n-orf00068 38595 38723 +3 8.05\n-orf00069 38795 38977 +2 9.33\n-orf00070 38992 39552 +1 10.38\n-orf00071 39554 40429 +2 10.15\n-orf00072 40469 42721 +2 13.23\n-orf00073 42758 43933 +2 8.98\n-orf00075 44229 44594 +3 6.09\n-orf00076 44623 45732 +1 7.78\n-orf00077 45939 46265 +3 3.96\n-orf00078 46357 46569 +1 7.30\n-orf00079 46662 46883 +3 1.89\n-orf00080 46919 47035 +2 4.09\n-orf00081 47044 47916 +1 7.65\n-orf00082 47969 48256 +2 6.67\n-orf00083 48280 48504 +1 12.14\n-orf00086 48720 49277 +3 6.24\n-orf00087 49281 49634 +3 13.23\n-orf00088 49645 49896 +1 8.41\n-orf00089 50212 50493 +1 5.34\n-orf00090 50503 50922 +1 8.63\n-orf00092 50958 51530 +3 7.72\n-orf00093 51541 51903 +1 10.81\n-orf00094 51903 52172 +3 6.98\n-orf00095 52298 52591 +2 10.52\n-orf00096 52615 52833 +1 2.29\n-orf00098 52985 53137 +2 9.37\n-orf00100 53221 53661 +1 6.06\n-orf00101 53685 53921 +3 6.18\n-orf00102 53923 54144 +1 3.66\n-orf00103 54225 54755 +3 10.26\n-orf00104 54826 56265 +1 11.52\n-orf00105 56342 56911 +2 12.15\n-orf00107 57009 57203 +3 7.65\n-orf00108 57206 57382 +2 7.01\n-orf00110 57624 57914 +3 9.59\n-orf00111 57925 58236 +1 5.34\n-orf00113 59706 58597 -1 7.23\n-orf00114 59749 60351 +1 9.61\n-orf00115 60354 62126 +3 12.46\n-orf00116 62137 63210 +1 10.'..b' 96877 -1 4.63\n-orf00193 97727 97404 -3 6.99\n-orf00194 98013 97756 -1 4.97\n-orf00195 98398 98015 -2 9.84\n-orf00196 98816 98409 -3 7.35\n-orf00197 98987 98817 -3 12.25\n-orf00198 99292 99059 -2 8.24\n-orf00199 99572 99303 -3 7.18\n-orf00200 99928 99593 -2 11.12\n-orf00201 100067 99939 -3 1.66\n-orf00202 100309 100169 -2 1.85\n-orf00204 100896 100375 -1 3.55\n-orf00205 101545 100922 -2 8.90\n-orf00206 101869 101597 -2 10.05\n-orf00207 102567 101872 -1 8.24\n-orf00208 103097 102567 -3 7.10\n-orf00210 103446 104255 +3 11.77\n-orf00211 104304 104819 +3 2.67\n-orf00212 105693 104839 -1 8.49\n-orf00213 106176 105709 -1 6.32\n-orf00214 106227 106781 +3 8.96\n-orf00215 106820 108547 +2 12.05\n-orf00216 108552 110618 +3 9.07\n-orf00217 110650 112575 +1 10.62\n-orf00218 112656 115742 +3 9.94\n-orf00219 115743 116735 +3 6.50\n-orf00220 116745 117608 +3 10.54\n-orf00221 117710 119422 +2 13.92\n-orf00222 119422 120090 +1 11.52\n-orf00223 120100 121485 +1 10.64\n-orf00224 121496 123247 +2 13.64\n-orf00225 123286 124212 +1 11.65\n-orf00226 124222 124968 +1 11.32\n-orf00228 125117 125872 +2 8.26\n-orf00229 125872 126369 +1 12.43\n-orf00230 126381 128186 +3 4.39\n-orf00231 128206 130197 +1 10.39\n-orf00232 130246 130731 +1 11.81\n-orf00233 130787 132361 +2 11.27\n-orf00234 132361 132603 +1 14.40\n-orf00235 132612 133016 +3 8.20\n-orf00237 133019 133666 +2 10.48\n-orf00238 133699 134487 +1 14.45\n-orf00239 134507 136075 +2 16.79\n-orf00241 136168 136806 +1 2.92\n-orf00242 136839 138128 +3 11.97\n-orf00243 138433 138852 +1 11.57\n-orf00244 138852 139028 +3 7.61\n-orf00245 139536 139303 -1 7.73\n-orf00246 141044 139545 -3 5.03\n-orf00247 141115 141738 +1 12.04\n-orf00248 141831 142142 +3 8.21\n-orf00249 142182 142751 +3 5.11\n-orf00250 142780 143313 +1 13.11\n-orf00251 143324 143599 +2 8.94\n-orf00252 143613 144131 +3 5.20\n-orf00253 144627 144163 -1 10.43\n-orf00254 145516 144677 -2 9.89\n-orf00255 145631 146506 +2 10.48\n-orf00256 146539 146856 +1 3.43\n-orf00257 146910 147029 +3 4.35\n-orf00258 147041 147352 +2 5.34\n-orf00259 147354 147710 +3 12.94\n-orf00260 147710 148234 +2 11.54\n-orf00261 148238 149257 +2 13.08\n-orf00262 149352 149828 +3 6.02\n-orf00263 149897 150346 +2 9.80\n-orf00264 150424 150684 +1 11.24\n-orf00266 150694 151143 +1 3.86\n-orf00267 151171 152604 +1 9.12\n-orf00268 152630 152893 +2 3.24\n-orf00269 152905 153741 +1 9.17\n-orf00270 153750 154019 +3 4.63\n-orf00271 154052 154534 +2 7.42\n-orf00273 154854 156977 +3 8.76\n-orf00274 157045 157287 +1 7.59\n-orf00275 157287 157781 +3 9.71\n-orf00276 157781 157987 +2 4.81\n-orf00277 158008 158259 +1 5.46\n-orf00278 158320 158511 +1 7.99\n-orf00279 158652 159179 +3 3.87\n-orf00280 159200 159667 +2 8.79\n-orf00281 159737 160702 +2 9.94\n-orf00282 160745 161413 +2 8.59\n-orf00284 161651 161950 +2 10.21\n-orf00285 162030 165803 +3 8.87\n-orf00286 165815 166927 +2 6.42\n-orf00287 166977 167645 +3 7.19\n-orf00288 167654 171466 +2 9.03\n-orf00289 171503 172030 +2 3.11\n-orf00290 172147 172794 +1 2.92\n-orf00291 172953 172795 -1 3.49\n-orf00292 173351 173061 -3 1.18\n-orf00293 174148 173351 -2 13.25\n-orf00295 174872 174453 -3 12.21\n-orf00298 175187 174939 -3 13.40\n-orf00299 175604 175224 -3 13.18\n-orf00300 176010 175636 -1 6.19\n' |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer/test-data/ConvGlim_Out.gff3 --- a/cpt_convert_glimmer/test-data/ConvGlim_Out.gff3 Fri May 20 08:41:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,517 +0,0 @@\n-##gff-version 3\n-Miro\tGlimmer3\tgene\t1\t900\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00001;\n-Miro\tGlimmer3\tCDS\t1\t900\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00001;Parent=Miro.orf00001;\n-Miro\tGlimmer3\tgene\t900\t3161\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00002;\n-Miro\tGlimmer3\tCDS\t900\t3161\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00002;Parent=Miro.orf00002;\n-Miro\tGlimmer3\tgene\t3172\t3408\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00003;\n-Miro\tGlimmer3\tCDS\t3172\t3408\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00003;Parent=Miro.orf00003;\n-Miro\tGlimmer3\tgene\t3412\t4020\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00004;\n-Miro\tGlimmer3\tCDS\t3412\t4020\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00004;Parent=Miro.orf00004;\n-Miro\tGlimmer3\tgene\t4038\t5324\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00005;\n-Miro\tGlimmer3\tCDS\t4038\t5324\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00005;Parent=Miro.orf00005;\n-Miro\tGlimmer3\tgene\t5324\t7222\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00007;\n-Miro\tGlimmer3\tCDS\t5324\t7222\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00007;Parent=Miro.orf00007;\n-Miro\tGlimmer3\tgene\t7290\t7403\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00009;\n-Miro\tGlimmer3\tCDS\t7290\t7403\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00009;Parent=Miro.orf00009;\n-Miro\tGlimmer3\tgene\t7454\t7894\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00010;\n-Miro\tGlimmer3\tCDS\t7454\t7894\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00010;Parent=Miro.orf00010;\n-Miro\tGlimmer3\tgene\t7917\t8384\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00011;\n-Miro\tGlimmer3\tCDS\t7917\t8384\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00011;Parent=Miro.orf00011;\n-Miro\tGlimmer3\tgene\t8488\t8733\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00012;\n-Miro\tGlimmer3\tCDS\t8488\t8733\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00012;Parent=Miro.orf00012;\n-Miro\tGlimmer3\tgene\t8763\t9359\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00013;\n-Miro\tGlimmer3\tCDS\t8763\t9359\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00013;Parent=Miro.orf00013;\n-Miro\tGlimmer3\tgene\t9399\t9728\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00015;\n-Miro\tGlimmer3\tCDS\t9399\t9728\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00015;Parent=Miro.orf00015;\n-Miro\tGlimmer3\tgene\t9788\t10012\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00016;\n-Miro\tGlimmer3\tCDS\t9788\t10012\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00016;Parent=Miro.orf00016;\n-Miro\tGlimmer3\tgene\t10086\t10349\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00017;\n-Miro\tGlimmer3\tCDS\t10086\t10349\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00017;Parent=Miro.orf00017;\n-Miro\tGlimmer3\tgene\t10438\t10707\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00018;\n-Miro\tGlimmer3\tCDS\t10438\t10707\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00018;Parent=Miro.orf00018;\n-Miro\tGlimmer3\tgene\t10737\t10961\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00020;\n-Miro\tGlimmer3\tCDS\t10737\t10961\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00020;Parent=Miro.orf00020;\n-Miro\tGlimmer3\tgene\t11178\t11441\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00021;\n-Miro\tGlimmer3\tCDS\t11178\t11441\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00021;Parent=Miro.orf00021;\n-Miro\tGlimmer3\tgene\t11456\t11701\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00022;\n-Miro\tGlimmer3\tCDS\t11456\t11701\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00022;Parent=Miro.orf00022;\n-Miro\tGlimmer3\tgene\t11728\t12117\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00023;\n-Miro\tGlimmer3\tCDS\t11728\t12117\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00023;Parent=Miro.orf00023;\n-Miro\tGlimmer3\tgene\t12399\t12707\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00025;\n-Miro\tGlimmer3\tCDS\t12399\t12707\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00025;Parent=Miro.orf00025;\n-Miro\tGlimmer3\tgene\t12732\t14003\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00026;\n-Miro\tGlimmer3\tCDS\t12732\t14003\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00026;Parent=Miro.orf00026;\n-Miro\tGlimmer3\tgene\t14057\t14347\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00027;\n-Miro\tGlimmer3\tCDS\t14057\t14347\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00027;Parent=Miro.orf00027;\n-Miro\tGlimmer3\tgene\t14529\t15065\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00028;\n-Miro\tGlimmer3\tCDS\t14529\t15065\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00028;Parent=Miro.orf00028;\n-Miro\tGlimmer3\tgene\t15073\t16098\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00029;\n-Miro\tGlimmer3\tCDS\t15073\t16098\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00029;Parent=Miro.or'..b'ID=Miro.cds_orf00273;Parent=Miro.orf00273;\n-Miro\tGlimmer3\tgene\t157045\t157287\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00274;\n-Miro\tGlimmer3\tCDS\t157045\t157287\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00274;Parent=Miro.orf00274;\n-Miro\tGlimmer3\tgene\t157287\t157781\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00275;\n-Miro\tGlimmer3\tCDS\t157287\t157781\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00275;Parent=Miro.orf00275;\n-Miro\tGlimmer3\tgene\t157781\t157987\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00276;\n-Miro\tGlimmer3\tCDS\t157781\t157987\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00276;Parent=Miro.orf00276;\n-Miro\tGlimmer3\tgene\t158008\t158259\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00277;\n-Miro\tGlimmer3\tCDS\t158008\t158259\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00277;Parent=Miro.orf00277;\n-Miro\tGlimmer3\tgene\t158320\t158511\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00278;\n-Miro\tGlimmer3\tCDS\t158320\t158511\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00278;Parent=Miro.orf00278;\n-Miro\tGlimmer3\tgene\t158652\t159179\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00279;\n-Miro\tGlimmer3\tCDS\t158652\t159179\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00279;Parent=Miro.orf00279;\n-Miro\tGlimmer3\tgene\t159200\t159667\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00280;\n-Miro\tGlimmer3\tCDS\t159200\t159667\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00280;Parent=Miro.orf00280;\n-Miro\tGlimmer3\tgene\t159737\t160702\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00281;\n-Miro\tGlimmer3\tCDS\t159737\t160702\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00281;Parent=Miro.orf00281;\n-Miro\tGlimmer3\tgene\t160745\t161413\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00282;\n-Miro\tGlimmer3\tCDS\t160745\t161413\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00282;Parent=Miro.orf00282;\n-Miro\tGlimmer3\tgene\t161651\t161950\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00284;\n-Miro\tGlimmer3\tCDS\t161651\t161950\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00284;Parent=Miro.orf00284;\n-Miro\tGlimmer3\tgene\t162030\t165803\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00285;\n-Miro\tGlimmer3\tCDS\t162030\t165803\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00285;Parent=Miro.orf00285;\n-Miro\tGlimmer3\tgene\t165815\t166927\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00286;\n-Miro\tGlimmer3\tCDS\t165815\t166927\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00286;Parent=Miro.orf00286;\n-Miro\tGlimmer3\tgene\t166977\t167645\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00287;\n-Miro\tGlimmer3\tCDS\t166977\t167645\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00287;Parent=Miro.orf00287;\n-Miro\tGlimmer3\tgene\t167654\t171466\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00288;\n-Miro\tGlimmer3\tCDS\t167654\t171466\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00288;Parent=Miro.orf00288;\n-Miro\tGlimmer3\tgene\t171503\t172030\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00289;\n-Miro\tGlimmer3\tCDS\t171503\t172030\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00289;Parent=Miro.orf00289;\n-Miro\tGlimmer3\tgene\t172147\t172794\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00290;\n-Miro\tGlimmer3\tCDS\t172147\t172794\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00290;Parent=Miro.orf00290;\n-Miro\tGlimmer3\tgene\t172795\t172953\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00291;\n-Miro\tGlimmer3\tCDS\t172795\t172953\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00291;Parent=Miro.orf00291;\n-Miro\tGlimmer3\tgene\t173061\t173351\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00292;\n-Miro\tGlimmer3\tCDS\t173061\t173351\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00292;Parent=Miro.orf00292;\n-Miro\tGlimmer3\tgene\t173351\t174148\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00293;\n-Miro\tGlimmer3\tCDS\t173351\t174148\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00293;Parent=Miro.orf00293;\n-Miro\tGlimmer3\tgene\t174453\t174872\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00295;\n-Miro\tGlimmer3\tCDS\t174453\t174872\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00295;Parent=Miro.orf00295;\n-Miro\tGlimmer3\tgene\t174939\t175187\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00298;\n-Miro\tGlimmer3\tCDS\t174939\t175187\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00298;Parent=Miro.orf00298;\n-Miro\tGlimmer3\tgene\t175224\t175604\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00299;\n-Miro\tGlimmer3\tCDS\t175224\t175604\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00299;Parent=Miro.orf00299;\n-Miro\tGlimmer3\tgene\t175636\t176010\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00300;\n-Miro\tGlimmer3\tCDS\t175636\t176010\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00300;Parent=Miro.orf00300;\n' |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer_to_gff3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer_to_gff3.py Mon Jun 05 02:40:30 2023 +0000 |
| [ |
| @@ -0,0 +1,91 @@ +#!/usr/bin/env python +import sys +import argparse +from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature +from Bio import SeqIO +from Bio.SeqFeature import SeqFeature +from Bio.SeqFeature import FeatureLocation +import logging + +logging.basicConfig(level=logging.INFO) + + +def glimmer3_to_gff3(glimmer, genome): + seq_dict = SeqIO.to_dict(SeqIO.parse(genome, "fasta")) + + current_record = None + for line in glimmer: + if line.startswith(">"): + chromId = line.strip().replace(">", "") + if chromId in seq_dict: + if current_record is not None: + yield current_record + current_record = seq_dict[chromId] + else: + raise Exception( + "Found results for sequence %s which was not in fasta file sequences (%s)" + % (chromId, ", ".join(seq_dict.keys())) + ) + + if not line.startswith(">"): + (gene_id, gstart, gend, phase, score) = line.strip().split() + gstart = int(gstart) + gend = int(gend) + + if "+" in phase: + strand = 1 + start = gstart + end = gend + else: + strand = -1 + start = gend + end = gstart + + # Correct for gff3 + start -= 1 + + if start > end: + # gene found on boundary (ex [4000, 200]) from glimmer assuming circular genome + # -------------start<=======|sequence end|========>end------ + if strand > 0: + end = len(current_record) + else: + start = 0 + gene_id += "_truncated" + + cds_feat = gffSeqFeature( + FeatureLocation(start, end), + type="CDS", + strand=strand, + id="%s.%s" % (current_record.id, gene_id), + qualifiers={ + "source": "Glimmer3", + "ID": "%s.cds_%s" % (current_record.id, gene_id), + }, + source="Glimmer3", + ) + + gene = gffSeqFeature( + FeatureLocation(start, end), + type="gene", + strand=strand, + id="%s.%s" % (current_record.id, gene_id), + qualifiers={ + "source": "Glimmer3", + "ID": "%s.%s" % (current_record.id, gene_id), + }, + source="Glimmer3", + ) + gene.sub_features = [cds_feat] + current_record.features.append(gene) + yield current_record + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Convert Glimmer to GFF3") + parser.add_argument("glimmer", type=argparse.FileType("r"), help="Glimmer3 Output") + parser.add_argument("genome", type=argparse.FileType("r"), help="Fasta Genome") + args = parser.parse_args() + + for result in glimmer3_to_gff3(**vars(args)): + gffWrite([result], sys.stdout) |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a cpt_convert_glimmer_to_gff3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer_to_gff3.xml Mon Jun 05 02:40:30 2023 +0000 |
| [ |
| @@ -0,0 +1,40 @@ +<tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0"> + <description>convert formats</description> + <macros> + <import>cpt-macros.xml</import> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +@GENOME_SELECTOR_PRE@ + +'python $__tool_directory__/cpt_convert_glimmer_to_gff3.py' +'$glimmer' +@GENOME_SELECTOR@ +> '$data' ]]> +</command> + <inputs> + <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/> + <expand macro="genome_selector"/> + </inputs> + <outputs> + <data format="gff3" name="data"> + </data> + </outputs> + <tests> + <test> + <param name="reference_genome_source" value="history"/> + <param name="genome_fasta" value="ConvGlim_In.fasta"/> + <param name="glimmer" value="ConvGlim_In.out"/> + <output name="data" file="ConvGlim_Out.gff3"/> + </test> + </tests> + <help> + **What it does** + + Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping + around over the sequence boundary (as if circular) then it will only convert the upstream fragment and + label it as "_truncated" in the resulting GFF. + </help> + <expand macro="citations"/> +</tool> |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 05 02:40:30 2023 +0000 |
| b |
| @@ -0,0 +1,74 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package">progressivemauve</requirement> + <!--<requirement type="package" version="2.7">python</requirement>--> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> + <xml name="citation/progressive_mauve"> + <citation type="doi">10.1371/journal.pone.0011147</citation> + </xml> + <xml name="citation/gepard"> + <citation type="doi">10.1093/bioinformatics/btm039</citation> + </xml> + <token name="@XMFA_INPUT@"> + '$xmfa' + </token> + <xml name="xmfa_input" token_formats="xmfa"> + <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/> + </xml> + <token name="@XMFA_FA_INPUT@"> + '$sequences' + </token> + <xml name="xmfa_fa_input"> + <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/> + </xml> + <xml name="genome_selector"> + <conditional name="reference_genome"> + <param name="reference_genome_source" type="select" label="Reference Genome"> + <option value="history" selected="True">From History</option> + <option value="cached">Locally Cached</option> + </param> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </when> + </conditional> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input"/> + <expand macro="genome_selector"/> + </xml> + <token name="@INPUT_GFF@"> + '$gff3_data' + </token> + <token name="@INPUT_FASTA@"> + #if str($reference_genome.reference_genome_source) == 'cached': + '${reference_genome.fasta_indexes.fields.path}' + #else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa + #end if + </token> + <token name="@GENOME_SELECTOR_PRE@"> + #if $reference_genome.reference_genome_source == 'history': + ln -s '$reference_genome.genome_fasta' genomeref.fa; + #end if + </token> + <token name="@GENOME_SELECTOR@"> + #if str($reference_genome.reference_genome_source) == 'cached': + '${reference_genome.fasta_indexes.fields.path}' + #else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa + #end if + </token> +</macros> |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a test-data/ConvGlim_In.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ConvGlim_In.fasta Mon Jun 05 02:40:30 2023 +0000 |
| b |
| b'@@ -0,0 +1,2936 @@\n+>Miro\n+TTAGTAATGGCTAAAACCATATGTAACATCAATCATGACTTTATAACGGCATACACGCAT\n+TTTTGCGTTATTGTAATCCACTGGGATCGCTACCACGTCAGCAGGATCCACCTTTACCTG\n+AATGACTCTACCAACACCGCCCCCGTAGTGTGGAAGGTATGATTTAGCCGCAACGTGTAG\n+GCCAGTAGAACAGGTGCGCGTTTTATCTTCGTCTACCATGTTTCGAGGCATGGAGACAGT\n+CACACCAGGACTATTATCAAATTTGCCAGTAGCGAGATCTTTATAGTTATCGCGCACACG\n+TTTCCAGGCAAGGAAACAACCATCATCGGTCAGTTCAATGTCATTATGTACAAGGAACCC\n+ATAAAGCTGGTATACAGCATCGCGTGAAGGGTTTCGCATCAACCGTTCAAAGAAGTTCAC\n+CAGATGTTCATACGGACGATCGTTATACATTTCGCGAATGATTCGTTGAGTGATATCAGA\n+ATCAAACACTACATCTTTATATAGAAGCTGATGACCAATGATTTTAATGTTGCCTTTGCT\n+ATAGGTTCGGATCGCTTCTTGAGTATCCAAACAAGTTACAGCACCTTTGACATCACCAGC\n+TTTCAGCATTTCATGCGCTTTCTTAAAGTTCGGATGTGTTTCACCCGCCATGAAAACGCG\n+CCCTTCGTATACAACCGTAATGAACGATTCAGATCCGATCATACGCGGTACAGTGTCTGA\n+TACTTTAGGCTTTTGTTTTACATCCCTTTTCTTAGGGAATTCCGCTAACTTGCGGTTGAT\n+AACGCGCCCAATGGTTCGGGCGCTTACGTTGAACTGTTGGGCCAGTGCTGTTTTACTTGC\n+CCCCGTCAACCATCCATTATAGATAGCTTTCTGTTGTACTTCGTCGAGAATTTTGACCAT\n+TATTTCCACCGTATTAATTTCTTAAACTCACTGAGATTCTTTTCGTTGTTGTAAATCGGA\n+CGAATTGAATAAGAATCGCTATGTTCAACAAGTGAAGCCAGTAACGGGTTTAGTGATTTA\n+AAGATTTCCCATGCCTGATCAACACGTTTTTTCATATTGCTGCGTTTAACGCGCATTGAT\n+GCTACGGACTCACGCAGAATCGGACAACGCACCCTGGAAAGATTTTTACCATCTTTCTCA\n+TACCCTTCCAGACACACTATACGTTCGAGGGTATCAACAATCTTATACAGTTTTTCATTA\n+TATCGGTTTTTCACAATCCGATCAAGCGATACACCGAAACGGCTATGCAATGCGTCTGTT\n+TCTGTTGAGTGATCCTTCCCAATCCATCCAGGCAAGCAATTATCTTTCAATGCCTTTTCA\n+GATTTAACATACTGCTTGCACAGCATATCATCAAAGCATACCAGATTTGAATCCGGGATC\n+CACTTCCAGAGGCTGTTACGTATAGCAAACACAACAGGGATCCCAGTATGGCGCATGATA\n+CGCGATAAAGTAGATTCTTTCATTGCTGAATCCATAGACAACCCGGAATTTTCACCATCT\n+AAGCGGCTATATTCATCAATACCATACAACCGAACACCTGGGGCTTTATCCAGTGATAAA\n+AACTCTGATTTTGTCATAAACAGAGAAGTTTTTGCCAGATTGCCGTTACTATCCAACTCA\n+TAACGATATACGGTCGGGGTTTTTGGGCGCGGTTCTGAATTTTTCGGTGCATATAGCGCT\n+TTTGATTTTTCGCGATCTGCATCATAGATCTCTTTTTCTTTTGTCATTTCACTGGTACGG\n+AGATACACAATTTCCGATTCATCAAAATGACCTTTCCGAACGATATCATTAACAATCTCA\n+CGCTTTGAATCACTATCGTAATATGCAACAAAGCTAACACGGCTTAGGTTATGCATTTTA\n+GCATACCCGACGATATACGGTTTAACCGTGTTGGTATCCACTTTTAACAGAATGAGTTTC\n+TTCTGTTTCCACGGATAATAAATGCGTGTGATGTCCTGGCGTTTGGTTGTTTCTGGCTTA\n+TACTTGCTCCAGCGGCCTCCGCTACCAGTTACCTGATACCATGCATCTTTACCGTCGTAT\n+TCGTTCGCCCAATACCCAGCAACATAATCATCATTATATTTGTTTGGTTTGACTAGTTCG\n+CTATGGATCCAGCCAATAGAATCACCATTGATGCGAAAATTAGCATCTTTACCAACAAAG\n+TTTTGTACCATTGAAGGCAGAGAATGGAACCACGTCAGTTTATCACGCACGGTTTGTAAC\n+TTATCGAATTCTGATTTAACTCGATTGAAATATACCCGGCTGATTTGTTTCAGACGTTCT\n+TTAACAATCCCTACTGTCATTTTATCCATACTCAACTCTTCGCGAGAAGGCATGAAATCA\n+AGTTCACCGATCGGGAAGTCAATAATATACGTATACTGGCTTTCTGTATAGCAATAGAAC\n+ATCGAGGTATCATACAAATCTTTATCCAGAGGATAAATGATGTTACCCATGCGAGCATAT\n+ACACCGCTAGTGTATGCTGATTTATGACGGATCACCCCGCTATCGTTGGTTGCTTCTTTC\n+GGCTGATAGTTGATTTTGAGAATAGAAGCACCAACAAAGTTAGGACGAATATCAGTAAAT\n+GATTCGTATACCCTTGCTGCTTCGTTTTCCCATTCTTTGATATCTTCAACCTTAACCGGA\n+ACAGTGATAGTAACCCCGTTAGGTTCATCGCTTTCAATCTCATACAGAGGATCGCAGAAA\n+GGTTCCCCATCATCCATATAGATTGTGTAACCGCATTTGATACCGTCTTTTACGGATTCC\n+ACCGTGAAAGCATCGGAATAGCAAAGCGGAGATTTGCAACCCAGACCCATAGAACCGATC\n+AGGTCGTTTGAATCATTTTTAGTTGATTCGAAGTAAACGGTAAACGCATCACTAACGAAA\n+TCAGGAGACATACCGATCCCGTAGTCACGAATAACAAAACGAGGATCAACAGCAGTTGGC\n+AACTGGACATCAAACGGGTTCTGATTTCCCGCTTCTTTGTGTCCATCAATCGCATTACAA\n+GACAGTTCGCGAATGATTGCGCGGATCTTGTATTTGTATACTGTCGAAGAAAGGATCTTA\n+TACGCTTTCTTGTTTGCGCGTAGAGATAGTTTGTTTCGTCCCTTGCTGGTATCTGTACCA\n+ACACGGTAGATGGTTTGCGGTGTATCTTCGCGTAATTTCATTGTTTATTTCTCACTTAAC\n+ATTAAAAATAACTTGGTCACAAGAGTACTTCGTTGGCTTTTTGTTCAGACCATATTCTAC\n+TACTTCACAATAGGTGTCAAGGAATTTTACCAATTTTTCTTCCTCGACCTGCTGTTTCTT\n+CATATCAAGGATACCCCACACGATAGCCCCGATAATGACAGAAAAGAACGCACAAAATCC\n+GAATATGGTCAGATATTTTCCCAACTTAGGCGCATTATAACGTGTCATACCTTACCCCTC\n+TTTGCGAATGTATGCAAGTTCTTCATGGGTTACTGGACGGATATACAGACGGCCTTTTGT\n+ATATGCCTTGCGCCCGCTGATCCAAATGTTTTTCATATCCTTAACACCGTTCATCACATC\n+GTTGTAAAACTTCTTATCAGCTTTAGCCTGATAGACTTCACGGCCTTGATAATCTTTCAT\n+GAACAAACAATAAAGGATCTCATTCTTATCAACTAGATTAGCATCCTTTGTAGTTGTTTT\n+ACTTGGTGAAGGTTTCGCACCCAGGCGCAAGGCCATAGCTTGCCACACTTTACCATGTTC\n+ATAACCGCGCCCGACAAGAGCATGAGCGATTTCGTGTAAAAGAGTGTCTAAAATATCCTC\n+GTAGATATCTTCCGCAACATGACGACCAGACAGTTCGATCAGTTTTTTGGTATAACTGCA\n+ACGG'..b'TCGGGTAATATCG\n+TTTGTGATGGGTGTGAAAACATGGAAACAATTGCTGATAAAAATAATTCTAATAATGGTT\n+ATGTTTCTTATGGTAGTAACTTGGTACAAATGGACTGATATATTCCCGATGATAAAAGGT\n+GCCCTTGTAGTCGATACAAGGGCTATCGAAATGGAAAGAACAGAAAAGTTTAATCAATCC\n+GCGTTGGAACAGTTGAGCATAGTTCATCTTACTTCCAACGCGGATTTTTCGGCGGTACTG\n+GCATTCAGACCAAAGAACATAAACTATTTTGTTGACATTGTAGAATATCAGGGAAAATTA\n+CCATCCCAAATCGATCCTAAAAACCTCGGTGGTTATCCGATCGATAAAACATCCGAAGAA\n+TACACGAATCATATAAATGGCTTGTACTATTCATCAACTACAGCAAGTTCCTACCTACCG\n+ACACGTGATTTTGTGCCAGTAGCTTATACTTTTAGTTGCCCTTATTTCAATCTTGATAAC\n+TACTATTCTGGATCGGTTTTGATGGAATGGTATGCAAAGCGGCCTGATATACCAGATATG\n+AAGATAAACATCATATGTGGACAGGCCGCGCGCATTTTAGGTCGAGCGAGGTGATTAACG\n+TAATGCTGGTGTTAAATTGTGTGATCTTCCAATAGCCCGTTTGATTGCTTTAAAGAAGTT\n+CATCACCGGGCTATTTTTCTCGTAAATATCCCAAACTTTCAATTTGTCCCACGGATCCGG\n+AACATAATCTTCATTCCTTGCCGAAACCCCCAACGTAACCCTCCTGTATCCAGCGCTGTC\n+GTGATAATACACGAAGAATGGCCTACCTATTGGCGCAACCTTACAACCTCTCTTAGCGGC\n+TCTCATAGCCTCATCGAACGTCATGGATTCCCCCAAAAATTTCTATGCATGAATGGTCGA\n+ATTCCGATAGTTTCACTCAAAATGAATATCGGATGATCTAGCTCATCGTGGTTTTCTTCG\n+TCAATGACGATATCCCAATCAGTAGCCTTTTGTTCTTCTACCGTGGCAATGAATACCTGG\n+TTTACTTCACACTTGCGGTGTGTACGTCTGATGATTGTATCCCCCTCACGAAACACAATC\n+ATATCAGGATTGGTAGTGCGGTACGCGGTTTTACCCGCGCACACTTCATTAAGCATATCT\n+TCGTATGTCATTATAAAACCTTTACACGTTGAACGATGGTTTGTTTAACGTCTTTGTATT\n+CTCCGTGCTCTTTAACGGTTGCTTTGAAAGTGATTTCATCACCTTCGTTTGCAATGTTAT\n+TACCGAAGTAAACAACAACATTACCATCAACATTAATTTTGGTCATGAATCTTTCTACAG\n+AAGTGTAGTAAGAAACTTGAGTATATCCCAGTGAAATCACTTTCTCAACGGTTCCGGTCA\n+TTTCCAGACGTTGTTTGATTTCACCGATGTGGTTAGCTTTAGAAATGCGTTCCTGGCGCT\n+CTTGTTCCCACTGTTCGCGGATTTCTTCGCGTTTGGCGATATAATCCTTTTCCAGTGCAA\n+CACCCATGCAGTAAGCGCACACAGCATCGAATACAGGGCTGTTTTTGTTGTCTTCTTTAG\n+ACTGGTCAGCCCACCAAAGAACAGTAAACATTGGCATTTCTGCAATTACTTCGCCTTTAC\n+GCTTGCCAATCGGCATGATCCCTTTTTCCAGCAGTTCCAGTTTTTCAGTATCGAACACTG\n+ACAGTTTACCGCGACGTTCGAACAGATCGAAATCTGCAAAGCCCTGGAATATCATTTTGA\n+AAGTATCAGTTTCAGTTAAACGGGCTGAAACACGGTCGAAATACTCACGCGCTTTCGCTT\n+CCGCTTTCTCCGGATCGGTAGATAAGTTGCAGATATAGTTATCAGAAGTATAACCGCCGC\n+CTCTACGCTCAACACGCAAGGTATACATTGCATTTTTACGACCAGAAGAAATGAAGTAAG\n+TGGTAGTAACTACGGTTGCGTTAGTCATGGTATTTCTCCTTAAAGGGTATCTCGTTTCGA\n+TATGGCTAATATAGCAAAAGCCCCTGACCGAAGTCAAGGGCTTTTTCATCATTCATTCGA\n+ATCTTTCATTGTTTTATGAAGATGAATATCAAAAATTTTCCAGTACGCCTTTCCGCGAGG\n+ATAAATTTTTGCTTTGTCAATATCGTTGTTGCTTCCCCATGTGTTGTTTGGGCCACGACA\n+TCGATTTTTTATATAATCTGTATGCCAGAATAAGCGCTGAACCGATGATTCCGTACCTAA\n+TGGATCTTCTTTACTGAACAGAATTTGTATACTCATAAGAAGAACCCAGTGCGAACAATC\n+AGATCGATTTTCTTTTCTGGTTCAAACGGTGATTTGCTATCGATGTTACACTGATAGAAC\n+ATACCAACATACTTTTCAGGAATGTTGGATTCACGCGCCCATTTCAGGTTATCATCGGTA\n+TTCGGCCCCAGCATGAGGTTAACAACATCAACAGCATAATCCTGTTCTTTGGTGTTGCCG\n+GAACCGTTTACATAATGCCCGTGGGCGGTTTTGAGGATCTCAATTACTTCGCTATCGTCA\n+GTTTCGACTTTGTAAAGCGTTGTATTTTCAGGAATTTCTTCAAGAATGATCAAAGCGGTT\n+TTCATCACACTTACCTTTGTGTTTCTGTTTACGTTTTGCTTCTTTAAATGCTCGCTTGCG\n+ATCGCGGTGAGTAGAAGCGCGGTTGAAATCATGTTTCGCTACCAAATTATTCATATAAGC\n+CCCTTAAAGAAAAATATTTAGGGGCTTTCGCCCCTGTATTAATCCAGCAATTTGCGGATC\n+TTGTCTGCGATACGTCCGGCGCGGGTTGCACTTGCAGTATGATCGCTTTCTTTTGAAGCC\n+AGTTCCGCCAGCTTACGCTGATGTTCTTCTTCTGCTGCTTGACGATCTGCTGCAACCTGT\n+GCAACCTGCTCATTATCGTGAGCAATACGCGCTTCCAGTTCAGACAGGGTTTTGTCGAAA\n+GTTGCTACGATTTCATCTACAGAACGAATTTTATTAAACAGTTTCATAATTTATCTCAAT\n+TGGTTAGTTTTAATCAGTATACATCAATATGGTTGAAATTCAAAATCATAAATGTCATTC\n+AGTGCGCGGTTCCACTCGGTGTAGTTTTCACCAGCACCATAACGCATTTGAATAGCACTT\n+TCGAACGTTGATCCGTTGAGGTTCGGGAAACCGAACAGGTTTTTGATTTTGTCATGTGCT\n+ACATAATACAGAGAAGCACTTTCCAGCATCGCAACCATCGCAGACGGTTCGTGTTCGCGG\n+CGCTTGATACGTAACAGAGTACGACTAGCACCAGTTTTACGGCGTTGATTTGGTGCTACG\n+TAGAAACGGAATACTACGCGCCCTGTTTTATCATCAACTACCAGGTAAAACCCGTTTTCT\n+TTCAGATCCACGCCTTCGAATTTCTTGAAGGTTCCGCGTTTCATGTCACCAATTTTAATT\n+GCATATTTGTGAATGTCAAGTCTTGTCAGAATTCTTTTCATATTTTTTAGATACCAGTTT\n+GCCTAATTTTGTAATTTCGCCTGTTTTTACGTTAACAAACAAGGCGATGCTCAGAAATGG\n+GATGCTAATCACTACGCTGATCAATGTAAACAGAAAACGTATCACAAAAAGAACAGCACG\n+TTCAAGATATCGTTGCATCCACGCGATTCCTAAACAACTATACCCTACTATAAAGGTGGT\n+TGCAACATAAAATGCACCAAATCCTTTACGAAATACGTAACCTTTCCCGGATTCTATCCG\n+GTCGTCGGCCCACATTTCACGGGCAGTTTTCAGAATAGATTCACCACTAGCGCGAGTTTC\n+GTTAGCCGAAGGCATGTTTTTAAATTTCATGATAGTCTCCTATGCGCCCAGAACTCTCCA\n+GGCGCGGTTGTTTAG\n' |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a test-data/ConvGlim_In.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ConvGlim_In.out Mon Jun 05 02:40:30 2023 +0000 |
| b |
| b'@@ -0,0 +1,259 @@\n+>Miro\n+orf00001 900 1 -1 9.03\n+orf00002 3161 900 -3 8.16\n+orf00003 3408 3172 -1 2.33\n+orf00004 4020 3412 -1 6.61\n+orf00005 5324 4038 -3 7.54\n+orf00007 7222 5324 -2 8.91\n+orf00009 7403 7290 -3 11.40\n+orf00010 7894 7454 -2 6.54\n+orf00011 8384 7917 -3 8.53\n+orf00012 8733 8488 -1 3.78\n+orf00013 9359 8763 -3 5.35\n+orf00015 9728 9399 -3 10.83\n+orf00016 10012 9788 -2 10.71\n+orf00017 10349 10086 -3 12.41\n+orf00018 10707 10438 -1 7.65\n+orf00020 10961 10737 -3 2.85\n+orf00021 11441 11178 -3 10.54\n+orf00022 11701 11456 -2 2.48\n+orf00023 12117 11728 -1 9.11\n+orf00025 12707 12399 -3 6.00\n+orf00026 14003 12732 -3 11.58\n+orf00027 14347 14057 -2 3.72\n+orf00028 15065 14529 -3 13.22\n+orf00029 16098 15073 -1 7.69\n+orf00030 16362 16102 -1 2.28\n+orf00031 16564 16418 -2 4.66\n+orf00032 17121 16633 -1 10.98\n+orf00033 17813 17127 -3 3.24\n+orf00034 18201 17839 -1 5.40\n+orf00035 18464 18228 -3 5.21\n+orf00037 18810 18556 -1 12.10\n+orf00039 19014 18889 -1 5.45\n+orf00040 20638 19202 -2 11.95\n+orf00042 20968 20648 -2 9.61\n+orf00044 22163 21006 -3 12.67\n+orf00045 24937 22238 -2 10.44\n+orf00046 25298 24984 -3 4.08\n+orf00047 25597 25310 -2 3.41\n+orf00048 26028 25666 -1 8.33\n+orf00049 26595 26032 -1 9.85\n+orf00050 27596 26598 -3 10.29\n+orf00051 28320 27655 -1 13.49\n+orf00052 28616 28347 -3 9.40\n+orf00053 29643 28672 -1 15.00\n+orf00055 30270 29659 -1 4.93\n+orf00056 30560 30315 -3 8.17\n+orf00057 30827 30564 -3 14.14\n+orf00058 31754 30837 -3 10.56\n+orf00059 32076 32603 +3 9.83\n+orf00060 32693 32815 +2 5.52\n+orf00061 32841 33134 +3 5.04\n+orf00062 33186 34217 +3 9.85\n+orf00063 34267 34491 +1 1.56\n+orf00064 34514 36172 +2 8.89\n+orf00065 36172 36363 +1 4.57\n+orf00066 36437 38146 +2 12.99\n+orf00067 38230 38496 +1 2.01\n+orf00068 38595 38723 +3 8.05\n+orf00069 38795 38977 +2 9.33\n+orf00070 38992 39552 +1 10.38\n+orf00071 39554 40429 +2 10.15\n+orf00072 40469 42721 +2 13.23\n+orf00073 42758 43933 +2 8.98\n+orf00075 44229 44594 +3 6.09\n+orf00076 44623 45732 +1 7.78\n+orf00077 45939 46265 +3 3.96\n+orf00078 46357 46569 +1 7.30\n+orf00079 46662 46883 +3 1.89\n+orf00080 46919 47035 +2 4.09\n+orf00081 47044 47916 +1 7.65\n+orf00082 47969 48256 +2 6.67\n+orf00083 48280 48504 +1 12.14\n+orf00086 48720 49277 +3 6.24\n+orf00087 49281 49634 +3 13.23\n+orf00088 49645 49896 +1 8.41\n+orf00089 50212 50493 +1 5.34\n+orf00090 50503 50922 +1 8.63\n+orf00092 50958 51530 +3 7.72\n+orf00093 51541 51903 +1 10.81\n+orf00094 51903 52172 +3 6.98\n+orf00095 52298 52591 +2 10.52\n+orf00096 52615 52833 +1 2.29\n+orf00098 52985 53137 +2 9.37\n+orf00100 53221 53661 +1 6.06\n+orf00101 53685 53921 +3 6.18\n+orf00102 53923 54144 +1 3.66\n+orf00103 54225 54755 +3 10.26\n+orf00104 54826 56265 +1 11.52\n+orf00105 56342 56911 +2 12.15\n+orf00107 57009 57203 +3 7.65\n+orf00108 57206 57382 +2 7.01\n+orf00110 57624 57914 +3 9.59\n+orf00111 57925 58236 +1 5.34\n+orf00113 59706 58597 -1 7.23\n+orf00114 59749 60351 +1 9.61\n+orf00115 60354 62126 +3 12.46\n+orf00116 62137 63210 +1 10.'..b' 96877 -1 4.63\n+orf00193 97727 97404 -3 6.99\n+orf00194 98013 97756 -1 4.97\n+orf00195 98398 98015 -2 9.84\n+orf00196 98816 98409 -3 7.35\n+orf00197 98987 98817 -3 12.25\n+orf00198 99292 99059 -2 8.24\n+orf00199 99572 99303 -3 7.18\n+orf00200 99928 99593 -2 11.12\n+orf00201 100067 99939 -3 1.66\n+orf00202 100309 100169 -2 1.85\n+orf00204 100896 100375 -1 3.55\n+orf00205 101545 100922 -2 8.90\n+orf00206 101869 101597 -2 10.05\n+orf00207 102567 101872 -1 8.24\n+orf00208 103097 102567 -3 7.10\n+orf00210 103446 104255 +3 11.77\n+orf00211 104304 104819 +3 2.67\n+orf00212 105693 104839 -1 8.49\n+orf00213 106176 105709 -1 6.32\n+orf00214 106227 106781 +3 8.96\n+orf00215 106820 108547 +2 12.05\n+orf00216 108552 110618 +3 9.07\n+orf00217 110650 112575 +1 10.62\n+orf00218 112656 115742 +3 9.94\n+orf00219 115743 116735 +3 6.50\n+orf00220 116745 117608 +3 10.54\n+orf00221 117710 119422 +2 13.92\n+orf00222 119422 120090 +1 11.52\n+orf00223 120100 121485 +1 10.64\n+orf00224 121496 123247 +2 13.64\n+orf00225 123286 124212 +1 11.65\n+orf00226 124222 124968 +1 11.32\n+orf00228 125117 125872 +2 8.26\n+orf00229 125872 126369 +1 12.43\n+orf00230 126381 128186 +3 4.39\n+orf00231 128206 130197 +1 10.39\n+orf00232 130246 130731 +1 11.81\n+orf00233 130787 132361 +2 11.27\n+orf00234 132361 132603 +1 14.40\n+orf00235 132612 133016 +3 8.20\n+orf00237 133019 133666 +2 10.48\n+orf00238 133699 134487 +1 14.45\n+orf00239 134507 136075 +2 16.79\n+orf00241 136168 136806 +1 2.92\n+orf00242 136839 138128 +3 11.97\n+orf00243 138433 138852 +1 11.57\n+orf00244 138852 139028 +3 7.61\n+orf00245 139536 139303 -1 7.73\n+orf00246 141044 139545 -3 5.03\n+orf00247 141115 141738 +1 12.04\n+orf00248 141831 142142 +3 8.21\n+orf00249 142182 142751 +3 5.11\n+orf00250 142780 143313 +1 13.11\n+orf00251 143324 143599 +2 8.94\n+orf00252 143613 144131 +3 5.20\n+orf00253 144627 144163 -1 10.43\n+orf00254 145516 144677 -2 9.89\n+orf00255 145631 146506 +2 10.48\n+orf00256 146539 146856 +1 3.43\n+orf00257 146910 147029 +3 4.35\n+orf00258 147041 147352 +2 5.34\n+orf00259 147354 147710 +3 12.94\n+orf00260 147710 148234 +2 11.54\n+orf00261 148238 149257 +2 13.08\n+orf00262 149352 149828 +3 6.02\n+orf00263 149897 150346 +2 9.80\n+orf00264 150424 150684 +1 11.24\n+orf00266 150694 151143 +1 3.86\n+orf00267 151171 152604 +1 9.12\n+orf00268 152630 152893 +2 3.24\n+orf00269 152905 153741 +1 9.17\n+orf00270 153750 154019 +3 4.63\n+orf00271 154052 154534 +2 7.42\n+orf00273 154854 156977 +3 8.76\n+orf00274 157045 157287 +1 7.59\n+orf00275 157287 157781 +3 9.71\n+orf00276 157781 157987 +2 4.81\n+orf00277 158008 158259 +1 5.46\n+orf00278 158320 158511 +1 7.99\n+orf00279 158652 159179 +3 3.87\n+orf00280 159200 159667 +2 8.79\n+orf00281 159737 160702 +2 9.94\n+orf00282 160745 161413 +2 8.59\n+orf00284 161651 161950 +2 10.21\n+orf00285 162030 165803 +3 8.87\n+orf00286 165815 166927 +2 6.42\n+orf00287 166977 167645 +3 7.19\n+orf00288 167654 171466 +2 9.03\n+orf00289 171503 172030 +2 3.11\n+orf00290 172147 172794 +1 2.92\n+orf00291 172953 172795 -1 3.49\n+orf00292 173351 173061 -3 1.18\n+orf00293 174148 173351 -2 13.25\n+orf00295 174872 174453 -3 12.21\n+orf00298 175187 174939 -3 13.40\n+orf00299 175604 175224 -3 13.18\n+orf00300 176010 175636 -1 6.19\n' |
| b |
| diff -r 3aac15f277c5 -r 843ea2c82e9a test-data/ConvGlim_Out.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ConvGlim_Out.gff3 Mon Jun 05 02:40:30 2023 +0000 |
| b |
| b'@@ -0,0 +1,517 @@\n+##gff-version 3\n+Miro\tGlimmer3\tgene\t1\t900\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00001;\n+Miro\tGlimmer3\tCDS\t1\t900\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00001;Parent=Miro.orf00001;\n+Miro\tGlimmer3\tgene\t900\t3161\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00002;\n+Miro\tGlimmer3\tCDS\t900\t3161\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00002;Parent=Miro.orf00002;\n+Miro\tGlimmer3\tgene\t3172\t3408\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00003;\n+Miro\tGlimmer3\tCDS\t3172\t3408\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00003;Parent=Miro.orf00003;\n+Miro\tGlimmer3\tgene\t3412\t4020\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00004;\n+Miro\tGlimmer3\tCDS\t3412\t4020\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00004;Parent=Miro.orf00004;\n+Miro\tGlimmer3\tgene\t4038\t5324\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00005;\n+Miro\tGlimmer3\tCDS\t4038\t5324\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00005;Parent=Miro.orf00005;\n+Miro\tGlimmer3\tgene\t5324\t7222\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00007;\n+Miro\tGlimmer3\tCDS\t5324\t7222\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00007;Parent=Miro.orf00007;\n+Miro\tGlimmer3\tgene\t7290\t7403\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00009;\n+Miro\tGlimmer3\tCDS\t7290\t7403\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00009;Parent=Miro.orf00009;\n+Miro\tGlimmer3\tgene\t7454\t7894\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00010;\n+Miro\tGlimmer3\tCDS\t7454\t7894\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00010;Parent=Miro.orf00010;\n+Miro\tGlimmer3\tgene\t7917\t8384\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00011;\n+Miro\tGlimmer3\tCDS\t7917\t8384\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00011;Parent=Miro.orf00011;\n+Miro\tGlimmer3\tgene\t8488\t8733\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00012;\n+Miro\tGlimmer3\tCDS\t8488\t8733\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00012;Parent=Miro.orf00012;\n+Miro\tGlimmer3\tgene\t8763\t9359\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00013;\n+Miro\tGlimmer3\tCDS\t8763\t9359\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00013;Parent=Miro.orf00013;\n+Miro\tGlimmer3\tgene\t9399\t9728\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00015;\n+Miro\tGlimmer3\tCDS\t9399\t9728\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00015;Parent=Miro.orf00015;\n+Miro\tGlimmer3\tgene\t9788\t10012\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00016;\n+Miro\tGlimmer3\tCDS\t9788\t10012\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00016;Parent=Miro.orf00016;\n+Miro\tGlimmer3\tgene\t10086\t10349\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00017;\n+Miro\tGlimmer3\tCDS\t10086\t10349\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00017;Parent=Miro.orf00017;\n+Miro\tGlimmer3\tgene\t10438\t10707\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00018;\n+Miro\tGlimmer3\tCDS\t10438\t10707\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00018;Parent=Miro.orf00018;\n+Miro\tGlimmer3\tgene\t10737\t10961\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00020;\n+Miro\tGlimmer3\tCDS\t10737\t10961\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00020;Parent=Miro.orf00020;\n+Miro\tGlimmer3\tgene\t11178\t11441\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00021;\n+Miro\tGlimmer3\tCDS\t11178\t11441\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00021;Parent=Miro.orf00021;\n+Miro\tGlimmer3\tgene\t11456\t11701\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00022;\n+Miro\tGlimmer3\tCDS\t11456\t11701\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00022;Parent=Miro.orf00022;\n+Miro\tGlimmer3\tgene\t11728\t12117\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00023;\n+Miro\tGlimmer3\tCDS\t11728\t12117\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00023;Parent=Miro.orf00023;\n+Miro\tGlimmer3\tgene\t12399\t12707\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00025;\n+Miro\tGlimmer3\tCDS\t12399\t12707\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00025;Parent=Miro.orf00025;\n+Miro\tGlimmer3\tgene\t12732\t14003\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00026;\n+Miro\tGlimmer3\tCDS\t12732\t14003\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00026;Parent=Miro.orf00026;\n+Miro\tGlimmer3\tgene\t14057\t14347\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00027;\n+Miro\tGlimmer3\tCDS\t14057\t14347\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00027;Parent=Miro.orf00027;\n+Miro\tGlimmer3\tgene\t14529\t15065\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00028;\n+Miro\tGlimmer3\tCDS\t14529\t15065\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00028;Parent=Miro.orf00028;\n+Miro\tGlimmer3\tgene\t15073\t16098\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00029;\n+Miro\tGlimmer3\tCDS\t15073\t16098\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00029;Parent=Miro.or'..b'ID=Miro.cds_orf00273;Parent=Miro.orf00273;\n+Miro\tGlimmer3\tgene\t157045\t157287\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00274;\n+Miro\tGlimmer3\tCDS\t157045\t157287\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00274;Parent=Miro.orf00274;\n+Miro\tGlimmer3\tgene\t157287\t157781\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00275;\n+Miro\tGlimmer3\tCDS\t157287\t157781\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00275;Parent=Miro.orf00275;\n+Miro\tGlimmer3\tgene\t157781\t157987\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00276;\n+Miro\tGlimmer3\tCDS\t157781\t157987\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00276;Parent=Miro.orf00276;\n+Miro\tGlimmer3\tgene\t158008\t158259\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00277;\n+Miro\tGlimmer3\tCDS\t158008\t158259\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00277;Parent=Miro.orf00277;\n+Miro\tGlimmer3\tgene\t158320\t158511\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00278;\n+Miro\tGlimmer3\tCDS\t158320\t158511\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00278;Parent=Miro.orf00278;\n+Miro\tGlimmer3\tgene\t158652\t159179\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00279;\n+Miro\tGlimmer3\tCDS\t158652\t159179\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00279;Parent=Miro.orf00279;\n+Miro\tGlimmer3\tgene\t159200\t159667\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00280;\n+Miro\tGlimmer3\tCDS\t159200\t159667\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00280;Parent=Miro.orf00280;\n+Miro\tGlimmer3\tgene\t159737\t160702\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00281;\n+Miro\tGlimmer3\tCDS\t159737\t160702\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00281;Parent=Miro.orf00281;\n+Miro\tGlimmer3\tgene\t160745\t161413\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00282;\n+Miro\tGlimmer3\tCDS\t160745\t161413\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00282;Parent=Miro.orf00282;\n+Miro\tGlimmer3\tgene\t161651\t161950\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00284;\n+Miro\tGlimmer3\tCDS\t161651\t161950\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00284;Parent=Miro.orf00284;\n+Miro\tGlimmer3\tgene\t162030\t165803\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00285;\n+Miro\tGlimmer3\tCDS\t162030\t165803\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00285;Parent=Miro.orf00285;\n+Miro\tGlimmer3\tgene\t165815\t166927\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00286;\n+Miro\tGlimmer3\tCDS\t165815\t166927\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00286;Parent=Miro.orf00286;\n+Miro\tGlimmer3\tgene\t166977\t167645\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00287;\n+Miro\tGlimmer3\tCDS\t166977\t167645\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00287;Parent=Miro.orf00287;\n+Miro\tGlimmer3\tgene\t167654\t171466\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00288;\n+Miro\tGlimmer3\tCDS\t167654\t171466\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00288;Parent=Miro.orf00288;\n+Miro\tGlimmer3\tgene\t171503\t172030\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00289;\n+Miro\tGlimmer3\tCDS\t171503\t172030\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00289;Parent=Miro.orf00289;\n+Miro\tGlimmer3\tgene\t172147\t172794\t.\t+\t.\tsource=Glimmer3;ID=Miro.orf00290;\n+Miro\tGlimmer3\tCDS\t172147\t172794\t.\t+\t0\tsource=Glimmer3;ID=Miro.cds_orf00290;Parent=Miro.orf00290;\n+Miro\tGlimmer3\tgene\t172795\t172953\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00291;\n+Miro\tGlimmer3\tCDS\t172795\t172953\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00291;Parent=Miro.orf00291;\n+Miro\tGlimmer3\tgene\t173061\t173351\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00292;\n+Miro\tGlimmer3\tCDS\t173061\t173351\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00292;Parent=Miro.orf00292;\n+Miro\tGlimmer3\tgene\t173351\t174148\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00293;\n+Miro\tGlimmer3\tCDS\t173351\t174148\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00293;Parent=Miro.orf00293;\n+Miro\tGlimmer3\tgene\t174453\t174872\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00295;\n+Miro\tGlimmer3\tCDS\t174453\t174872\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00295;Parent=Miro.orf00295;\n+Miro\tGlimmer3\tgene\t174939\t175187\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00298;\n+Miro\tGlimmer3\tCDS\t174939\t175187\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00298;Parent=Miro.orf00298;\n+Miro\tGlimmer3\tgene\t175224\t175604\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00299;\n+Miro\tGlimmer3\tCDS\t175224\t175604\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00299;Parent=Miro.orf00299;\n+Miro\tGlimmer3\tgene\t175636\t176010\t.\t-\t.\tsource=Glimmer3;ID=Miro.orf00300;\n+Miro\tGlimmer3\tCDS\t175636\t176010\t.\t-\t0\tsource=Glimmer3;ID=Miro.cds_orf00300;Parent=Miro.orf00300;\n' |