| Next changeset 1:aeef53d23c03 (2022-05-19) |
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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 000000000000 -r d09ed5271c24 cpt_convert_glimmer/cpt-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/cpt-macros.xml Fri May 13 17:56:15 2022 +0000 |
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| @@ -0,0 +1,115 @@ +<?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@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + 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 + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 000000000000 -r d09ed5271c24 cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.py Fri May 13 17:56:15 2022 +0000 |
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| @@ -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) |
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| diff -r 000000000000 -r d09ed5271c24 cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml Fri May 13 17:56:15 2022 +0000 |
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| @@ -0,0 +1,41 @@ +<?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 000000000000 -r d09ed5271c24 cpt_convert_glimmer/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/macros.xml Fri May 13 17:56:15 2022 +0000 |
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| @@ -0,0 +1,66 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.77">biopython</requirement> + <requirement type="package" version="1.1.3">cpt_gffparser</requirement> + <yield/> + </requirements> + </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> + <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 000000000000 -r d09ed5271c24 cpt_convert_glimmer/test-data/ConvGlim_In.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/test-data/ConvGlim_In.fasta Fri May 13 17:56:15 2022 +0000 |
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| 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' 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| diff -r 000000000000 -r d09ed5271c24 cpt_convert_glimmer/test-data/ConvGlim_In.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/test-data/ConvGlim_In.out Fri May 13 17:56:15 2022 +0000 |
| b |
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| b |
| diff -r 000000000000 -r d09ed5271c24 cpt_convert_glimmer/test-data/ConvGlim_Out.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_convert_glimmer/test-data/ConvGlim_Out.gff3 Fri May 13 17:56:15 2022 +0000 |
| b |
| b'@@ -0,0 +1,517 @@\n+##gff-version 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=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' |