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Commit message:
planemo upload commit edc74553919d09dcbe27fcadf144612c1ad3a2a2 |
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added:
cpt-macros.xml gff3_splitgff.py gff3_splitgff.xml macros.xml test-data/Miro_SplitIn.gff3 test-data/Miro_SplitOut.fa test-data/Miro_SplitOut.gff3 |
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removed:
cpt_gff_split/cpt-macros.xml cpt_gff_split/gff3_splitgff.py cpt_gff_split/gff3_splitgff.xml cpt_gff_split/macros.xml cpt_gff_split/test-data/Miro_SplitIn.gff3 cpt_gff_split/test-data/Miro_SplitOut.fa cpt_gff_split/test-data/Miro_SplitOut.gff3 |
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| diff -r e7762a585e3d -r 8bd03ba8510a cpt-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt-macros.xml Fri Apr 28 01:35:25 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@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + 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 e7762a585e3d -r 8bd03ba8510a cpt_gff_split/cpt-macros.xml --- a/cpt_gff_split/cpt-macros.xml Fri May 20 08:53:34 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 e7762a585e3d -r 8bd03ba8510a cpt_gff_split/gff3_splitgff.py --- a/cpt_gff_split/gff3_splitgff.py Fri May 20 08:53:34 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,35 +0,0 @@ -#!/usr/bin/env python -import sys -import argparse -from Bio import SeqIO -from Bio.Seq import Seq -from CPT_GFFParser import gffParse, gffWrite - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Sample script to add an attribute to a feature via web services" - ) - parser.add_argument("data", type=argparse.FileType("r"), help="GFF3 File") - parser.add_argument( - "--gff", - type=argparse.FileType("w"), - help="Output Annotations", - default="data.gff3", - ) - parser.add_argument( - "--fasta", - type=argparse.FileType("w"), - help="Output Sequence", - default="data.fa", - ) - args = parser.parse_args() - - for record in gffParse(args.data): - gffWrite([record], args.gff) - record.description = "" - - if isinstance(record.seq, str): - record.seq = Seq(record.seq) - - SeqIO.write([record], args.fasta, "fasta") - sys.exit() |
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| diff -r e7762a585e3d -r 8bd03ba8510a cpt_gff_split/gff3_splitgff.xml --- a/cpt_gff_split/gff3_splitgff.xml Fri May 20 08:53:34 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,36 +0,0 @@ -<?xml version="1.0"?> -<tool id="edu.tamu.cpt2.gff3.splitGff" name="Split GFF3+Fasta into separate parts" version="22.0.0"> - <description></description> - <macros> - <import>macros.xml</import> - <import>cpt-macros.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[ -python $__tool_directory__/gff3_splitgff.py -$input - ---gff $gff_out ---fasta $fasta_out -]]></command> - <inputs> - <param label="Combined GFF3/Fasta File" name="input" type="data" format="gff,gff3"/> - </inputs> - <outputs> - <data format="gff3" label="GFF Portion of ${input.name}" name="gff_out"/> - <data format="fasta" label="Fasta Portion of ${input.name}" name="fasta_out"/> - </outputs> - <tests> - <test> - <param name="input" value="Miro_SplitIn.gff3" /> - <output name="gff" file="Miro_SplitOut.gff3" /> - <output name="fasta" file="Miro_SplitOut.fa" /> - </test> - </tests> - <help><![CDATA[ -**What it does** - -Splits apart the GFF3/Fasta data in a combined file into separate fasta and gff3 files. - ]]></help> - <expand macro="citations" /> -</tool> |
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| diff -r e7762a585e3d -r 8bd03ba8510a cpt_gff_split/macros.xml --- a/cpt_gff_split/macros.xml Fri May 20 08:53:34 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,85 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="3.8.13">python</requirement> - <requirement type="package" version="1.79">biopython</requirement> - <requirement type="package" version="1.2.2">cpt_gffparser</requirement> - <yield/> - </requirements> - </xml> - <token name="@BLAST_TSV@"> - "$blast_tsv" - </token> - <xml name="blast_tsv"> - <param label="Blast Results" help="TSV/tabular (25 Column)" - name="blast_tsv" type="data" format="tabular" /> - </xml> - - <token name="@BLAST_XML@"> - "$blast_xml" - </token> - <xml name="blast_xml"> - <param label="Blast Results" help="XML format" - name="blast_xml" type="data" format="blastxml" /> - </xml> - <xml name="gff3_with_fasta"> - <param label="Genome Sequences" name="fasta" type="data" format="fasta" /> - <param label="Genome Annotations" name="gff3" type="data" format="gff3" /> - </xml> - <xml name="genome_selector"> - <conditional name="reference_genome"> - <param name="reference_genome_source" type="select" label="Reference Genome"> - <option value="history" selected="True">From History</option> - <option value="cached">Locally Cached</option> - </param> - <when value="cached"> - <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> - <options from_data_table="all_fasta"/> - </param> - </when> - <when value="history"> - <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> - </when> - </conditional> - </xml> - <xml name="gff3_input"> - <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> - </xml> - <xml name="input/gff3+fasta"> - <expand macro="gff3_input" /> - <expand macro="genome_selector" /> - </xml> - <token name="@INPUT_GFF@"> - "$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 e7762a585e3d -r 8bd03ba8510a cpt_gff_split/test-data/Miro_SplitIn.gff3 --- a/cpt_gff_split/test-data/Miro_SplitIn.gff3 Fri May 20 08:53:34 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,3763 +0,0 @@\n-##gff-version 3\n-Miro\tfeature\tgene\t7454\t7906\t.\t-\t.\tID=Miro_8\n-Miro\tGenBank\tCDS\t7454\t7894\t.\t-\t1\tID=Miro_8.CDS;Name=Miro_8;Parent=Miro_8;obsolete_name=Miro_156;product=hypothetical conserved\n-Miro\tGenBank\tShine_Dalgarno_sequence\t7903\t7906\t.\t-\t1\tAlias=Miro_8;ID=Miro_8.RBS;Name=Miro_8;Parent=Miro_8\n-Miro\tfeature\tgene\t7917\t8512\t.\t-\t.\tID=Miro_9\n-Miro\tGenBank\tCDS\t7917\t8501\t.\t-\t1\tID=Miro_9.CDS;Name=Miro_9;Parent=Miro_9;obsolete_name=Miro_155;product=hypothetical conserved\n-Miro\tGenBank\tShine_Dalgarno_sequence\t8509\t8512\t.\t-\t1\tAlias=Miro_9;ID=Miro_9.RBS;Name=Miro_9;Parent=Miro_9\n-Miro\tfeature\tgene\t123276\t124212\t.\t+\t.\tID=Miro_206\n-Miro\tGenBank\tCDS\t123286\t124212\t.\t+\t1\tAlias=Miro_206;ID=Miro_206.CDS;Name=Miro_206;Parent=Miro_206;obsolete_name=Miro_234;product=hypothetical conserved\n-Miro\tGenBank\tShine_Dalgarno_sequence\t123276\t123279\t.\t+\t1\tID=Miro_206.rbs;Name=Miro_206;Parent=Miro_206\n-Miro\tfeature\tgene\t68490\t70715\t.\t-\t.\tID=Miro_117\n-Miro\tGenBank\tCDS\t68490\t70706\t.\t-\t1\tID=Miro_117.CDS;Name=Miro_117;Note=contains von Willebrand factor%2C type A;Parent=Miro_117;obsolete_name=Miro_047;product=hypothetical conserved\n-Miro\tGenBank\tShine_Dalgarno_sequence\t70713\t70715\t.\t-\t1\tAlias=Miro_117;ID=Miro_117.RBS;Name=Miro_117;Parent=Miro_117\n-Miro\tfeature\tgene\t115729\t116735\t.\t+\t.\tID=Miro_200\n-Miro\tGenBank\tCDS\t115743\t116735\t.\t+\t1\tAlias=Miro_200;ID=Miro_200.CDS;Name=Miro_200;Note=T4 gp6-like;Parent=Miro_200;obsolete_name=Miro_240;product=baseplate structural protein\n-Miro\tGenBank\tShine_Dalgarno_sequence\t115729\t115732\t.\t+\t1\tID=Miro_200.RBS;Name=Miro_200;Parent=Miro_200\n-Miro\tfeature\tgene\t116735\t117608\t.\t+\t.\tID=Miro_201\n-Miro\tGenBank\tCDS\t116745\t117608\t.\t+\t1\tAlias=Miro_201;ID=Miro_201.CDS;Name=Miro_201;Note=T4 gp9/gp10-like;Parent=Miro_201;obsolete_name=Miro_239;product=baseplate structural protein\n-Miro\tGenBank\tShine_Dalgarno_sequence\t116735\t116738\t.\t+\t1\tID=Miro_201.RBS;Name=Miro_201;Parent=Miro_201\n-Miro\tfeature\tgene\t117595\t119422\t.\t+\t.\tID=Miro_202\n-Miro\tGenBank\tCDS\t117605\t119422\t.\t+\t1\tAlias=Miro_202;ID=Miro_202.CDS;Name=Miro_202;Note=T4 gp9/gp10-like;Parent=Miro_202;obsolete_name=Miro_238;product=baseplate structural protein\n-Miro\tGenBank\tShine_Dalgarno_sequence\t117595\t117597\t.\t+\t1\tID=Miro_202.RBS;Name=Miro_202;Parent=Miro_202\n-Miro\tfeature\tgene\t119412\t120090\t.\t+\t.\tID=Miro_203\n-Miro\tGenBank\tCDS\t119422\t120090\t.\t+\t1\tAlias=Miro_203;ID=Miro_203.CDS;Name=Miro_203;Note=T4 gp11-like;Parent=Miro_203;obsolete_name=Miro_237;product=baseplate to short tail fiber connector protein\n-Miro\tGenBank\tShine_Dalgarno_sequence\t119412\t119415\t.\t+\t1\tID=Miro_203.RBS;Name=Miro_203;Parent=Miro_203\n-Miro\tfeature\tgene\t81829\t81940\t.\t-\t.\tID=Miro_142\n-Miro\tGenBank\tCDS\t81829\t81927\t.\t-\t1\tID=Miro_142.CDS;Name=Miro_142;Parent=Miro_142;obsolete_name=Miro_022;product=hypothetical conserved;tmhelix=1 TMD %284-26%29 N out%2C C in\n-Miro\tGenBank\tShine_Dalgarno_sequence\t81938\t81940\t.\t-\t1\tAlias=Miro_142;ID=Miro_142.RBS;Name=Miro_142;Parent=Miro_142\n-Miro\tfeature\tgene\t1\t910\t.\t-\t.\tID=Miro_1\n-Miro\tGenBank\tCDS\t1\t900\t.\t-\t1\tID=Miro_1.CDS;Name=Miro_1;Parent=Miro_1;obsolete_name=Miro_163;product=rIIb\n-Miro\tGenBank\tShine_Dalgarno_sequence\t908\t910\t.\t-\t1\tAlias=Miro_1;ID=Miro_1.RBS;Name=Miro_1;Parent=Miro_1\n-Miro\tfeature\tgene\t900\t3173\t.\t-\t.\tID=Miro_2\n-Miro\tGenBank\tCDS\t900\t3161\t.\t-\t1\tID=Miro_2.CDS;Name=Miro_2;Parent=Miro_2;obsolete_name=Miro_162;product=rIIa\n-Miro\tGenBank\tShine_Dalgarno_sequence\t3171\t3173\t.\t-\t1\tAlias=Miro_2;ID=Miro_2.RBS;Name=Miro_2;Parent=Miro_2\n-Miro\tfeature\tgene\t3172\t3417\t.\t-\t.\tID=Miro_3\n-Miro\tGenBank\tCDS\t3172\t3408\t.\t-\t1\tID=Miro_3.CDS;Name=Miro_3;Parent=Miro_3;obsolete_name=Miro_161;product=hypothetical conserved;tmhelix=1 TMD %2812-34%29 N in%2C C out\n-Miro\tGenBank\tShine_Dalgarno_sequence\t3414\t3417\t.\t-\t1\tAlias=Miro_3;ID=Miro_3.RBS;Name=Miro_3;Parent=Miro_3\n-Miro\tfeature\tgene\t3412\t3979\t.\t-\t.\tID=Miro_4\n-Miro\tGenBank\tCDS\t3412\t3966\t.\t-\t1\tID=Miro_4.CDS;Name=Miro_4;Note=contains SprT domain;Parent=Miro_4;obsolete_name=Miro_160;product=hypothetical conserved\n-Miro\tGenBank\tShine_D'..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 e7762a585e3d -r 8bd03ba8510a cpt_gff_split/test-data/Miro_SplitOut.fa --- a/cpt_gff_split/test-data/Miro_SplitOut.fa Fri May 20 08:53:34 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| 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 e7762a585e3d -r 8bd03ba8510a cpt_gff_split/test-data/Miro_SplitOut.gff3 --- a/cpt_gff_split/test-data/Miro_SplitOut.gff3 Fri May 20 08:53:34 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,825 +0,0 @@\n-##gff-version 3\n-##sequence-region Miro 1 176055\n-Miro\tfeature\tgene\t7454\t7906\t.\t-\t.\tID=Miro_8;\n-Miro\tGenBank\tCDS\t7454\t7894\t.\t-\t1\tID=Miro_8.CDS;Name=Miro_8;Parent=Miro_8;obsolete_name=Miro_156;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t7903\t7906\t.\t-\t1\tAlias=Miro_8;ID=Miro_8.RBS;Name=Miro_8;Parent=Miro_8;\n-Miro\tfeature\tgene\t7917\t8512\t.\t-\t.\tID=Miro_9;\n-Miro\tGenBank\tCDS\t7917\t8501\t.\t-\t1\tID=Miro_9.CDS;Name=Miro_9;Parent=Miro_9;obsolete_name=Miro_155;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t8509\t8512\t.\t-\t1\tAlias=Miro_9;ID=Miro_9.RBS;Name=Miro_9;Parent=Miro_9;\n-Miro\tfeature\tgene\t123276\t124212\t.\t+\t.\tID=Miro_206;\n-Miro\tGenBank\tCDS\t123286\t124212\t.\t+\t1\tAlias=Miro_206;ID=Miro_206.CDS;Name=Miro_206;Parent=Miro_206;obsolete_name=Miro_234;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t123276\t123279\t.\t+\t1\tID=Miro_206.rbs;Name=Miro_206;Parent=Miro_206;\n-Miro\tfeature\tgene\t68490\t70715\t.\t-\t.\tID=Miro_117;\n-Miro\tGenBank\tCDS\t68490\t70706\t.\t-\t1\tID=Miro_117.CDS;Name=Miro_117;Note=contains von Willebrand factor%2C type A;Parent=Miro_117;obsolete_name=Miro_047;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t70713\t70715\t.\t-\t1\tAlias=Miro_117;ID=Miro_117.RBS;Name=Miro_117;Parent=Miro_117;\n-Miro\tfeature\tgene\t115729\t116735\t.\t+\t.\tID=Miro_200;\n-Miro\tGenBank\tCDS\t115743\t116735\t.\t+\t1\tAlias=Miro_200;ID=Miro_200.CDS;Name=Miro_200;Note=T4 gp6-like;Parent=Miro_200;obsolete_name=Miro_240;product=baseplate structural protein;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t115729\t115732\t.\t+\t1\tID=Miro_200.RBS;Name=Miro_200;Parent=Miro_200;\n-Miro\tfeature\tgene\t116735\t117608\t.\t+\t.\tID=Miro_201;\n-Miro\tGenBank\tCDS\t116745\t117608\t.\t+\t1\tAlias=Miro_201;ID=Miro_201.CDS;Name=Miro_201;Note=T4 gp9/gp10-like;Parent=Miro_201;obsolete_name=Miro_239;product=baseplate structural protein;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t116735\t116738\t.\t+\t1\tID=Miro_201.RBS;Name=Miro_201;Parent=Miro_201;\n-Miro\tfeature\tgene\t117595\t119422\t.\t+\t.\tID=Miro_202;\n-Miro\tGenBank\tCDS\t117605\t119422\t.\t+\t1\tAlias=Miro_202;ID=Miro_202.CDS;Name=Miro_202;Note=T4 gp9/gp10-like;Parent=Miro_202;obsolete_name=Miro_238;product=baseplate structural protein;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t117595\t117597\t.\t+\t1\tID=Miro_202.RBS;Name=Miro_202;Parent=Miro_202;\n-Miro\tfeature\tgene\t119412\t120090\t.\t+\t.\tID=Miro_203;\n-Miro\tGenBank\tCDS\t119422\t120090\t.\t+\t1\tAlias=Miro_203;ID=Miro_203.CDS;Name=Miro_203;Note=T4 gp11-like;Parent=Miro_203;obsolete_name=Miro_237;product=baseplate to short tail fiber connector protein;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t119412\t119415\t.\t+\t1\tID=Miro_203.RBS;Name=Miro_203;Parent=Miro_203;\n-Miro\tfeature\tgene\t81829\t81940\t.\t-\t.\tID=Miro_142;\n-Miro\tGenBank\tCDS\t81829\t81927\t.\t-\t1\tID=Miro_142.CDS;Name=Miro_142;Parent=Miro_142;obsolete_name=Miro_022;product=hypothetical conserved;tmhelix=1 TMD (4-26) N out%2C C in;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t81938\t81940\t.\t-\t1\tAlias=Miro_142;ID=Miro_142.RBS;Name=Miro_142;Parent=Miro_142;\n-Miro\tfeature\tgene\t1\t910\t.\t-\t.\tID=Miro_1;\n-Miro\tGenBank\tCDS\t1\t900\t.\t-\t1\tID=Miro_1.CDS;Name=Miro_1;Parent=Miro_1;obsolete_name=Miro_163;product=rIIb;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t908\t910\t.\t-\t1\tAlias=Miro_1;ID=Miro_1.RBS;Name=Miro_1;Parent=Miro_1;\n-Miro\tfeature\tgene\t900\t3173\t.\t-\t.\tID=Miro_2;\n-Miro\tGenBank\tCDS\t900\t3161\t.\t-\t1\tID=Miro_2.CDS;Name=Miro_2;Parent=Miro_2;obsolete_name=Miro_162;product=rIIa;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t3171\t3173\t.\t-\t1\tAlias=Miro_2;ID=Miro_2.RBS;Name=Miro_2;Parent=Miro_2;\n-Miro\tfeature\tgene\t3172\t3417\t.\t-\t.\tID=Miro_3;\n-Miro\tGenBank\tCDS\t3172\t3408\t.\t-\t1\tID=Miro_3.CDS;Name=Miro_3;Parent=Miro_3;obsolete_name=Miro_161;product=hypothetical conserved;tmhelix=1 TMD (12-34) N in%2C C out;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t3414\t3417\t.\t-\t1\tAlias=Miro_3;ID=Miro_3.RBS;Name=Miro_3;Parent=Miro_3;\n-Miro\tfeature\tgene\t3412\t3979\t.\t-\t.\tID=Miro_4;\n-Miro\tGenBank\tCDS\t3412\t3966\t.\t-\t1\tID=Miro_4.CDS;Name=Miro_4;Note=contains SprT domain;Parent=Miro_4;obsolete_name='..b'ro_066;product=hypothetical conserved;tmhelix=2TMDs (7-26%2C 31-53) N in%2C C in;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t57368\t57372\t.\t+\t1\tID=Miro_98.RBS;Name=Miro_98;Parent=Miro_98;\n-Miro\tfeature\tgene\t57613\t57914\t.\t+\t.\tID=Miro_99;\n-Miro\tGenBank\tCDS\t57624\t57914\t.\t+\t1\tAlias=Miro_99;ID=Miro_99.CDS;Name=Miro_99;Parent=Miro_99;obsolete_name=Miro_065;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t57613\t57616\t.\t+\t1\tID=Miro_99.RBS;Name=Miro_99;Parent=Miro_99;\n-Miro\tfeature\tgene\t81924\t82086\t.\t-\t.\tID=Miro_143;\n-Miro\tGenBank\tCDS\t81924\t82079\t.\t-\t1\tID=Miro_143.CDS;Name=Miro_143;Parent=Miro_143;obsolete_name=Miro_021;product=hypothetical conserved;tmhelix=1 TMD (15-37) N out%2C C in;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t82084\t82086\t.\t-\t1\tAlias=Miro_143;ID=Miro_143.RBS;Name=Miro_143;Parent=Miro_143;\n-Miro\tfeature\tgene\t67179\t67658\t.\t-\t.\tID=Miro_114;\n-Miro\tGenBank\tCDS\t67179\t67649\t.\t-\t1\tID=Miro_114.CDS;Name=Miro_114;Parent=Miro_114;obsolete_name=Miro_050;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t67656\t67658\t.\t-\t1\tAlias=Miro_114;ID=Miro_114.RBS;Name=Miro_114;Parent=Miro_114;\n-Miro\tfeature\tgene\t81366\t81851\t.\t-\t.\tID=Miro_141;\n-Miro\tGenBank\tCDS\t81366\t81839\t.\t-\t1\tID=Miro_141.CDS;Name=Miro_141;Note=contains macro domain;Parent=Miro_141;obsolete_name=Miro_023;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t81849\t81851\t.\t-\t1\tAlias=Miro_141;ID=Miro_141.RBS;Name=Miro_141;Parent=Miro_141;\n-Miro\tfeature\tgene\t81076\t81376\t.\t-\t.\tID=Miro_140;\n-Miro\tGenBank\tCDS\t81076\t81363\t.\t-\t1\tID=Miro_140.CDS;Name=Miro_140;Parent=Miro_140;obsolete_name=Miro_024;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t81374\t81376\t.\t-\t1\tAlias=Miro_140;ID=Miro_140.RBS;Name=Miro_140;Parent=Miro_140;\n-Miro\tfeature\tgene\t83223\t83630\t.\t-\t.\tID=Miro_147;\n-Miro\tGenBank\tCDS\t83223\t83618\t.\t-\t1\tID=Miro_147.CDS;Name=Miro_147;Parent=Miro_147;obsolete_name=Miro_017;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t83627\t83630\t.\t-\t1\tAlias=Miro_147;ID=Miro_147.RBS;Name=Miro_147;Parent=Miro_147;\n-Miro\tfeature\tgene\t83066\t83224\t.\t-\t.\tID=Miro_146;\n-Miro\tGenBank\tCDS\t83066\t83212\t.\t-\t1\tID=Miro_146.CDS;Name=Miro_146;Parent=Miro_146;obsolete_name=Miro_018;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t83221\t83224\t.\t-\t1\tAlias=Miro_146;ID=Miro_146.RBS;Name=Miro_146;Parent=Miro_146;\n-Miro\tfeature\tgene\t82479\t83083\t.\t-\t.\tID=Miro_145;\n-Miro\tGenBank\tCDS\t82479\t83069\t.\t-\t1\tID=Miro_145.CDS;Name=Miro_145;Parent=Miro_145;obsolete_name=Miro_019;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t83080\t83083\t.\t-\t1\tAlias=Miro_145;ID=Miro_145.RBS;Name=Miro_145;Parent=Miro_145;\n-Miro\tfeature\tgene\t67646\t67816\t.\t-\t.\tID=Miro_115;\n-Miro\tGenBank\tCDS\t67646\t67804\t.\t-\t1\tID=Miro_115.CDS;Name=Miro_115;Parent=Miro_115;obsolete_name=Miro_049;product=hypothetical conserved;tmhelix=2TMDs (2-21%2C 31-50) N in%2C C in;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t67814\t67816\t.\t-\t1\tAlias=Miro_115;ID=Miro_115.RBS;Name=Miro_115;Parent=Miro_115;\n-Miro\tfeature\tgene\t84392\t84959\t.\t-\t.\tID=Miro_149;\n-Miro\tGenBank\tCDS\t84392\t84946\t.\t-\t1\tID=Miro_149.CDS;Name=Miro_149;Parent=Miro_149;obsolete_name=Miro_015;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t84955\t84959\t.\t-\t1\tAlias=Miro_149;ID=Miro_149.RBS;Name=Miro_149;Parent=Miro_149;\n-Miro\tfeature\tgene\t83686\t84337\t.\t-\t.\tID=Miro_148;\n-Miro\tGenBank\tCDS\t83686\t84327\t.\t-\t1\tID=Miro_148.CDS;Name=Miro_148;Note=T4 RegB-like;Parent=Miro_148;obsolete_name=Miro_016;product=endoribonuclease;signal=signal peptidase II cleavage site 12-13;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t84334\t84337\t.\t-\t1\tAlias=Miro_148;ID=Miro_148.RBS;Name=Miro_148;Parent=Miro_148;\n-Miro\tfeature\tgene\t67801\t68461\t.\t-\t.\tID=Miro_116;\n-Miro\tGenBank\tCDS\t67801\t68451\t.\t-\t1\tID=Miro_116.CDS;Name=Miro_116;Parent=Miro_116;obsolete_name=Miro_048;product=hypothetical conserved;\n-Miro\tGenBank\tShine_Dalgarno_sequence\t68457\t68461\t.\t-\t1\tAlias=Miro_116;ID=Miro_116.RBS;Name=Miro_116;Parent=Miro_116;\n' |
| b |
| diff -r e7762a585e3d -r 8bd03ba8510a gff3_splitgff.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_splitgff.py Fri Apr 28 01:35:25 2023 +0000 |
| [ |
| @@ -0,0 +1,35 @@ +#!/usr/bin/env python +import sys +import argparse +from Bio import SeqIO +from Bio.Seq import Seq +from CPT_GFFParser import gffParse, gffWrite + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Sample script to add an attribute to a feature via web services" + ) + parser.add_argument("data", type=argparse.FileType("r"), help="GFF3 File") + parser.add_argument( + "--gff", + type=argparse.FileType("w"), + help="Output Annotations", + default="data.gff3", + ) + parser.add_argument( + "--fasta", + type=argparse.FileType("w"), + help="Output Sequence", + default="data.fa", + ) + args = parser.parse_args() + + for record in gffParse(args.data): + gffWrite([record], args.gff) + record.description = "" + + if isinstance(record.seq, str): + record.seq = Seq(record.seq) + + SeqIO.write([record], args.fasta, "fasta") + sys.exit() |
| b |
| diff -r e7762a585e3d -r 8bd03ba8510a gff3_splitgff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_splitgff.xml Fri Apr 28 01:35:25 2023 +0000 |
| [ |
| @@ -0,0 +1,35 @@ +<tool id="edu.tamu.cpt2.gff3.splitGff" name="Split GFF3+Fasta into separate parts" version="22.0.0"> + <description/> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +'python $__tool_directory__/gff3_splitgff.py' +'$input' + +--gff '$gff_out' +--fasta '$fasta_out' +]]></command> + <inputs> + <param label="Combined GFF3/Fasta File" name="input" type="data" format="gff,gff3"/> + </inputs> + <outputs> + <data format="gff3" label="GFF Portion of ${input.name}" name="gff_out"/> + <data format="fasta" label="Fasta Portion of ${input.name}" name="fasta_out"/> + </outputs> + <tests> + <test> + <param name="input" value="Miro_SplitIn.gff3"/> + <output name="gff" file="Miro_SplitOut.gff3"/> + <output name="fasta" file="Miro_SplitOut.fa"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Splits apart the GFF3/Fasta data in a combined file into separate fasta and gff3 files. + ]]></help> + <expand macro="citations"/> +</tool> |
| b |
| diff -r e7762a585e3d -r 8bd03ba8510a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Apr 28 01:35:25 2023 +0000 |
| b |
| @@ -0,0 +1,74 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package">progressivemauve</requirement> + <!--<requirement type="package" version="2.7">python</requirement>--> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> + <xml name="citation/progressive_mauve"> + <citation type="doi">10.1371/journal.pone.0011147</citation> + </xml> + <xml name="citation/gepard"> + <citation type="doi">10.1093/bioinformatics/btm039</citation> + </xml> + <token name="@XMFA_INPUT@"> + '$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 e7762a585e3d -r 8bd03ba8510a test-data/Miro_SplitIn.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Miro_SplitIn.gff3 Fri Apr 28 01:35:25 2023 +0000 |
| b |
| b'@@ -0,0 +1,3763 @@\n+##gff-version 3\n+Miro\tfeature\tgene\t7454\t7906\t.\t-\t.\tID=Miro_8\n+Miro\tGenBank\tCDS\t7454\t7894\t.\t-\t1\tID=Miro_8.CDS;Name=Miro_8;Parent=Miro_8;obsolete_name=Miro_156;product=hypothetical conserved\n+Miro\tGenBank\tShine_Dalgarno_sequence\t7903\t7906\t.\t-\t1\tAlias=Miro_8;ID=Miro_8.RBS;Name=Miro_8;Parent=Miro_8\n+Miro\tfeature\tgene\t7917\t8512\t.\t-\t.\tID=Miro_9\n+Miro\tGenBank\tCDS\t7917\t8501\t.\t-\t1\tID=Miro_9.CDS;Name=Miro_9;Parent=Miro_9;obsolete_name=Miro_155;product=hypothetical conserved\n+Miro\tGenBank\tShine_Dalgarno_sequence\t8509\t8512\t.\t-\t1\tAlias=Miro_9;ID=Miro_9.RBS;Name=Miro_9;Parent=Miro_9\n+Miro\tfeature\tgene\t123276\t124212\t.\t+\t.\tID=Miro_206\n+Miro\tGenBank\tCDS\t123286\t124212\t.\t+\t1\tAlias=Miro_206;ID=Miro_206.CDS;Name=Miro_206;Parent=Miro_206;obsolete_name=Miro_234;product=hypothetical conserved\n+Miro\tGenBank\tShine_Dalgarno_sequence\t123276\t123279\t.\t+\t1\tID=Miro_206.rbs;Name=Miro_206;Parent=Miro_206\n+Miro\tfeature\tgene\t68490\t70715\t.\t-\t.\tID=Miro_117\n+Miro\tGenBank\tCDS\t68490\t70706\t.\t-\t1\tID=Miro_117.CDS;Name=Miro_117;Note=contains von Willebrand factor%2C type A;Parent=Miro_117;obsolete_name=Miro_047;product=hypothetical conserved\n+Miro\tGenBank\tShine_Dalgarno_sequence\t70713\t70715\t.\t-\t1\tAlias=Miro_117;ID=Miro_117.RBS;Name=Miro_117;Parent=Miro_117\n+Miro\tfeature\tgene\t115729\t116735\t.\t+\t.\tID=Miro_200\n+Miro\tGenBank\tCDS\t115743\t116735\t.\t+\t1\tAlias=Miro_200;ID=Miro_200.CDS;Name=Miro_200;Note=T4 gp6-like;Parent=Miro_200;obsolete_name=Miro_240;product=baseplate structural protein\n+Miro\tGenBank\tShine_Dalgarno_sequence\t115729\t115732\t.\t+\t1\tID=Miro_200.RBS;Name=Miro_200;Parent=Miro_200\n+Miro\tfeature\tgene\t116735\t117608\t.\t+\t.\tID=Miro_201\n+Miro\tGenBank\tCDS\t116745\t117608\t.\t+\t1\tAlias=Miro_201;ID=Miro_201.CDS;Name=Miro_201;Note=T4 gp9/gp10-like;Parent=Miro_201;obsolete_name=Miro_239;product=baseplate structural protein\n+Miro\tGenBank\tShine_Dalgarno_sequence\t116735\t116738\t.\t+\t1\tID=Miro_201.RBS;Name=Miro_201;Parent=Miro_201\n+Miro\tfeature\tgene\t117595\t119422\t.\t+\t.\tID=Miro_202\n+Miro\tGenBank\tCDS\t117605\t119422\t.\t+\t1\tAlias=Miro_202;ID=Miro_202.CDS;Name=Miro_202;Note=T4 gp9/gp10-like;Parent=Miro_202;obsolete_name=Miro_238;product=baseplate structural protein\n+Miro\tGenBank\tShine_Dalgarno_sequence\t117595\t117597\t.\t+\t1\tID=Miro_202.RBS;Name=Miro_202;Parent=Miro_202\n+Miro\tfeature\tgene\t119412\t120090\t.\t+\t.\tID=Miro_203\n+Miro\tGenBank\tCDS\t119422\t120090\t.\t+\t1\tAlias=Miro_203;ID=Miro_203.CDS;Name=Miro_203;Note=T4 gp11-like;Parent=Miro_203;obsolete_name=Miro_237;product=baseplate to short tail fiber connector protein\n+Miro\tGenBank\tShine_Dalgarno_sequence\t119412\t119415\t.\t+\t1\tID=Miro_203.RBS;Name=Miro_203;Parent=Miro_203\n+Miro\tfeature\tgene\t81829\t81940\t.\t-\t.\tID=Miro_142\n+Miro\tGenBank\tCDS\t81829\t81927\t.\t-\t1\tID=Miro_142.CDS;Name=Miro_142;Parent=Miro_142;obsolete_name=Miro_022;product=hypothetical conserved;tmhelix=1 TMD %284-26%29 N out%2C C in\n+Miro\tGenBank\tShine_Dalgarno_sequence\t81938\t81940\t.\t-\t1\tAlias=Miro_142;ID=Miro_142.RBS;Name=Miro_142;Parent=Miro_142\n+Miro\tfeature\tgene\t1\t910\t.\t-\t.\tID=Miro_1\n+Miro\tGenBank\tCDS\t1\t900\t.\t-\t1\tID=Miro_1.CDS;Name=Miro_1;Parent=Miro_1;obsolete_name=Miro_163;product=rIIb\n+Miro\tGenBank\tShine_Dalgarno_sequence\t908\t910\t.\t-\t1\tAlias=Miro_1;ID=Miro_1.RBS;Name=Miro_1;Parent=Miro_1\n+Miro\tfeature\tgene\t900\t3173\t.\t-\t.\tID=Miro_2\n+Miro\tGenBank\tCDS\t900\t3161\t.\t-\t1\tID=Miro_2.CDS;Name=Miro_2;Parent=Miro_2;obsolete_name=Miro_162;product=rIIa\n+Miro\tGenBank\tShine_Dalgarno_sequence\t3171\t3173\t.\t-\t1\tAlias=Miro_2;ID=Miro_2.RBS;Name=Miro_2;Parent=Miro_2\n+Miro\tfeature\tgene\t3172\t3417\t.\t-\t.\tID=Miro_3\n+Miro\tGenBank\tCDS\t3172\t3408\t.\t-\t1\tID=Miro_3.CDS;Name=Miro_3;Parent=Miro_3;obsolete_name=Miro_161;product=hypothetical conserved;tmhelix=1 TMD %2812-34%29 N in%2C C out\n+Miro\tGenBank\tShine_Dalgarno_sequence\t3414\t3417\t.\t-\t1\tAlias=Miro_3;ID=Miro_3.RBS;Name=Miro_3;Parent=Miro_3\n+Miro\tfeature\tgene\t3412\t3979\t.\t-\t.\tID=Miro_4\n+Miro\tGenBank\tCDS\t3412\t3966\t.\t-\t1\tID=Miro_4.CDS;Name=Miro_4;Note=contains SprT domain;Parent=Miro_4;obsolete_name=Miro_160;product=hypothetical conserved\n+Miro\tGenBank\tShine_D'..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 e7762a585e3d -r 8bd03ba8510a test-data/Miro_SplitOut.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Miro_SplitOut.fa Fri Apr 28 01:35:25 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 e7762a585e3d -r 8bd03ba8510a test-data/Miro_SplitOut.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Miro_SplitOut.gff3 Fri Apr 28 01:35:25 2023 +0000 |
| b |
| b'@@ -0,0 +1,825 @@\n+##gff-version 3\n+##sequence-region Miro 1 176055\n+Miro\tfeature\tgene\t7454\t7906\t.\t-\t.\tID=Miro_8;\n+Miro\tGenBank\tCDS\t7454\t7894\t.\t-\t1\tID=Miro_8.CDS;Name=Miro_8;Parent=Miro_8;obsolete_name=Miro_156;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t7903\t7906\t.\t-\t1\tAlias=Miro_8;ID=Miro_8.RBS;Name=Miro_8;Parent=Miro_8;\n+Miro\tfeature\tgene\t7917\t8512\t.\t-\t.\tID=Miro_9;\n+Miro\tGenBank\tCDS\t7917\t8501\t.\t-\t1\tID=Miro_9.CDS;Name=Miro_9;Parent=Miro_9;obsolete_name=Miro_155;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t8509\t8512\t.\t-\t1\tAlias=Miro_9;ID=Miro_9.RBS;Name=Miro_9;Parent=Miro_9;\n+Miro\tfeature\tgene\t123276\t124212\t.\t+\t.\tID=Miro_206;\n+Miro\tGenBank\tCDS\t123286\t124212\t.\t+\t1\tAlias=Miro_206;ID=Miro_206.CDS;Name=Miro_206;Parent=Miro_206;obsolete_name=Miro_234;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t123276\t123279\t.\t+\t1\tID=Miro_206.rbs;Name=Miro_206;Parent=Miro_206;\n+Miro\tfeature\tgene\t68490\t70715\t.\t-\t.\tID=Miro_117;\n+Miro\tGenBank\tCDS\t68490\t70706\t.\t-\t1\tID=Miro_117.CDS;Name=Miro_117;Note=contains von Willebrand factor%2C type A;Parent=Miro_117;obsolete_name=Miro_047;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t70713\t70715\t.\t-\t1\tAlias=Miro_117;ID=Miro_117.RBS;Name=Miro_117;Parent=Miro_117;\n+Miro\tfeature\tgene\t115729\t116735\t.\t+\t.\tID=Miro_200;\n+Miro\tGenBank\tCDS\t115743\t116735\t.\t+\t1\tAlias=Miro_200;ID=Miro_200.CDS;Name=Miro_200;Note=T4 gp6-like;Parent=Miro_200;obsolete_name=Miro_240;product=baseplate structural protein;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t115729\t115732\t.\t+\t1\tID=Miro_200.RBS;Name=Miro_200;Parent=Miro_200;\n+Miro\tfeature\tgene\t116735\t117608\t.\t+\t.\tID=Miro_201;\n+Miro\tGenBank\tCDS\t116745\t117608\t.\t+\t1\tAlias=Miro_201;ID=Miro_201.CDS;Name=Miro_201;Note=T4 gp9/gp10-like;Parent=Miro_201;obsolete_name=Miro_239;product=baseplate structural protein;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t116735\t116738\t.\t+\t1\tID=Miro_201.RBS;Name=Miro_201;Parent=Miro_201;\n+Miro\tfeature\tgene\t117595\t119422\t.\t+\t.\tID=Miro_202;\n+Miro\tGenBank\tCDS\t117605\t119422\t.\t+\t1\tAlias=Miro_202;ID=Miro_202.CDS;Name=Miro_202;Note=T4 gp9/gp10-like;Parent=Miro_202;obsolete_name=Miro_238;product=baseplate structural protein;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t117595\t117597\t.\t+\t1\tID=Miro_202.RBS;Name=Miro_202;Parent=Miro_202;\n+Miro\tfeature\tgene\t119412\t120090\t.\t+\t.\tID=Miro_203;\n+Miro\tGenBank\tCDS\t119422\t120090\t.\t+\t1\tAlias=Miro_203;ID=Miro_203.CDS;Name=Miro_203;Note=T4 gp11-like;Parent=Miro_203;obsolete_name=Miro_237;product=baseplate to short tail fiber connector protein;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t119412\t119415\t.\t+\t1\tID=Miro_203.RBS;Name=Miro_203;Parent=Miro_203;\n+Miro\tfeature\tgene\t81829\t81940\t.\t-\t.\tID=Miro_142;\n+Miro\tGenBank\tCDS\t81829\t81927\t.\t-\t1\tID=Miro_142.CDS;Name=Miro_142;Parent=Miro_142;obsolete_name=Miro_022;product=hypothetical conserved;tmhelix=1 TMD (4-26) N out%2C C in;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t81938\t81940\t.\t-\t1\tAlias=Miro_142;ID=Miro_142.RBS;Name=Miro_142;Parent=Miro_142;\n+Miro\tfeature\tgene\t1\t910\t.\t-\t.\tID=Miro_1;\n+Miro\tGenBank\tCDS\t1\t900\t.\t-\t1\tID=Miro_1.CDS;Name=Miro_1;Parent=Miro_1;obsolete_name=Miro_163;product=rIIb;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t908\t910\t.\t-\t1\tAlias=Miro_1;ID=Miro_1.RBS;Name=Miro_1;Parent=Miro_1;\n+Miro\tfeature\tgene\t900\t3173\t.\t-\t.\tID=Miro_2;\n+Miro\tGenBank\tCDS\t900\t3161\t.\t-\t1\tID=Miro_2.CDS;Name=Miro_2;Parent=Miro_2;obsolete_name=Miro_162;product=rIIa;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t3171\t3173\t.\t-\t1\tAlias=Miro_2;ID=Miro_2.RBS;Name=Miro_2;Parent=Miro_2;\n+Miro\tfeature\tgene\t3172\t3417\t.\t-\t.\tID=Miro_3;\n+Miro\tGenBank\tCDS\t3172\t3408\t.\t-\t1\tID=Miro_3.CDS;Name=Miro_3;Parent=Miro_3;obsolete_name=Miro_161;product=hypothetical conserved;tmhelix=1 TMD (12-34) N in%2C C out;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t3414\t3417\t.\t-\t1\tAlias=Miro_3;ID=Miro_3.RBS;Name=Miro_3;Parent=Miro_3;\n+Miro\tfeature\tgene\t3412\t3979\t.\t-\t.\tID=Miro_4;\n+Miro\tGenBank\tCDS\t3412\t3966\t.\t-\t1\tID=Miro_4.CDS;Name=Miro_4;Note=contains SprT domain;Parent=Miro_4;obsolete_name='..b'ro_066;product=hypothetical conserved;tmhelix=2TMDs (7-26%2C 31-53) N in%2C C in;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t57368\t57372\t.\t+\t1\tID=Miro_98.RBS;Name=Miro_98;Parent=Miro_98;\n+Miro\tfeature\tgene\t57613\t57914\t.\t+\t.\tID=Miro_99;\n+Miro\tGenBank\tCDS\t57624\t57914\t.\t+\t1\tAlias=Miro_99;ID=Miro_99.CDS;Name=Miro_99;Parent=Miro_99;obsolete_name=Miro_065;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t57613\t57616\t.\t+\t1\tID=Miro_99.RBS;Name=Miro_99;Parent=Miro_99;\n+Miro\tfeature\tgene\t81924\t82086\t.\t-\t.\tID=Miro_143;\n+Miro\tGenBank\tCDS\t81924\t82079\t.\t-\t1\tID=Miro_143.CDS;Name=Miro_143;Parent=Miro_143;obsolete_name=Miro_021;product=hypothetical conserved;tmhelix=1 TMD (15-37) N out%2C C in;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t82084\t82086\t.\t-\t1\tAlias=Miro_143;ID=Miro_143.RBS;Name=Miro_143;Parent=Miro_143;\n+Miro\tfeature\tgene\t67179\t67658\t.\t-\t.\tID=Miro_114;\n+Miro\tGenBank\tCDS\t67179\t67649\t.\t-\t1\tID=Miro_114.CDS;Name=Miro_114;Parent=Miro_114;obsolete_name=Miro_050;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t67656\t67658\t.\t-\t1\tAlias=Miro_114;ID=Miro_114.RBS;Name=Miro_114;Parent=Miro_114;\n+Miro\tfeature\tgene\t81366\t81851\t.\t-\t.\tID=Miro_141;\n+Miro\tGenBank\tCDS\t81366\t81839\t.\t-\t1\tID=Miro_141.CDS;Name=Miro_141;Note=contains macro domain;Parent=Miro_141;obsolete_name=Miro_023;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t81849\t81851\t.\t-\t1\tAlias=Miro_141;ID=Miro_141.RBS;Name=Miro_141;Parent=Miro_141;\n+Miro\tfeature\tgene\t81076\t81376\t.\t-\t.\tID=Miro_140;\n+Miro\tGenBank\tCDS\t81076\t81363\t.\t-\t1\tID=Miro_140.CDS;Name=Miro_140;Parent=Miro_140;obsolete_name=Miro_024;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t81374\t81376\t.\t-\t1\tAlias=Miro_140;ID=Miro_140.RBS;Name=Miro_140;Parent=Miro_140;\n+Miro\tfeature\tgene\t83223\t83630\t.\t-\t.\tID=Miro_147;\n+Miro\tGenBank\tCDS\t83223\t83618\t.\t-\t1\tID=Miro_147.CDS;Name=Miro_147;Parent=Miro_147;obsolete_name=Miro_017;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t83627\t83630\t.\t-\t1\tAlias=Miro_147;ID=Miro_147.RBS;Name=Miro_147;Parent=Miro_147;\n+Miro\tfeature\tgene\t83066\t83224\t.\t-\t.\tID=Miro_146;\n+Miro\tGenBank\tCDS\t83066\t83212\t.\t-\t1\tID=Miro_146.CDS;Name=Miro_146;Parent=Miro_146;obsolete_name=Miro_018;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t83221\t83224\t.\t-\t1\tAlias=Miro_146;ID=Miro_146.RBS;Name=Miro_146;Parent=Miro_146;\n+Miro\tfeature\tgene\t82479\t83083\t.\t-\t.\tID=Miro_145;\n+Miro\tGenBank\tCDS\t82479\t83069\t.\t-\t1\tID=Miro_145.CDS;Name=Miro_145;Parent=Miro_145;obsolete_name=Miro_019;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t83080\t83083\t.\t-\t1\tAlias=Miro_145;ID=Miro_145.RBS;Name=Miro_145;Parent=Miro_145;\n+Miro\tfeature\tgene\t67646\t67816\t.\t-\t.\tID=Miro_115;\n+Miro\tGenBank\tCDS\t67646\t67804\t.\t-\t1\tID=Miro_115.CDS;Name=Miro_115;Parent=Miro_115;obsolete_name=Miro_049;product=hypothetical conserved;tmhelix=2TMDs (2-21%2C 31-50) N in%2C C in;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t67814\t67816\t.\t-\t1\tAlias=Miro_115;ID=Miro_115.RBS;Name=Miro_115;Parent=Miro_115;\n+Miro\tfeature\tgene\t84392\t84959\t.\t-\t.\tID=Miro_149;\n+Miro\tGenBank\tCDS\t84392\t84946\t.\t-\t1\tID=Miro_149.CDS;Name=Miro_149;Parent=Miro_149;obsolete_name=Miro_015;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t84955\t84959\t.\t-\t1\tAlias=Miro_149;ID=Miro_149.RBS;Name=Miro_149;Parent=Miro_149;\n+Miro\tfeature\tgene\t83686\t84337\t.\t-\t.\tID=Miro_148;\n+Miro\tGenBank\tCDS\t83686\t84327\t.\t-\t1\tID=Miro_148.CDS;Name=Miro_148;Note=T4 RegB-like;Parent=Miro_148;obsolete_name=Miro_016;product=endoribonuclease;signal=signal peptidase II cleavage site 12-13;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t84334\t84337\t.\t-\t1\tAlias=Miro_148;ID=Miro_148.RBS;Name=Miro_148;Parent=Miro_148;\n+Miro\tfeature\tgene\t67801\t68461\t.\t-\t.\tID=Miro_116;\n+Miro\tGenBank\tCDS\t67801\t68451\t.\t-\t1\tID=Miro_116.CDS;Name=Miro_116;Parent=Miro_116;obsolete_name=Miro_048;product=hypothetical conserved;\n+Miro\tGenBank\tShine_Dalgarno_sequence\t68457\t68461\t.\t-\t1\tAlias=Miro_116;ID=Miro_116.RBS;Name=Miro_116;Parent=Miro_116;\n' |