| Next changeset 1:cba42189acbf (2022-05-20) |
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cpt_intersect_adj/cpt-macros.xml cpt_intersect_adj/intersect_and_adjacent.py cpt_intersect_adj/intersect_and_adjacent.xml cpt_intersect_adj/macros.xml cpt_intersect_adj/test-data/T7_IntersectAIn.gff3 cpt_intersect_adj/test-data/T7_IntersectAOut.gff3 cpt_intersect_adj/test-data/T7_IntersectBIn.gff3 cpt_intersect_adj/test-data/T7_IntersectBOut.gff3 |
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| diff -r 000000000000 -r 4c72b6accdee cpt_intersect_adj/cpt-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/cpt-macros.xml Fri May 13 05:05:59 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@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + 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 + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 4c72b6accdee cpt_intersect_adj/intersect_and_adjacent.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/intersect_and_adjacent.py Fri May 13 05:05:59 2022 +0000 |
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| b"@@ -0,0 +1,242 @@\n+#!/usr/bin/env python\n+import logging\n+import argparse\n+from intervaltree import IntervalTree, Interval\n+from CPT_GFFParser import gffParse, gffWrite\n+from Bio.SeqRecord import SeqRecord\n+from Bio.Seq import Seq\n+\n+logging.basicConfig(level=logging.INFO)\n+log = logging.getLogger(__name__)\n+\n+def validFeat(rec):\n+ for feat in rec.features:\n+ if feat.type != 'remark' and feat.type != 'annotation':\n+ return True\n+ return False\n+\n+def treeFeatures(features, window):\n+ for feat in features:\n+ # Interval(begin, end, data)\n+ yield Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end) + int(window),\n+ feat.id,\n+ )\n+def treeFeatures_noRem(features, window):\n+ for feat in features:\n+ if feat.type == 'remark' or feat.type == 'annotation':\n+ continue\n+ # Interval(begin, end, data)\n+ yield Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end) + int(window),\n+ feat.id,\n+ )\n+\n+\n+def intersect(a, b, window, stranding):\n+ rec_a = list(gffParse(a))\n+ rec_b = list(gffParse(b))\n+ rec_a_out = []\n+ rec_b_out = []\n+ maxLen = min(len(rec_a), len(rec_b))\n+ iterate = 0\n+ \n+\n+ if maxLen > 0:\n+ while iterate < maxLen:\n+ rec_a_i = rec_a[iterate]\n+ rec_b_i = rec_b[iterate]\n+\n+ if (not validFeat(rec_a_i)) or (not validFeat(rec_b_i)):\n+ rec_a_out.append(SeqRecord(rec_a[iterate].seq, rec_a[iterate].id, rec_a[iterate].name, rec_a[iterate].description, rec_a[iterate].dbxrefs, [], rec_a[iterate].annotations))\n+ rec_b_out.append(SeqRecord(rec_b[iterate].seq, rec_b[iterate].id, rec_b[iterate].name, rec_b[iterate].description, rec_b[iterate].dbxrefs, [], rec_b[iterate].annotations))\n+ iterate += 1\n+ continue\n+\n+ a_neg = []\n+ a_pos = []\n+ b_neg = []\n+ b_pos = []\n+ tree_a = []\n+ tree_b = []\n+ if stranding == True:\n+ for feat in rec_a_i.features:\n+ if feat.type == 'remark' or feat.type == 'annotation':\n+ continue\n+ if feat.strand > 0:\n+ a_pos.append(\n+ Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end) + int(window),\n+ feat.id,\n+ )\n+ )\n+ else:\n+ a_neg.append(\n+ Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end) + int(window),\n+ feat.id,\n+ )\n+ )\n+\n+ for feat in rec_b_i.features:\n+ if feat.type == 'remark' or feat.type == 'annotation':\n+ continue\n+ if feat.strand > 0:\n+ b_pos.append(\n+ Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end) + int(window),\n+ feat.id,\n+ )\n+ )\n+ else:\n+ b_neg.append(\n+ Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end) + int(window),\n+ feat.id,\n+ )\n+ )\n+\n+ else:\n+ for feat in rec_a_i.features:\n+ if feat.type == 'remark' or feat.type == 'annotation':\n+ continue\n+ tree_a.append(\n+ Interval(\n+ int(feat.location.start) - int(window),\n+ int(feat.location.end)"..b'feature.location.start), int(feature.location.end)))\n+\n+ if feature.type == "remark" or feature.type == "annotation":\n+ continue\n+\n+ if stranding == False:\n+ hits = tree_b[int(feature.location.start) : int(feature.location.end)]\n+ \n+ \n+ # feature id is saved in interval result.data, use map to get full feature\n+ for hit in hits:\n+ rec_a_hits_in_b.append(rec_b_map[hit.data])\n+\n+ else:\n+ if feature.strand > 0:\n+ hits_pos = tree_b_pos[\n+ int(feature.location.start) : int(feature.location.end)\n+ ]\n+ for hit in hits_pos:\n+ rec_a_hits_in_b.append(rec_b_map[hit.data])\n+ else:\n+ hits_neg = tree_b_neg[\n+ int(feature.location.start) : int(feature.location.end)\n+ ]\n+ for hit in hits_neg:\n+ rec_a_hits_in_b.append(rec_b_map[hit.data])\n+\n+ for feature in rec_b_i.features:\n+ if feature.type == "remark" or feature.type == "annotation":\n+ continue\n+\n+ if stranding == False:\n+ hits = tree_a[int(feature.location.start) : int(feature.location.end)]\n+\n+ # feature id is saved in interval result.data, use map to get full feature\n+ for hit in hits:\n+ rec_b_hits_in_a.append(rec_a_map[hit.data])\n+\n+ else:\n+ if feature.strand > 0:\n+ hits_pos = tree_a_pos[\n+ int(feature.location.start) : int(feature.location.end)\n+ ]\n+ for hit in hits_pos:\n+ rec_b_hits_in_a.append(rec_a_map[hit.data])\n+ else:\n+ hits_neg = tree_a_neg[\n+ int(feature.location.start) : int(feature.location.end)\n+ ]\n+ for hit in hits_neg:\n+ rec_b_hits_in_a.append(rec_a_map[hit.data])\n+\n+ # Remove duplicate features using sets\n+ rec_a_out.append(SeqRecord(rec_a[iterate].seq, rec_a[iterate].id, rec_a[iterate].name, rec_a[iterate].description, rec_a[iterate].dbxrefs, sorted(set(rec_a_hits_in_b), key=lambda feat: feat.location.start), rec_a[iterate].annotations))\n+ rec_b_out.append(SeqRecord(rec_b[iterate].seq, rec_b[iterate].id, rec_b[iterate].name, rec_b[iterate].description, rec_b[iterate].dbxrefs, sorted(set(rec_b_hits_in_a), key=lambda feat: feat.location.start), rec_b[iterate].annotations))\n+ iterate += 1\n+ \n+ else:\n+ # If one input is empty, output two empty result files.\n+ rec_a_out = [SeqRecord(Seq(""), "none")]\n+ rec_b_out = [SeqRecord(Seq(""), "none")]\n+ return rec_a_out, rec_b_out\n+\n+\n+if __name__ == "__main__":\n+ parser = argparse.ArgumentParser(\n+ description="rebase gff3 features against parent locations", epilog=""\n+ )\n+ parser.add_argument("a", type=argparse.FileType("r"))\n+ parser.add_argument("b", type=argparse.FileType("r"))\n+ parser.add_argument(\n+ "window",\n+ type=int,\n+ default=50,\n+ help="Allows features this far away to still be considered \'adjacent\'",\n+ )\n+ parser.add_argument(\n+ "-stranding",\n+ action="store_true",\n+ help="Only allow adjacency for same-strand features",\n+ )\n+ parser.add_argument("--oa", type=str, default="a_hits_near_b.gff")\n+ parser.add_argument("--ob", type=str, default="b_hits_near_a.gff")\n+ args = parser.parse_args()\n+\n+ b, a = intersect(args.a, args.b, args.window, args.stranding)\n+\n+ with open(args.oa, "w") as handle:\n+ for rec in a:\n+ gffWrite([rec], handle)\n+\n+ with open(args.ob, "w") as handle:\n+ for rec in b:\n+ gffWrite([rec], handle)\n' |
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| diff -r 000000000000 -r 4c72b6accdee cpt_intersect_adj/intersect_and_adjacent.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/intersect_and_adjacent.xml Fri May 13 05:05:59 2022 +0000 |
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| @@ -0,0 +1,52 @@ +<?xml version="1.0"?> +<tool id="edu.tamu.cpt.gff3.intersect_and_adjacent" name="Intersect and Adjacent" version="21.0.0"> + <description>Outputs nearby top-level GFF features from two GFF3 files</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.79">biopython</requirement> + <requirement type="package" version="1.1.3">cpt_gffparser</requirement> + <requirement type="package" version="3.0.2">intervaltree</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +$__tool_directory__/intersect_and_adjacent.py +"$gff3_data_a" +"$gff3_data_b" +$window +$stranding +--oa $oa +--ob $ob +]]></command> + <inputs> + <param label="GFF3 Annotations A" name="gff3_data_a" type="data" format="gff3"/> + <param label="GFF3 Annotations B" name="gff3_data_b" type="data" format="gff3"/> + <param label="Adjacency Window Size" name="window" type="integer" value = "0"/> + <param label="Only allow adjacencies for features on the same strand" name="stranding" type="boolean" checked="false" truevalue="-stranding" falsevalue="" /> + </inputs> + <outputs> + <data format="gff3" name="oa" label="GFF3 Annotations from ${gff3_data_a.name} in ${gff3_data_b.name}"/> + <data format="gff3" name="ob" label="GFF3 Annotations from ${gff3_data_b.name} in ${gff3_data_a.name}"/> + </outputs> + <tests> + <test> + <param name="gff3_data_a" value="T7_IntersectAIn.gff3" /> + <param name="gff3_data_b" value="T7_IntersectBIn.gff3" /> + <param name="window" value= "50" /> + <param name="stranding" value= "-stranding"/> + <output name="oa" file="T7_IntersectAOut.gff3"/> + <output name="ob" file="T7_IntersectBOut.gff3"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Given two input files, this tool computes the members of A that are within +"Window" nucleotides of a member of B, and vice versa. It then produces +two gff3 outputs, one being the features of GFF A that pass this check, +and the other being the features of GFF B that pass. +]]></help> + <expand macro="citations-2020" /> +</tool> |
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| diff -r 000000000000 -r 4c72b6accdee cpt_intersect_adj/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/macros.xml Fri May 13 05:05:59 2022 +0000 |
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| @@ -0,0 +1,85 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.6">python</requirement> + <requirement type="package" version="1.77">biopython</requirement> + <requirement type="package" version="1.1.3">cpt_gffparser</requirement> + <yield/> + </requirements> + </xml> + <token name="@BLAST_TSV@"> + "$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 000000000000 -r 4c72b6accdee cpt_intersect_adj/test-data/T7_IntersectAIn.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/test-data/T7_IntersectAIn.gff3 Fri May 13 05:05:59 2022 +0000 |
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| b'@@ -0,0 +1,202 @@\n+##gff-version 3\n+##sequence-region NC_001604 1 39847\n+NC_001604\tfeature\tChain\t545\t634\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171;Note=Transmembrane protein - N in C out;Target=ORF.0.2506_0.167028375883.CDS\n+NC_001604\tTMHMM\tTopological domain\t620\t637\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171\n+NC_001604\tTMHMM\tTransmembrane\t551\t619\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171\n+NC_001604\tTMHMM\tTopological domain\t545\t550\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171\n+NC_001604\tfeature\tChain\t1499\t1636\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e;Note=Transmembrane protein - N out C in;Target=ORF.0.566_0.38534199341.CDS\n+NC_001604\tTMHMM\tTopological domain\t1496\t1561\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e\n+NC_001604\tTMHMM\tTransmembrane\t1562\t1630\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e\n+NC_001604\tTMHMM\tTopological domain\t1631\t1636\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e\n+NC_001604\tfeature\tChain\t1505\t1636\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65;Note=Transmembrane protein - N out C in;Target=ORF.0.567_0.804461971525.CDS\n+NC_001604\tTMHMM\tTopological domain\t1502\t1543\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65\n+NC_001604\tTMHMM\tTransmembrane\t1544\t1612\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65\n+NC_001604\tTMHMM\tTopological domain\t1613\t1636\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65\n+NC_001604\tfeature\tChain\t1782\t2018\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b;Note=Transmembrane protein - N in C out;Target=ORF.0.3347_0.667378729511.CDS\n+NC_001604\tTMHMM\tTopological domain\t1986\t2021\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b\n+NC_001604\tTMHMM\tTransmembrane\t1917\t1985\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b\n+NC_001604\tTMHMM\tTopological domain\t1782\t1916\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b\n+NC_001604\tfeature\tChain\t2801\t2896\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_5-727cd513-bd63-4234-b5d0-04c3b0e3e553;Note=Transmembrane protein - N in C out;Target=ORF.0.2482_0.370811900925.CDS\n+NC_001604\tTMHMM\tTopological domain\t2864\t2899\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_5-727cd513-bd63-4234-b5d0-04c3b0e3e553\n+NC_001604\tTMHMM\tTransmembrane\t2804\t2863\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_5-727cd513-bd63-4234-b5d0-04c3b0e3e553\n+NC_001604\tTMHMM\tTopological domain\t2801\t2803\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_5-727cd513-bd63-4234-b5d0-04c3b0e3e553\n+NC_001604\tfeature\tChain\t2997\t3089\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_6-378e5997-850e-46f8-8e45-49106261d847;Note=Transmembrane protein - N in C out;Target=ORF.0.1442_0.301385622759.CDS\n+NC_001604\tTMHMM\tTopological domain\t2994\t3011\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_6-378e5997-850e-46f8-8e45-49106261d847\n+NC_001604\tTMHMM\tTransmembrane\t3012\t3071\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_6-378e5997-850e-46f8-8e45-49106261d847\n+NC_001604\tTMHMM\tTopological domain\t3072\t3089\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_6-378e5997-850e-46f8-8e45-49106261d847\n+NC_001604\tfeature\tChain\t4106\t4408\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_7-cd8efeae-028d-4b07-876f-435d36998a1d;Note=Transmembrane protein - N out C in;Target=ORF.0.2446_0.195161217306.CDS\n+NC_001604\tTMHMM\tTopological domain\t4187\t4411\t.\t-\t.\tParent=tmhmm_tmd_7-cd8efeae-028d-4b07-876f-435d36998a1d\n+NC_001604\tTMHMM\tTransmembrane\t4118\t4186\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_7-cd8efeae-028d-4b07-876f-435d36998a1d\n+NC_001604\tTMHMM\tTopological domain\t4106\t4117\t.\t-\t.\tNote=Cytoplasmic;Parent=tm'..b'rotein;ID=tmhmm_tmd_40-5f3b3b76-c62e-4936-8d3d-78e71f81949a;Note=Transmembrane protein - N out C in;Target=ORF.0.1264_0.997259655684.CDS\n+NC_001604\tTMHMM\tTopological domain\t31289\t31315\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_40-5f3b3b76-c62e-4936-8d3d-78e71f81949a\n+NC_001604\tTMHMM\tTransmembrane\t31316\t31372\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_40-5f3b3b76-c62e-4936-8d3d-78e71f81949a\n+NC_001604\tTMHMM\tTopological domain\t31373\t31426\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_40-5f3b3b76-c62e-4936-8d3d-78e71f81949a\n+NC_001604\tfeature\tChain\t33913\t34548\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_41-366d135b-3f32-4e85-a42b-79d65e6f26d6;Note=Transmembrane protein - N in C out;Target=ORF.0.470_0.0223503021819.CDS\n+NC_001604\tTMHMM\tTopological domain\t33910\t33990\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_41-366d135b-3f32-4e85-a42b-79d65e6f26d6\n+NC_001604\tTMHMM\tTransmembrane\t33991\t34059\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_41-366d135b-3f32-4e85-a42b-79d65e6f26d6\n+NC_001604\tTMHMM\tTopological domain\t34060\t34548\t.\t+\t.\tParent=tmhmm_tmd_41-366d135b-3f32-4e85-a42b-79d65e6f26d6\n+NC_001604\tfeature\tChain\t36347\t36544\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_42-e8edf813-5edf-4572-b01e-a338e0b87f22;Note=Transmembrane protein - N out C in;Target=ORF.0.1312_0.680684781715.CDS\n+NC_001604\tTMHMM\tTopological domain\t36344\t36451\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_42-e8edf813-5edf-4572-b01e-a338e0b87f22\n+NC_001604\tTMHMM\tTransmembrane\t36452\t36508\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_42-e8edf813-5edf-4572-b01e-a338e0b87f22\n+NC_001604\tTMHMM\tTopological domain\t36509\t36544\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_42-e8edf813-5edf-4572-b01e-a338e0b87f22\n+NC_001604\tfeature\tChain\t37001\t37102\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_43-a4f91c3c-dde7-4dd4-8420-df0050dd1146;Note=Transmembrane protein - N in C out;Target=ORF.0.2065_0.772127826341.CDS\n+NC_001604\tTMHMM\tTopological domain\t37073\t37105\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_43-a4f91c3c-dde7-4dd4-8420-df0050dd1146\n+NC_001604\tTMHMM\tTransmembrane\t37004\t37072\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_43-a4f91c3c-dde7-4dd4-8420-df0050dd1146\n+NC_001604\tTMHMM\tTopological domain\t37001\t37003\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_43-a4f91c3c-dde7-4dd4-8420-df0050dd1146\n+NC_001604\tfeature\tChain\t37035\t37280\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd;Note=Transmembrane protein - N in C out;Target=ORF.0.1961_0.261039005028.CDS\n+NC_001604\tTMHMM\tTopological domain\t37032\t37112\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd\n+NC_001604\tTMHMM\tTransmembrane\t37113\t37181\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd\n+NC_001604\tTMHMM\tTopological domain\t37182\t37280\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd\n+NC_001604\tfeature\tChain\t39392\t39535\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3;Note=Transmembrane protein - N in C out;Target=ORF.0.1414_0.296990322019.CDS\n+NC_001604\tTMHMM\tTopological domain\t39389\t39424\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3\n+NC_001604\tTMHMM\tTransmembrane\t39425\t39478\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3\n+NC_001604\tTMHMM\tTopological domain\t39479\t39535\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3\n+NC_001604\tfeature\tChain\t39456\t39554\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164;Note=Transmembrane protein - N out C in;Target=ORF.0.2021_0.203671539857.CDS\n+NC_001604\tTMHMM\tTopological domain\t39453\t39494\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164\n+NC_001604\tTMHMM\tTransmembrane\t39495\t39548\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164\n+NC_001604\tTMHMM\tTopological domain\t39549\t39554\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164\n' |
| b |
| diff -r 000000000000 -r 4c72b6accdee cpt_intersect_adj/test-data/T7_IntersectAOut.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/test-data/T7_IntersectAOut.gff3 Fri May 13 05:05:59 2022 +0000 |
| b |
| b'@@ -0,0 +1,82 @@\n+##gff-version 3\n+##sequence-region NC_001604 1 39937\n+NC_001604\tfeature\tChain\t545\t634\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171;Note=Transmembrane protein - N in C out;Target=ORF.0.2506_0.167028375883.CDS;\n+NC_001604\tTMHMM\tTopological domain\t620\t637\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171;\n+NC_001604\tTMHMM\tTransmembrane\t551\t619\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171;\n+NC_001604\tTMHMM\tTopological domain\t545\t550\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_1-f21272ae-496f-4fc1-8d6e-c0ea75f90171;\n+NC_001604\tfeature\tChain\t1499\t1636\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e;Note=Transmembrane protein - N out C in;Target=ORF.0.566_0.38534199341.CDS;\n+NC_001604\tTMHMM\tTopological domain\t1496\t1561\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e;\n+NC_001604\tTMHMM\tTransmembrane\t1562\t1630\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e;\n+NC_001604\tTMHMM\tTopological domain\t1631\t1636\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_2-82f21b97-6a7e-4ddd-9c7a-a6043f5b598e;\n+NC_001604\tfeature\tChain\t1505\t1636\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65;Note=Transmembrane protein - N out C in;Target=ORF.0.567_0.804461971525.CDS;\n+NC_001604\tTMHMM\tTopological domain\t1502\t1543\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65;\n+NC_001604\tTMHMM\tTransmembrane\t1544\t1612\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65;\n+NC_001604\tTMHMM\tTopological domain\t1613\t1636\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_3-86aae52d-c800-485f-8895-a9287e122d65;\n+NC_001604\tfeature\tChain\t1782\t2018\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b;Note=Transmembrane protein - N in C out;Target=ORF.0.3347_0.667378729511.CDS;\n+NC_001604\tTMHMM\tTopological domain\t1986\t2021\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b;\n+NC_001604\tTMHMM\tTransmembrane\t1917\t1985\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b;\n+NC_001604\tTMHMM\tTopological domain\t1782\t1916\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_4-69abcd70-170f-472f-8d52-eeb29376d71b;\n+NC_001604\tfeature\tChain\t7611\t7760\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_15-06ae012d-7e0c-43f2-b065-b3d75bad06ce;Note=Transmembrane protein - N in C in;Target=ORF.0.1571_0.432752129598.CDS;\n+NC_001604\tTMHMM\tTopological domain\t7608\t7619\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_15-06ae012d-7e0c-43f2-b065-b3d75bad06ce;\n+NC_001604\tTMHMM\tTransmembrane\t7620\t7679\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_15-06ae012d-7e0c-43f2-b065-b3d75bad06ce;\n+NC_001604\tTMHMM\tTopological domain\t7680\t7688\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_15-06ae012d-7e0c-43f2-b065-b3d75bad06ce;\n+NC_001604\tTMHMM\tTransmembrane\t7689\t7757\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_15-06ae012d-7e0c-43f2-b065-b3d75bad06ce;\n+NC_001604\tTMHMM\tTopological domain\t7758\t7760\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_15-06ae012d-7e0c-43f2-b065-b3d75bad06ce;\n+NC_001604\tfeature\tChain\t8241\t8393\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_17-acc5c4e6-6a78-4138-b96b-e14da7269fa4;Note=Transmembrane protein - N in C in;Target=ORF.0.3260_0.786396696237.CDS;\n+NC_001604\tTMHMM\tTopological domain\t8385\t8396\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_17-acc5c4e6-6a78-4138-b96b-e14da7269fa4;\n+NC_001604\tTMHMM\tTransmembrane\t8325\t8384\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_17-acc5c4e6-6a78-4138-b96b-e14da7269fa4;\n+NC_001604\tTMHMM\tTopological domain\t8313\t8324\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_17-acc5c4e6-6a78-4138-b96b-e14da7269fa4;\n+NC_001604\tTMHMM\tTransmembrane\t8244\t8312\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_17-acc5c4e6-6a78-4138-b96b-e14da7269fa4;\n+NC_001604\tTMHMM\tTopological domain\t8241\t8243\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_17-acc5c4e6-6a78-4138-b96b-e'..b'-35e7ba119b92;Note=Transmembrane protein - N in C out;Target=ORF.0.2827_0.307040161403.CDS;\n+NC_001604\tTMHMM\tTopological domain\t15316\t15375\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_25-fea2e54b-e2fa-47d6-8a46-35e7ba119b92;\n+NC_001604\tTMHMM\tTransmembrane\t15247\t15315\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_25-fea2e54b-e2fa-47d6-8a46-35e7ba119b92;\n+NC_001604\tTMHMM\tTopological domain\t15202\t15246\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_25-fea2e54b-e2fa-47d6-8a46-35e7ba119b92;\n+NC_001604\tfeature\tChain\t18397\t18504\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_33-5de09f17-eff3-46d8-abe6-96ae4dfd69fc;Note=Transmembrane protein - N out C in;Target=ORF.0.298_0.896134049513.CDS;\n+NC_001604\tTMHMM\tTopological domain\t18394\t18405\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_33-5de09f17-eff3-46d8-abe6-96ae4dfd69fc;\n+NC_001604\tTMHMM\tTransmembrane\t18406\t18465\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_33-5de09f17-eff3-46d8-abe6-96ae4dfd69fc;\n+NC_001604\tTMHMM\tTopological domain\t18466\t18504\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_33-5de09f17-eff3-46d8-abe6-96ae4dfd69fc;\n+NC_001604\tfeature\tChain\t19351\t19761\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_35-6ad75bad-a355-49a8-ae3b-b61762d6bde7;Note=Transmembrane protein - N out C in;Target=ORF.0.2751_0.199850521186.CDS;\n+NC_001604\tTMHMM\tTopological domain\t19588\t19764\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_35-6ad75bad-a355-49a8-ae3b-b61762d6bde7;\n+NC_001604\tTMHMM\tTransmembrane\t19519\t19587\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_35-6ad75bad-a355-49a8-ae3b-b61762d6bde7;\n+NC_001604\tTMHMM\tTopological domain\t19351\t19518\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_35-6ad75bad-a355-49a8-ae3b-b61762d6bde7;\n+NC_001604\tfeature\tChain\t28523\t29278\t.\t-\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_36-7ccd4500-53cb-4119-b088-ef9b6866ee18;Note=Transmembrane protein - N in C out;Target=ORF.0.2112_0.388955799353.CDS;\n+NC_001604\tTMHMM\tTopological domain\t28784\t29281\t.\t-\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_36-7ccd4500-53cb-4119-b088-ef9b6866ee18;\n+NC_001604\tTMHMM\tTransmembrane\t28715\t28783\t.\t-\t.\tNote=Helical;Parent=tmhmm_tmd_36-7ccd4500-53cb-4119-b088-ef9b6866ee18;\n+NC_001604\tTMHMM\tTopological domain\t28523\t28714\t.\t-\t.\tNote=Extracellular;Parent=tmhmm_tmd_36-7ccd4500-53cb-4119-b088-ef9b6866ee18;\n+NC_001604\tfeature\tChain\t37035\t37280\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd;Note=Transmembrane protein - N in C out;Target=ORF.0.1961_0.261039005028.CDS;\n+NC_001604\tTMHMM\tTopological domain\t37032\t37112\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd;\n+NC_001604\tTMHMM\tTransmembrane\t37113\t37181\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd;\n+NC_001604\tTMHMM\tTopological domain\t37182\t37280\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_44-b4121b3a-f384-4f27-8abb-e14261bfd2fd;\n+NC_001604\tfeature\tChain\t39392\t39535\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3;Note=Transmembrane protein - N in C out;Target=ORF.0.1414_0.296990322019.CDS;\n+NC_001604\tTMHMM\tTopological domain\t39389\t39424\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3;\n+NC_001604\tTMHMM\tTransmembrane\t39425\t39478\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3;\n+NC_001604\tTMHMM\tTopological domain\t39479\t39535\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_45-ec6c20e1-8a25-47bf-8ded-cbe854809ce3;\n+NC_001604\tfeature\tChain\t39456\t39554\t.\t+\t.\tDescription=Transmembrane protein;ID=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164;Note=Transmembrane protein - N out C in;Target=ORF.0.2021_0.203671539857.CDS;\n+NC_001604\tTMHMM\tTopological domain\t39453\t39494\t.\t+\t.\tNote=Extracellular;Parent=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164;\n+NC_001604\tTMHMM\tTransmembrane\t39495\t39548\t.\t+\t.\tNote=Helical;Parent=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164;\n+NC_001604\tTMHMM\tTopological domain\t39549\t39554\t.\t+\t.\tNote=Cytoplasmic;Parent=tmhmm_tmd_46-bb7be945-aca9-4ef4-93f5-4de3337ea164;\n' |
| b |
| diff -r 000000000000 -r 4c72b6accdee cpt_intersect_adj/test-data/T7_IntersectBIn.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/test-data/T7_IntersectBIn.gff3 Fri May 13 05:05:59 2022 +0000 |
| b |
| b'@@ -0,0 +1,492 @@\n+##gff-version 3\n+##sequence-region NC_001604 1 39937\n+NC_001604\tcpt.fixModel\tgene\t627\t824\t.\t-\t.\tID=ORF.0.3363_0.587331907045\n+NC_001604\tcpt.fixModel\tmRNA\t627\t824\t.\t-\t.\tID=ORF.0.3363_0.587331907045.mRNA;Parent=ORF.0.3363_0.587331907045\n+NC_001604\tgetOrfsOrCds\tCDS\t627\t824\t.\t-\t0\tID=ORF.0.3363_0.587331907045.CDS;Parent=ORF.0.3363_0.587331907045.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t837\t839\t.\t-\t.\tID=ORF.0.3363_0.587331907045.rbs-0;Parent=ORF.0.3363_0.587331907045\n+NC_001604\tCPT_LipoRy\tLipobox\t693\t704\t.\t-\t.\tID=ORF.0.3363_0.587331907045.lipobox;Parent=ORF.0.3363_0.587331907045;sequence=FTLC\n+NC_001604\tcpt.fixModel\tgene\t627\t734\t.\t-\t.\tID=ORF.0.3367_0.864588620692\n+NC_001604\tcpt.fixModel\tmRNA\t627\t734\t.\t-\t.\tID=ORF.0.3367_0.864588620692.mRNA;Parent=ORF.0.3367_0.864588620692\n+NC_001604\tgetOrfsOrCds\tCDS\t627\t734\t.\t-\t0\tID=ORF.0.3367_0.864588620692.CDS;Parent=ORF.0.3367_0.864588620692.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t745\t747\t.\t-\t.\tID=ORF.0.3367_0.864588620692.rbs-0;Parent=ORF.0.3367_0.864588620692\n+NC_001604\tCPT_LipoRy\tLipobox\t693\t704\t.\t-\t.\tID=ORF.0.3367_0.864588620692.lipobox;Parent=ORF.0.3367_0.864588620692;sequence=FTLC\n+NC_001604\tcpt.fixModel\tgene\t1182\t1298\t.\t-\t.\tID=ORF.0.3359_0.0923195020918\n+NC_001604\tcpt.fixModel\tmRNA\t1182\t1298\t.\t-\t.\tID=ORF.0.3359_0.0923195020918.mRNA;Parent=ORF.0.3359_0.0923195020918\n+NC_001604\tgetOrfsOrCds\tCDS\t1182\t1298\t.\t-\t0\tID=ORF.0.3359_0.0923195020918.CDS;Parent=ORF.0.3359_0.0923195020918.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1308\t1310\t.\t-\t.\tID=ORF.0.3359_0.0923195020918.rbs-0;Parent=ORF.0.3359_0.0923195020918\n+NC_001604\tCPT_LipoRy\tLipobox\t1188\t1199\t.\t-\t.\tID=ORF.0.3359_0.0923195020918.lipobox;Parent=ORF.0.3359_0.0923195020918;sequence=IVNC\n+NC_001604\tcpt.fixModel\tgene\t1496\t1639\t.\t+\t.\tID=ORF.0.566_0.38534199341\n+NC_001604\tcpt.fixModel\tmRNA\t1496\t1639\t.\t+\t.\tID=ORF.0.566_0.38534199341.mRNA;Parent=ORF.0.566_0.38534199341\n+NC_001604\tgetOrfsOrCds\tCDS\t1496\t1639\t.\t+\t0\tID=ORF.0.566_0.38534199341.CDS;Parent=ORF.0.566_0.38534199341.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1487\t1490\t.\t+\t.\tID=ORF.0.566_0.38534199341.rbs-0;Parent=ORF.0.566_0.38534199341\n+NC_001604\tCPT_LipoRy\tLipobox\t1589\t1600\t.\t+\t.\tID=ORF.0.566_0.38534199341.lipobox;Parent=ORF.0.566_0.38534199341;sequence=FTAC\n+NC_001604\tcpt.fixModel\tgene\t1502\t1639\t.\t+\t.\tID=ORF.0.567_0.804461971525\n+NC_001604\tcpt.fixModel\tmRNA\t1502\t1639\t.\t+\t.\tID=ORF.0.567_0.804461971525.mRNA;Parent=ORF.0.567_0.804461971525\n+NC_001604\tgetOrfsOrCds\tCDS\t1502\t1639\t.\t+\t0\tID=ORF.0.567_0.804461971525.CDS;Parent=ORF.0.567_0.804461971525.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1487\t1490\t.\t+\t.\tID=ORF.0.567_0.804461971525.rbs-0;Parent=ORF.0.567_0.804461971525\n+NC_001604\tCPT_LipoRy\tLipobox\t1589\t1600\t.\t+\t.\tID=ORF.0.567_0.804461971525.lipobox;Parent=ORF.0.567_0.804461971525;sequence=FTAC\n+NC_001604\tcpt.fixModel\tgene\t1779\t2021\t.\t-\t.\tID=ORF.0.3347_0.667378729511\n+NC_001604\tcpt.fixModel\tmRNA\t1779\t2021\t.\t-\t.\tID=ORF.0.3347_0.667378729511.mRNA;Parent=ORF.0.3347_0.667378729511\n+NC_001604\tgetOrfsOrCds\tCDS\t1779\t2021\t.\t-\t0\tID=ORF.0.3347_0.667378729511.CDS;Parent=ORF.0.3347_0.667378729511.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t2030\t2032\t.\t-\t.\tID=ORF.0.3347_0.667378729511.rbs-0;Parent=ORF.0.3347_0.667378729511\n+NC_001604\tCPT_LipoRy\tLipobox\t1896\t1907\t.\t-\t.\tID=ORF.0.3347_0.667378729511.lipobox;Parent=ORF.0.3347_0.667378729511;sequence=ALSC\n+NC_001604\tcpt.fixModel\tgene\t1779\t1979\t.\t-\t.\tID=ORF.0.3349_0.219533700187\n+NC_001604\tcpt.fixModel\tmRNA\t1779\t1979\t.\t-\t.\tID=ORF.0.3349_0.219533700187.mRNA;Parent=ORF.0.3349_0.219533700187\n+NC_001604\tgetOrfsOrCds\tCDS\t1779\t1979\t.\t-\t0\tID=ORF.0.3349_0.219533700187.CDS;Parent=ORF.0.3349_0.219533700187.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1992\t1994\t.\t-\t.\tID=ORF.0.3349_0.219533700187.rbs-0;Parent=ORF.0.3349_0.219533700187\n+NC_001604\tCPT_LipoRy\tLipobox\t1896\t1907\t.\t-\t.\tID=ORF.0.3349_0.219533700187.lipobox;Parent=ORF.0.3349_0.219533700187;sequence=ALSC\n+NC_001604\tcpt.fi'..b'odel\tgene\t36800\t36898\t.\t+\t.\tID=ORF.0.1325_0.813429946488\n+NC_001604\tcpt.fixModel\tmRNA\t36800\t36898\t.\t+\t.\tID=ORF.0.1325_0.813429946488.mRNA;Parent=ORF.0.1325_0.813429946488\n+NC_001604\tgetOrfsOrCds\tCDS\t36800\t36898\t.\t+\t0\tID=ORF.0.1325_0.813429946488.CDS;Parent=ORF.0.1325_0.813429946488.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t36787\t36789\t.\t+\t.\tID=ORF.0.1325_0.813429946488.rbs-0;Parent=ORF.0.1325_0.813429946488\n+NC_001604\tCPT_LipoRy\tLipobox\t36851\t36862\t.\t+\t.\tID=ORF.0.1325_0.813429946488.lipobox;Parent=ORF.0.1325_0.813429946488;sequence=LYGC\n+NC_001604\tcpt.fixModel\tgene\t37032\t37283\t.\t+\t.\tID=ORF.0.1961_0.261039005028\n+NC_001604\tcpt.fixModel\tmRNA\t37032\t37283\t.\t+\t.\tID=ORF.0.1961_0.261039005028.mRNA;Parent=ORF.0.1961_0.261039005028\n+NC_001604\tgetOrfsOrCds\tCDS\t37032\t37283\t.\t+\t0\tID=ORF.0.1961_0.261039005028.CDS;Parent=ORF.0.1961_0.261039005028.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t37020\t37026\t.\t+\t.\tID=ORF.0.1961_0.261039005028.rbs-0;Parent=ORF.0.1961_0.261039005028\n+NC_001604\tCPT_LipoRy\tLipobox\t37167\t37178\t.\t+\t.\tID=ORF.0.1961_0.261039005028.lipobox;Parent=ORF.0.1961_0.261039005028;sequence=ISGC\n+NC_001604\tcpt.fixModel\tgene\t37083\t37283\t.\t+\t.\tID=ORF.0.1964_0.894779255809\n+NC_001604\tcpt.fixModel\tmRNA\t37083\t37283\t.\t+\t.\tID=ORF.0.1964_0.894779255809.mRNA;Parent=ORF.0.1964_0.894779255809\n+NC_001604\tgetOrfsOrCds\tCDS\t37083\t37283\t.\t+\t0\tID=ORF.0.1964_0.894779255809.CDS;Parent=ORF.0.1964_0.894779255809.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t37074\t37076\t.\t+\t.\tID=ORF.0.1964_0.894779255809.rbs-0;Parent=ORF.0.1964_0.894779255809\n+NC_001604\tCPT_LipoRy\tLipobox\t37167\t37178\t.\t+\t.\tID=ORF.0.1964_0.894779255809.lipobox;Parent=ORF.0.1964_0.894779255809;sequence=ISGC\n+NC_001604\tcpt.fixModel\tgene\t37213\t37368\t.\t-\t.\tID=ORF.0.2528_0.841717806577\n+NC_001604\tcpt.fixModel\tmRNA\t37213\t37368\t.\t-\t.\tID=ORF.0.2528_0.841717806577.mRNA;Parent=ORF.0.2528_0.841717806577\n+NC_001604\tgetOrfsOrCds\tCDS\t37213\t37368\t.\t-\t0\tID=ORF.0.2528_0.841717806577.CDS;Parent=ORF.0.2528_0.841717806577.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t37377\t37379\t.\t-\t.\tID=ORF.0.2528_0.841717806577.rbs-0;Parent=ORF.0.2528_0.841717806577\n+NC_001604\tCPT_LipoRy\tLipobox\t37315\t37326\t.\t-\t.\tID=ORF.0.2528_0.841717806577.lipobox;Parent=ORF.0.2528_0.841717806577;sequence=IVSC\n+NC_001604\tcpt.fixModel\tgene\t38016\t38273\t.\t+\t.\tID=ORF.0.1988_0.755408274882\n+NC_001604\tcpt.fixModel\tmRNA\t38016\t38273\t.\t+\t.\tID=ORF.0.1988_0.755408274882.mRNA;Parent=ORF.0.1988_0.755408274882\n+NC_001604\tgetOrfsOrCds\tCDS\t38016\t38273\t.\t+\t0\tID=ORF.0.1988_0.755408274882.CDS;Parent=ORF.0.1988_0.755408274882.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t38006\t38009\t.\t+\t.\tID=ORF.0.1988_0.755408274882.rbs-0;Parent=ORF.0.1988_0.755408274882\n+NC_001604\tCPT_LipoRy\tLipobox\t38091\t38102\t.\t+\t.\tID=ORF.0.1988_0.755408274882.lipobox;Parent=ORF.0.1988_0.755408274882;sequence=LLLC\n+NC_001604\tcpt.fixModel\tgene\t38376\t38513\t.\t+\t.\tID=ORF.0.2003_0.337942263367\n+NC_001604\tcpt.fixModel\tmRNA\t38376\t38513\t.\t+\t.\tID=ORF.0.2003_0.337942263367.mRNA;Parent=ORF.0.2003_0.337942263367\n+NC_001604\tgetOrfsOrCds\tCDS\t38376\t38513\t.\t+\t0\tID=ORF.0.2003_0.337942263367.CDS;Parent=ORF.0.2003_0.337942263367.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t38361\t38364\t.\t+\t.\tID=ORF.0.2003_0.337942263367.rbs-0;Parent=ORF.0.2003_0.337942263367\n+NC_001604\tCPT_LipoRy\tLipobox\t38490\t38501\t.\t+\t.\tID=ORF.0.2003_0.337942263367.lipobox;Parent=ORF.0.2003_0.337942263367;sequence=VTLC\n+NC_001604\tcpt.fixModel\tgene\t39389\t39538\t.\t+\t.\tID=ORF.0.1414_0.296990322019\n+NC_001604\tcpt.fixModel\tmRNA\t39389\t39538\t.\t+\t.\tID=ORF.0.1414_0.296990322019.mRNA;Parent=ORF.0.1414_0.296990322019\n+NC_001604\tgetOrfsOrCds\tCDS\t39389\t39538\t.\t+\t0\tID=ORF.0.1414_0.296990322019.CDS;Parent=ORF.0.1414_0.296990322019.mRNA\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t39378\t39382\t.\t+\t.\tID=ORF.0.1414_0.296990322019.rbs-0;Parent=ORF.0.1414_0.296990322019\n+NC_001604\tCPT_LipoRy\tLipobox\t39443\t39454\t.\t+\t.\tID=ORF.0.1414_0.296990322019.lipobox;Parent=ORF.0.1414_0.296990322019;sequence=VVLC\n' |
| b |
| diff -r 000000000000 -r 4c72b6accdee cpt_intersect_adj/test-data/T7_IntersectBOut.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_intersect_adj/test-data/T7_IntersectBOut.gff3 Fri May 13 05:05:59 2022 +0000 |
| b |
| b'@@ -0,0 +1,102 @@\n+##gff-version 3\n+##sequence-region NC_001604 1 39847\n+NC_001604\tcpt.fixModel\tgene\t627\t824\t.\t-\t.\tID=ORF.0.3363_0.587331907045;\n+NC_001604\tcpt.fixModel\tmRNA\t627\t824\t.\t-\t.\tID=ORF.0.3363_0.587331907045.mRNA;Parent=ORF.0.3363_0.587331907045;\n+NC_001604\tgetOrfsOrCds\tCDS\t627\t824\t.\t-\t0\tID=ORF.0.3363_0.587331907045.CDS;Parent=ORF.0.3363_0.587331907045.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t837\t839\t.\t-\t.\tID=ORF.0.3363_0.587331907045.rbs-0;Parent=ORF.0.3363_0.587331907045;\n+NC_001604\tCPT_LipoRy\tLipobox\t693\t704\t.\t-\t.\tID=ORF.0.3363_0.587331907045.lipobox;Parent=ORF.0.3363_0.587331907045;sequence=FTLC;\n+NC_001604\tcpt.fixModel\tgene\t627\t734\t.\t-\t.\tID=ORF.0.3367_0.864588620692;\n+NC_001604\tcpt.fixModel\tmRNA\t627\t734\t.\t-\t.\tID=ORF.0.3367_0.864588620692.mRNA;Parent=ORF.0.3367_0.864588620692;\n+NC_001604\tgetOrfsOrCds\tCDS\t627\t734\t.\t-\t0\tID=ORF.0.3367_0.864588620692.CDS;Parent=ORF.0.3367_0.864588620692.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t745\t747\t.\t-\t.\tID=ORF.0.3367_0.864588620692.rbs-0;Parent=ORF.0.3367_0.864588620692;\n+NC_001604\tCPT_LipoRy\tLipobox\t693\t704\t.\t-\t.\tID=ORF.0.3367_0.864588620692.lipobox;Parent=ORF.0.3367_0.864588620692;sequence=FTLC;\n+NC_001604\tcpt.fixModel\tgene\t1496\t1639\t.\t+\t.\tID=ORF.0.566_0.38534199341;\n+NC_001604\tcpt.fixModel\tmRNA\t1496\t1639\t.\t+\t.\tID=ORF.0.566_0.38534199341.mRNA;Parent=ORF.0.566_0.38534199341;\n+NC_001604\tgetOrfsOrCds\tCDS\t1496\t1639\t.\t+\t0\tID=ORF.0.566_0.38534199341.CDS;Parent=ORF.0.566_0.38534199341.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1487\t1490\t.\t+\t.\tID=ORF.0.566_0.38534199341.rbs-0;Parent=ORF.0.566_0.38534199341;\n+NC_001604\tCPT_LipoRy\tLipobox\t1589\t1600\t.\t+\t.\tID=ORF.0.566_0.38534199341.lipobox;Parent=ORF.0.566_0.38534199341;sequence=FTAC;\n+NC_001604\tcpt.fixModel\tgene\t1502\t1639\t.\t+\t.\tID=ORF.0.567_0.804461971525;\n+NC_001604\tcpt.fixModel\tmRNA\t1502\t1639\t.\t+\t.\tID=ORF.0.567_0.804461971525.mRNA;Parent=ORF.0.567_0.804461971525;\n+NC_001604\tgetOrfsOrCds\tCDS\t1502\t1639\t.\t+\t0\tID=ORF.0.567_0.804461971525.CDS;Parent=ORF.0.567_0.804461971525.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1487\t1490\t.\t+\t.\tID=ORF.0.567_0.804461971525.rbs-0;Parent=ORF.0.567_0.804461971525;\n+NC_001604\tCPT_LipoRy\tLipobox\t1589\t1600\t.\t+\t.\tID=ORF.0.567_0.804461971525.lipobox;Parent=ORF.0.567_0.804461971525;sequence=FTAC;\n+NC_001604\tcpt.fixModel\tgene\t1779\t1979\t.\t-\t.\tID=ORF.0.3349_0.219533700187;\n+NC_001604\tcpt.fixModel\tmRNA\t1779\t1979\t.\t-\t.\tID=ORF.0.3349_0.219533700187.mRNA;Parent=ORF.0.3349_0.219533700187;\n+NC_001604\tgetOrfsOrCds\tCDS\t1779\t1979\t.\t-\t0\tID=ORF.0.3349_0.219533700187.CDS;Parent=ORF.0.3349_0.219533700187.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t1992\t1994\t.\t-\t.\tID=ORF.0.3349_0.219533700187.rbs-0;Parent=ORF.0.3349_0.219533700187;\n+NC_001604\tCPT_LipoRy\tLipobox\t1896\t1907\t.\t-\t.\tID=ORF.0.3349_0.219533700187.lipobox;Parent=ORF.0.3349_0.219533700187;sequence=ALSC;\n+NC_001604\tcpt.fixModel\tgene\t1779\t2021\t.\t-\t.\tID=ORF.0.3347_0.667378729511;\n+NC_001604\tcpt.fixModel\tmRNA\t1779\t2021\t.\t-\t.\tID=ORF.0.3347_0.667378729511.mRNA;Parent=ORF.0.3347_0.667378729511;\n+NC_001604\tgetOrfsOrCds\tCDS\t1779\t2021\t.\t-\t0\tID=ORF.0.3347_0.667378729511.CDS;Parent=ORF.0.3347_0.667378729511.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t2030\t2032\t.\t-\t.\tID=ORF.0.3347_0.667378729511.rbs-0;Parent=ORF.0.3347_0.667378729511;\n+NC_001604\tCPT_LipoRy\tLipobox\t1896\t1907\t.\t-\t.\tID=ORF.0.3347_0.667378729511.lipobox;Parent=ORF.0.3347_0.667378729511;sequence=ALSC;\n+NC_001604\tcpt.fixModel\tgene\t7608\t7763\t.\t+\t.\tID=ORF.0.1571_0.432752129598;\n+NC_001604\tcpt.fixModel\tmRNA\t7608\t7763\t.\t+\t.\tID=ORF.0.1571_0.432752129598.mRNA;Parent=ORF.0.1571_0.432752129598;\n+NC_001604\tgetOrfsOrCds\tCDS\t7608\t7763\t.\t+\t0\tID=ORF.0.1571_0.432752129598.CDS;Parent=ORF.0.1571_0.432752129598.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t7596\t7600\t.\t+\t.\tID=ORF.0.1571_0.432752129598.rbs-0;Parent=ORF.0.1571_0.432752129598;\n+NC_001604\tCPT_LipoRy\tLipobox\t7728\t7739\t.\t+\t.\tID=ORF.0.1571_0.432752129598.lipobox;Parent=ORF.0.1571_0.432752129598;sequen'..b'8406\t.\t+\t.\tID=ORF.0.808_0.284208778955;\n+NC_001604\tcpt.fixModel\tmRNA\t17918\t18406\t.\t+\t.\tID=ORF.0.808_0.284208778955.mRNA;Parent=ORF.0.808_0.284208778955;\n+NC_001604\tgetOrfsOrCds\tCDS\t17918\t18406\t.\t+\t0\tID=ORF.0.808_0.284208778955.CDS;Parent=ORF.0.808_0.284208778955.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t17905\t17908\t.\t+\t.\tID=ORF.0.808_0.284208778955.rbs-0;Parent=ORF.0.808_0.284208778955;\n+NC_001604\tCPT_LipoRy\tLipobox\t17999\t18010\t.\t+\t.\tID=ORF.0.808_0.284208778955.lipobox;Parent=ORF.0.808_0.284208778955;sequence=IPNC;\n+NC_001604\tcpt.fixModel\tgene\t18375\t18503\t.\t+\t.\tID=ORF.0.1782_0.36618964442;\n+NC_001604\tcpt.fixModel\tmRNA\t18375\t18503\t.\t+\t.\tID=ORF.0.1782_0.36618964442.mRNA;Parent=ORF.0.1782_0.36618964442;\n+NC_001604\tgetOrfsOrCds\tCDS\t18375\t18503\t.\t+\t0\tID=ORF.0.1782_0.36618964442.CDS;Parent=ORF.0.1782_0.36618964442.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t18362\t18364\t.\t+\t.\tID=ORF.0.1782_0.36618964442.rbs-0;Parent=ORF.0.1782_0.36618964442;\n+NC_001604\tCPT_LipoRy\tLipobox\t18420\t18431\t.\t+\t.\tID=ORF.0.1782_0.36618964442.lipobox;Parent=ORF.0.1782_0.36618964442;sequence=GSLC;\n+NC_001604\tcpt.fixModel\tgene\t19348\t19764\t.\t-\t.\tID=ORF.0.2751_0.199850521186;\n+NC_001604\tcpt.fixModel\tmRNA\t19348\t19764\t.\t-\t.\tID=ORF.0.2751_0.199850521186.mRNA;Parent=ORF.0.2751_0.199850521186;\n+NC_001604\tgetOrfsOrCds\tCDS\t19348\t19764\t.\t-\t0\tID=ORF.0.2751_0.199850521186.CDS;Parent=ORF.0.2751_0.199850521186.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t19770\t19772\t.\t-\t.\tID=ORF.0.2751_0.199850521186.rbs-0;Parent=ORF.0.2751_0.199850521186;\n+NC_001604\tCPT_LipoRy\tLipobox\t19684\t19695\t.\t-\t.\tID=ORF.0.2751_0.199850521186.lipobox;Parent=ORF.0.2751_0.199850521186;sequence=AAAC;\n+NC_001604\tcpt.fixModel\tgene\t29038\t29148\t.\t-\t.\tID=ORF.0.2627_0.865400195799;\n+NC_001604\tcpt.fixModel\tmRNA\t29038\t29148\t.\t-\t.\tID=ORF.0.2627_0.865400195799.mRNA;Parent=ORF.0.2627_0.865400195799;\n+NC_001604\tgetOrfsOrCds\tCDS\t29038\t29148\t.\t-\t0\tID=ORF.0.2627_0.865400195799.CDS;Parent=ORF.0.2627_0.865400195799.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t29157\t29159\t.\t-\t.\tID=ORF.0.2627_0.865400195799.rbs-0;Parent=ORF.0.2627_0.865400195799;\n+NC_001604\tCPT_LipoRy\tLipobox\t29047\t29058\t.\t-\t.\tID=ORF.0.2627_0.865400195799.lipobox;Parent=ORF.0.2627_0.865400195799;sequence=LISC;\n+NC_001604\tcpt.fixModel\tgene\t37032\t37283\t.\t+\t.\tID=ORF.0.1961_0.261039005028;\n+NC_001604\tcpt.fixModel\tmRNA\t37032\t37283\t.\t+\t.\tID=ORF.0.1961_0.261039005028.mRNA;Parent=ORF.0.1961_0.261039005028;\n+NC_001604\tgetOrfsOrCds\tCDS\t37032\t37283\t.\t+\t0\tID=ORF.0.1961_0.261039005028.CDS;Parent=ORF.0.1961_0.261039005028.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t37020\t37026\t.\t+\t.\tID=ORF.0.1961_0.261039005028.rbs-0;Parent=ORF.0.1961_0.261039005028;\n+NC_001604\tCPT_LipoRy\tLipobox\t37167\t37178\t.\t+\t.\tID=ORF.0.1961_0.261039005028.lipobox;Parent=ORF.0.1961_0.261039005028;sequence=ISGC;\n+NC_001604\tcpt.fixModel\tgene\t37083\t37283\t.\t+\t.\tID=ORF.0.1964_0.894779255809;\n+NC_001604\tcpt.fixModel\tmRNA\t37083\t37283\t.\t+\t.\tID=ORF.0.1964_0.894779255809.mRNA;Parent=ORF.0.1964_0.894779255809;\n+NC_001604\tgetOrfsOrCds\tCDS\t37083\t37283\t.\t+\t0\tID=ORF.0.1964_0.894779255809.CDS;Parent=ORF.0.1964_0.894779255809.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t37074\t37076\t.\t+\t.\tID=ORF.0.1964_0.894779255809.rbs-0;Parent=ORF.0.1964_0.894779255809;\n+NC_001604\tCPT_LipoRy\tLipobox\t37167\t37178\t.\t+\t.\tID=ORF.0.1964_0.894779255809.lipobox;Parent=ORF.0.1964_0.894779255809;sequence=ISGC;\n+NC_001604\tcpt.fixModel\tgene\t39389\t39538\t.\t+\t.\tID=ORF.0.1414_0.296990322019;\n+NC_001604\tcpt.fixModel\tmRNA\t39389\t39538\t.\t+\t.\tID=ORF.0.1414_0.296990322019.mRNA;Parent=ORF.0.1414_0.296990322019;\n+NC_001604\tgetOrfsOrCds\tCDS\t39389\t39538\t.\t+\t0\tID=ORF.0.1414_0.296990322019.CDS;Parent=ORF.0.1414_0.296990322019.mRNA;\n+NC_001604\tCPT_ShineFind\tShine_Dalgarno_sequence\t39378\t39382\t.\t+\t.\tID=ORF.0.1414_0.296990322019.rbs-0;Parent=ORF.0.1414_0.296990322019;\n+NC_001604\tCPT_LipoRy\tLipobox\t39443\t39454\t.\t+\t.\tID=ORF.0.1414_0.296990322019.lipobox;Parent=ORF.0.1414_0.296990322019;sequence=VVLC;\n' |