| Next changeset 1:497c6bb3b717 (2015-06-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e |
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added:
jbrowse.py jbrowse.xml macros.xml readme.rst test-data/interpro.gff test-data/merlin.fa test-data/merlin.gff tool_dependencies.xml |
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| diff -r 000000000000 -r 2c9e5136b416 jbrowse.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse.py Mon May 04 17:21:38 2015 -0400 |
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| @@ -0,0 +1,59 @@ +#!/usr/bin/env python +import os +import shutil +import argparse +import subprocess +import hashlib + +TN_TABLE = { + 'gff3': '--gff', + 'gff': '--gff', + 'bed': '--bed', + # 'genbank': '--gbk', +} + + +def process_genome(jbrowse_dir, genome): + subprocess.check_output(['perl', 'bin/prepare-refseqs.pl', '--fasta', genome], cwd=jbrowse_dir) + + +def process_annotations(jbrowse_dir, annot_file, annot_label, annot_format, + **kwargs): + key = hashlib.md5(annot_file).hexdigest() + + cmd = ['perl', 'bin/flatfile-to-json.pl', TN_TABLE.get(annot_format, 'gff'), + annot_file, '--trackLabel', key, '--key', annot_label] + subprocess.check_output(cmd, cwd=jbrowse_dir) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description="", epilog="") + parser.add_argument('genome', type=file, help='Input genome file') + + parser.add_argument('--gff3', type=file, nargs='*', help='GFF3/BED/GBK File') + parser.add_argument('--gff3_format', choices=['gff3', 'gff', 'bed', 'gbk'], nargs='*', help='GFF3/BED/GBK Format') + parser.add_argument('--gff3_label', type=str, nargs='*', help='GFF3/BED/GBK Label') + + parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') + parser.add_argument('--outdir', help='Output directory', default='out') + args = parser.parse_args() + + jbrowse_dir = os.path.join(args.outdir, 'JBrowse-1.11.6') + shutil.copytree(args.jbrowse, jbrowse_dir) + + process_genome(jbrowse_dir, os.path.realpath(args.genome.name)) + + for gff3, gff3_format, gff3_label in zip(args.gff3, args.gff3_format, args.gff3_label): + gff3_path = os.path.realpath(gff3.name) + process_annotations(jbrowse_dir, gff3_path, gff3_label, gff3_format) + + print """ + <html> + <body> + <script type="text/javascript"> + window.location=JBrowse-1.11.6/index.html + </script> + <a href="JBrowse-1.11.6/index.html">Go to JBrowse</a> + </body> + </html> + """ |
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| diff -r 000000000000 -r 2c9e5136b416 jbrowse.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse.xml Mon May 04 17:21:38 2015 -0400 |
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| @@ -0,0 +1,44 @@ +<tool id="jbrowse" name="JBrowse" version="0.1"> + <description>genome browser</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <version_command>python jbrowse.py --version</version_command> + <command interpreter="python"><![CDATA[jbrowse.py +$positional_1 + +#set data_files = '" "'.join([ str($var.gff3) for $var in $data_tracks ]) +#set data_formats = '" "'.join([ str($var.gff3.ext) for $var in $data_tracks ]) +#set data_labels = '" "'.join([ str($var.gff3_label) for $var in $data_tracks ]) + +--gff3 "$data_files" +--gff3_format "$data_formats" +--gff3_label "$data_labels" + + +--jbrowse \${JBROWSE_SOURCE_DIR} +--outdir $default.files_path +> $default]]></command> + <inputs> + <param label="Genome" name="positional_1" type="data" format="fasta"/> + <repeat name="data_tracks" title="Annotation Track"> + <param label="Annotation Data" help="in GFF, GFF3, or BED formats" + format="gff,gff3,bed" name="gff3" type="data"/> + <param label="Dataset Label" name="gff3_label" type="text"/> + </repeat> + </inputs> + <outputs> + <data format="html" name="default" label="JBrowse on $positional_1.name"/> + </outputs> + <help><![CDATA[ +Deploy a static JBrowse visualization of a genome and some associated datasets + +@ATTRIBUTION@ +]]></help> + <citations> + <citation type="doi">10.1101/gr.094607.109</citation> + </citations> +</tool> + |
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| diff -r 000000000000 -r 2c9e5136b416 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon May 04 17:21:38 2015 -0400 |
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| @@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.11.6">jbrowse</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">1.0</token> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <token name="@ATTRIBUTION@"><![CDATA[ +**Attribution** + +This Galaxy tool relies on the JBrowse, maintained by the GMOD Community +]]> + </token> +</macros> |
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| diff -r 000000000000 -r 2c9e5136b416 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Mon May 04 17:21:38 2015 -0400 |
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| @@ -0,0 +1,40 @@ +JBrowse in Galaxy +================= + + JBrowse is a fast, embeddable genome browser built completely with + JavaScript and HTML5 + +Thus, it makes an ideal fit with Galaxy, especially for use as a +workflow summary. E.g. annotate a genome, then visualise all of the +associated datasets as an interactive HTML page. + +Installation +============ + +It is recommended to install this wrapper via the Galaxy Tool Shed + +History +======= + +- 0.1 Initial public release + +Wrapper License (MIT/BSD Style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the names +of the contributors or copyright holders not be used in advertising or +publicity pertaining to distribution of the software without specific +prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR +CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF +USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR +OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR +PERFORMANCE OF THIS SOFTWARE. |
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| diff -r 000000000000 -r 2c9e5136b416 test-data/interpro.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interpro.gff Mon May 04 17:21:38 2015 -0400 |
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| b'@@ -0,0 +1,558 @@\n+##gff-version 3\n+##sequence-region Merlin 1 172788\n+Merlin\tannotation\tremark\t1\t172788\t.\t.\t.\tgff-version=3;sequence-region=%28%27Merlin%27%2C 0%2C 172788%29\n+Merlin\tfeature\tpolypeptide\t1\t229\t.\t+\t.\tID=Merlin_1;md5=4d58b2b569c2fe52e2945e3f6e380c48\n+Merlin\tGene3D\tprotein_match\t2\t50\t2.9E-21\t+\t.\tID=match%2477_2_50;Name=G3DSA:3.90.176.10;Target=Merlin_1 2 50;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t106\t165\t2.9E-21\t+\t.\tID=match%2477_106_165;Name=G3DSA:3.90.176.10;Target=Merlin_1 106 165;date=23-02-2015;status=T\n+Merlin\tPfam\tprotein_match\t7\t162\t1.9E-12\t+\t.\tDbxref=InterPro:IPR003540;ID=match%2478_7_162;Name=PF03496;Ontology_term=GO:0005576%22%2C%22GO:0009405;Target=Merlin_1 7 162;date=23-02-2015;signature_desc=ADP-ribosyltransferase exoenzyme;status=T\n+Merlin\tSUPERFAMILY\tprotein_match\t2\t48\t.\t+\t.\tID=match%2479_2_48;Name=SSF56399;Target=Merlin_1 2 48;date=23-02-2015;status=T\n+Merlin\tSUPERFAMILY\tprotein_match\t104\t164\t.\t+\t.\tID=match%2479_104_164;Name=SSF56399;Target=Merlin_1 104 164;date=23-02-2015;status=T\n+Merlin\tfeature\tpolypeptide\t1698\t2011\t.\t-\t.\tID=Merlin_3;md5=6b220b99a5d2dd40f55bb664a8dbdfb3\n+Merlin\tPfam\tprotein_match\t1912\t2011\t1.5E-8\t-\t.\tDbxref=InterPro:IPR010667;ID=match%24113_149_248;Name=PF06841;Ontology_term=GO:0005198;Target=Merlin_3 149 248;date=23-02-2015;signature_desc=T4-like virus tail tube protein gp19;status=T\n+Merlin\tfeature\tpolypeptide\t2716\t3066\t.\t-\t.\tID=Merlin_4;md5=bdb226d471fe35e28ce6a9ed4649a1f8\n+Merlin\tPfam\tprotein_match\t2725\t3066\t1.6E-150\t-\t.\tDbxref=InterPro:IPR024389;ID=match%24361_4_345;Name=PF11091;Target=Merlin_4 4 345;date=23-02-2015;signature_desc=Tail-tube assembly protein;status=T\n+Merlin\tfeature\tpolypeptide\t5144\t5317\t.\t-\t.\tID=Merlin_6;md5=c61e0e2dba259054b9c93fd931056fdd\n+Merlin\tPfam\tprotein_match\t5166\t5317\t1.5E-59\t-\t.\tDbxref=InterPro:IPR024342;ID=match%24360_21_172;Name=PF11110;Target=Merlin_6 21 172;date=23-02-2015;signature_desc=Baseplate hub distal subunit;status=T\n+Merlin\tfeature\tpolypeptide\t6052\t6431\t.\t-\t.\tID=Merlin_7;md5=b51a60ffef9f07b672e0d12d26d27bbc\n+Merlin\tSUPERFAMILY\tprotein_match\t6256\t6431\t.\t-\t.\tID=match%24227_199_374;Name=SSF69279;Target=Merlin_7 199 374;date=23-02-2015;status=T\n+Merlin\tSUPERFAMILY\tprotein_match\t6238\t6431\t.\t-\t.\tID=match%24228_5_198;Name=SSF69279;Target=Merlin_7 5 198;date=23-02-2015;status=T\n+Merlin\tPfam\tprotein_match\t6237\t6431\t4.3E-96\t-\t.\tDbxref=InterPro:IPR015181;ID=match%24229_4_198;Name=PF09097;Target=Merlin_7 4 198;date=23-02-2015;signature_desc=Baseplate structural protein,domain 1;status=T\n+Merlin\tGene3D\tprotein_match\t6320\t6431\t1.4E-54\t-\t.\tID=match%24230_3_114;Name=G3DSA:2.40.10.10;Target=Merlin_7 3 114;date=23-02-2015;status=T\n+Merlin\tPfam\tprotein_match\t6263\t6431\t3.9E-83\t-\t.\tDbxref=InterPro:IPR015180;ID=match%24231_201_369;Name=PF09096;Target=Merlin_7 201 369;date=23-02-2015;signature_desc=Baseplate structural protein,domain 2;status=T\n+Merlin\tfeature\tpolypeptide\t6931\t7180\t.\t-\t.\tID=Merlin_8;md5=78306f53371e5e47b051cad8a16b86e5\n+Merlin\tPfam\tprotein_match\t6985\t7180\t9.8E-56\t-\t.\tDbxref=InterPro:IPR024364;ID=match%24348_5_200;Name=PF12322;Target=Merlin_8 5 200;date=23-02-2015;signature_desc=T4 bacteriophage base plate protein;status=T\n+Merlin\tfeature\tpolypeptide\t7227\t7435\t.\t+\t.\tID=Merlin_9;md5=5ced4f78a57bd34e165ccf7b43ed3ef1\n+Merlin\tPfam\tprotein_match\t7231\t7433\t6.3E-63\t+\t.\tDbxref=InterPro:IPR024364;ID=match%24164_5_207;Name=PF12322;Target=Merlin_9 5 207;date=23-02-2015;signature_desc=T4 bacteriophage base plate protein;status=T\n+Merlin\tfeature\tpolypeptide\t7856\t7970\t.\t+\t.\tID=Merlin_10;md5=b0c491c633f373b9340ede7359636469\n+Merlin\tPfam\tprotein_match\t7863\t7956\t1.6E-17\t+\t.\tDbxref=InterPro:IPR007048;ID=match%2416_8_101;Name=PF04965;Target=Merlin_10 8 101;date=23-02-2015;signature_desc=Gene 25-like lysozyme;status=T\n+Merlin\tSUPERFAMILY\tprotein_match\t7862\t7957\t.\t+\t.\tID=match%2417_7_102;Name=SSF160719;Target=Merlin_10 7 102;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t7857\t7959\t9.3E-27\t+\t.\tDbxref=InterPro:IPR015801;ID=match%2418_2_104;N'..b'Pro:IPR023214;ID=match%24167_7_211;Name=SSF56784;Target=Merlin_302 7 211;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t166428\t166561\t5.5E-6\t+\t.\tDbxref=InterPro:IPR023214;ID=match%24168_78_211;Name=G3DSA:3.40.50.1000;Target=Merlin_302 78 211;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t166359\t166371\t5.5E-6\t+\t.\tDbxref=InterPro:IPR023214;ID=match%24168_9_21;Name=G3DSA:3.40.50.1000;Target=Merlin_302 9 21;date=23-02-2015;status=T\n+Merlin\tfeature\tpolypeptide\t167486\t167970\t.\t+\t.\tID=Merlin_304;md5=283a418fea20ac001bffdcbf72299ca8\n+Merlin\tSUPERFAMILY\tprotein_match\t167619\t167850\t.\t+\t.\tID=match%24122_134_365;Name=SSF56091;Target=Merlin_304 134 365;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t167834\t167952\t5.9E-8\t+\t.\tDbxref=InterPro:IPR012340;ID=match%24123_349_467;Name=G3DSA:2.40.50.140;Target=Merlin_304 349 467;date=23-02-2015;status=T\n+Merlin\tProSitePatterns\tprotein_match\t167827\t167850\t.\t+\t.\tDbxref=InterPro:IPR016059%22%2C%22Reactome:REACT_216;ID=match%24124_342_365;Name=PS00333;Ontology_term=GO:0003909%22%2C%22GO:0051103;Target=Merlin_304 342 365;date=23-02-2015;signature_desc=ATP-dependent DNA ligase signature 2.;status=T\n+Merlin\tPfam\tprotein_match\t167620\t167850\t9.0E-28\t+\t.\tDbxref=InterPro:IPR012310%22%2C%22Reactome:REACT_216;ID=match%24125_135_365;Name=PF01068;Ontology_term=GO:0003910%22%2C%22GO:0005524%22%2C%22GO:0006281%22%2C%22GO:0006310;Target=Merlin_304 135 365;date=23-02-2015;signature_desc=ATP dependent DNA ligase domain;status=T\n+Merlin\tProSitePatterns\tprotein_match\t167642\t167650\t.\t+\t.\tDbxref=InterPro:IPR016059%22%2C%22Reactome:REACT_216;ID=match%24126_157_165;Name=PS00697;Ontology_term=GO:0003909%22%2C%22GO:0051103;Target=Merlin_304 157 165;date=23-02-2015;signature_desc=ATP-dependent DNA ligase AMP-binding site.;status=T\n+Merlin\tGene3D\tprotein_match\t167803\t167833\t8.5E-8\t+\t.\tID=match%24127_318_348;Name=G3DSA:3.30.1490.70;Target=Merlin_304 318 348;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t167621\t167646\t8.5E-8\t+\t.\tID=match%24127_136_161;Name=G3DSA:3.30.1490.70;Target=Merlin_304 136 161;date=23-02-2015;status=T\n+Merlin\tSUPERFAMILY\tprotein_match\t167823\t167930\t.\t+\t.\tDbxref=InterPro:IPR012340;ID=match%24128_338_445;Name=SSF50249;Target=Merlin_304 338 445;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t167661\t167794\t1.2E-4\t+\t.\tID=match%24129_176_309;Name=G3DSA:3.30.470.30;Target=Merlin_304 176 309;date=23-02-2015;status=T\n+Merlin\tfeature\tpolypeptide\t169174\t169869\t.\t+\t.\tID=Merlin_306;md5=3f61e1cb18fb135a3dc061968bcd879c\n+Merlin\tSUPERFAMILY\tprotein_match\t169736\t169781\t.\t+\t.\tID=match%24253_563_608;Name=SSF56399;Target=Merlin_306 563 608;date=23-02-2015;status=T\n+Merlin\tSUPERFAMILY\tprotein_match\t169590\t169696\t.\t+\t.\tID=match%24253_417_523;Name=SSF56399;Target=Merlin_306 417 523;date=23-02-2015;status=T\n+Merlin\tPfam\tprotein_match\t169589\t169781\t1.6E-22\t+\t.\tDbxref=InterPro:IPR003540;ID=match%24254_416_608;Name=PF03496;Ontology_term=GO:0005576%22%2C%22GO:0009405;Target=Merlin_306 416 608;date=23-02-2015;signature_desc=ADP-ribosyltransferase exoenzyme;status=T\n+Merlin\tGene3D\tprotein_match\t169597\t169698\t2.1E-28\t+\t.\tID=match%24255_424_525;Name=G3DSA:3.90.176.10;Target=Merlin_306 424 525;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t169738\t169784\t2.1E-28\t+\t.\tID=match%24255_565_611;Name=G3DSA:3.90.176.10;Target=Merlin_306 565 611;date=23-02-2015;status=T\n+Merlin\tfeature\tpolypeptide\t171300\t171794\t.\t+\t.\tID=Merlin_307;md5=0f4b8b0843334ccf18e5a4a7cbdf67b2\n+Merlin\tSUPERFAMILY\tprotein_match\t171723\t171792\t.\t+\t.\tID=match%24339_424_493;Name=SSF56399;Target=Merlin_307 424 493;date=23-02-2015;status=T\n+Merlin\tGene3D\tprotein_match\t171722\t171791\t5.2E-11\t+\t.\tID=match%24340_423_492;Name=G3DSA:3.90.176.10;Target=Merlin_307 423 492;date=23-02-2015;status=T\n+Merlin\tPfam\tprotein_match\t171723\t171791\t2.0E-9\t+\t.\tDbxref=InterPro:IPR003540;ID=match%24341_424_492;Name=PF03496;Ontology_term=GO:0005576%22%2C%22GO:0009405;Target=Merlin_307 424 492;date=23-02-2015;signature_desc=ADP-ribosyltransferase exoenzyme;status=T\n' |
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| diff -r 000000000000 -r 2c9e5136b416 test-data/merlin.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merlin.fa Mon May 04 17:21:38 2015 -0400 |
| b |
| b'@@ -0,0 +1,2881 @@\n+>Merlin\n+TCGTTTAGACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACATTCGA\n+GCATAACGCAGAGAATAAGTTGTTCTATTTCAGAAACTACGTTTCAACTTCATTAAAGCC\n+TCTGATCTTTGGTGAATTTGGTCGTATGTTTATGGCACTAGATGACGATACTACAATTTA\n+TACTGCTGAGACGCCTGATGATTATAATCGTTTCGCAAACCCAGAAGATATAATTGATAT\n+TGGCGCTACTCAAAAAGACTCATTTGACGATAACAATAATGATGGAACATCTATTAATAT\n+CGGCAAACAAGTTAATTTAGGATTCGTTATTTCCGGTGCTGAAAATGTTCGAGTTATTGT\n+TCCAGGTTCTTTAACTGAATATCCAGAAGAAGCGGAAGTTATTCTGCCTCGTGGTACTCT\n+TTTGAAGATCAATAAAATCACTACTCAAGTAGATAAACGCTCGAATAAGTTCATGGTTGA\n+AGGTTCAATCGTTCCGCCTTCTGAGCAAATTGATGAATCTGTTGAGATTTATGACGGTGA\n+TCTGTTCATGGAAACAGGTGAAGTAGTAAAACTGTCCGGATTCATGCAGTTCGTCAACGA\n+ATCTGCATACGATGAAGAGCAAAACCAGATGGCTGCTGAGATTCTGTCTGGATTCTTGGA\n+CATTGATGACATGCCACGTAAGTTCCGCTAGCCGTTTACATCCACATGGAAGTGGATTAT\n+AATGGCTCTACGTTAACAAGAGGAAAACAACATGAAATCAATTTTTCGTATCAACGGTGT\n+AGAAATTGTAGTTGAAGATGTAGTTCCTATGTCTTATGAATTCAATGAAGTTGTTTTCAA\n+AGAGCTTAAGAAAATTTTAGGCGATAAGAAGCTTCAAAGTACTCCAATTGGACGTTTTGG\n+AATGAAAGAAAACGTTGATACTTATATTGAAAGTGTAGTGACAGGGCAGTTAGAAGGTGA\n+ATTTTCTGTAGCAGTTCAAACTGTAGAAAATGATGAAGTTATTTTAACTTTACCAGCTTT\n+CGTAATTTTCCGCAAATAAAACAATGGGGAGCTATGCTCCCCATTTTTACAATCCAAGTA\n+TTTTCGAAGTAGAGTTTCGGGTCGAATTAATGACGTGAGACAACCCTCCAGCAGCTCCTC\n+CAAGTCTAGATAATCTACTTAAACTTCCATTAAGAGACATTTCACTATTAATTCCAGTTA\n+TAGAATTAACAGCTCTATCTTCAATCCAATCAAGAGCAGCTTGACGTCCAACAGCACCCG\n+TTTGCATTACTCTGTAAGCAAATGTAACATCGAAAACCGCAATTTGGTTATCTCCTTCAT\n+ATGTAAGCTCAGGAGCTCCACACGCAACAGGAACACAACCTGTGAACATTATCACAGTAT\n+GAGGTAATCCATTTCGAGCATGAAGGTTAACCTGAATGTCAGCTTCGACGTCAGTTGGTA\n+ATGCTCGCAATCCAGTAACCGGGTCTTGAACGGAGTTCACCCAATCTTGCATTGCACGAT\n+AGTTACTTGCTTCGGGATCCATTCTGAATGATATAGTTAACGGATCGAGTTCACGTCCAG\n+TTATTCTAATATTCGGTGAGTTATGGTTGAAATCCATTTCATGAGACAATCTGTTCTCTG\n+GAATTTTGACCGAATAAATCATCAATCCAGATTGCGGATAAGCCATGTTAAAGAAGTCTA\n+ACAAATAAGTTCCGACTTCAAATTCACCTAATAAAGACTGAACAACACGATTGCTCATTG\n+CTCCAATAAGATATTTCGATACACCAGACTTTCTTACCAGCTGTTGAGTACCGGCAGTGA\n+TAATTGAGGTGAGTCCTGATGTGAACTCACCTTGTGTTAATCCAAGCCAGTCATTATTCA\n+ACGGAAGGTTATTAAAGAGCATACCGCCAAATTGATCGAGTAATTGTTGAGACTTTGCTG\n+ACGGAGTAGTTGCAAATACACAACTAAACATATTAGTACGCTGAAAGTCTATATTACCCG\n+CTTGGTTTTTAAATTCATCTAAAGTTAGCATCAGAATCCTTCCGCATATACTGAAGCTCG\n+GTTCAATGTCAAGATTTCACGCATAGTAATTTCTAATGTGAATGTACTTGGCAGGTTTGG\n+AGCTATAGCTAAACCGTTAAAGTTTCCATTTGGAGTTTTATCAAAACGGATACTCTGAAT\n+TTGACATGGACCGAATACTTCAGCACGTCCATCGAATTTACTTGTGGTTCCAAAGTTTCT\n+GACGAACCACACAGTAGGGTTACTTACAACAATAACATTACTTAAGAATGAAGTTATTTT\n+CTCAAAAACAGTGTCATTTTTATTAGCTTCATCTGGAGTTAATGTATCAAGGAAAGTTGA\n+TTTATACCATTCATCTAATTGAGACTTAACTTCTTTTGCATAAGTAGACGTTCCCGTTTC\n+GCCATAACTATAGTAGTTAAAGTATTCATAGATCTCGATAATAGCAATAAGATCTTGTAC\n+TGATCGAGGAGTTAAATCCCACGTGAATACCTTCGTACGGTTATCTGCGCCGCCATACAT\n+TGATCGAGCAGTGTTATAGATCTGCTCGTTATGGTCAGCCATTAATCCTTGAGTCAATGA\n+CTCTAATCCGCCAAAGACAGCAGTAGATGCAACGTTACTTAATACCCCTGTAGCAGTACC\n+GCCGCCACGAGAAATAAGTGAATCTCCAACGTCATTAAATTTATGAGAAACTGATTCAAC\n+ATCTGATTTCGAGCGTGGAAGTAAAATATTCACTACTGGAATTTTATCAACTTTATTAGT\n+ATTTGTTCCAGTGATTGATTTCACTACACTATTTGCAGTACGTTTCATTTCACCTAAACG\n+CATGCTACGCATATCACCGGTTGTACGAGAATTCATATCATACGCAGTGAACAACAACCC\n+GTTCTTATAAAGATCATGAACTCGTAAAGAACCAGATGTGTCATTACCAGCTGAACGTTC\n+AGACGGATATTGCGCAGTTATAGTGGATTTTATTTTTGCTGATTGTGAACTTTGACCAGC\n+GGAGGTTTTAACTCCGCTAATTAAAGCATCAGTCTTATCATCTAATTCTCTGACTTTAAT\n+GCTCATTAATTAACTCCTGTTGCCCCGAATACTCCAGGAGCTGGAGTAGCCGTGACTGTT\n+TGAACCTGGTGAATAGTCTTACTATTATTTACGTTATTAACCTGAGTGTTAGCAACATTC\n+ATATCACCGGTTGATTTTTTAGATTGCTCTTTAGCATTTTCAGCTTTTTGAATATTTTGA\n+ACTCGTTGATTATCTTCCGAAGTAGCTGGAGCCGCAGGCTTCGGAGTGTTATCTTCTTTG\n+AGCTTCTGATACTTGGATTCTACTCGTTGGAATCTTTTATCGAGTTCCTTTTTAGTAGCT\n+GGTTGATCACTTATAGCAGAATCACTAATAGACTTTTTGGCACTGTTATATGCCTTCTCT\n+AAAGATTGCATATTAGTTGGATTCTCTGGATCAACATCACCAATATATTTTTCTAAACGC\n+TGAACAGCTGCACGAGCTTCGTTTTGTTTGATCAGTGTTTCTTCGCGTTTTTCAGGAGCC\n+ATTGCTTTAAGATTCTGAGTCTCTTGATCACGGTCAGATGCTTGTGTAGAATCGATTTTA\n+TTCTCTCTTCCTAGTACCCAATCAAATGCACGAGTTTTAAATTCGCCAGCTTTATCAATA\n+ATTCCAGGACCTTCTTCAATACGCTTACTCTGATATTTAGCCAAAGCTTTTTGATCATCT\n+TCAGACAATGAATTACCAGTGCGTTCCTGGAATCCTTCTAGTGCTGAACCACGAATAGTA\n+GTTGCTGCATTTTCAAAGCCAAGTGCATCGAGTATAGAAGCAGATATCTTTGAAATTCCC\n+AA'..b'ATTTCCATGAGGTTACTGGGTTATGAGTTATAAAATTCTTTT\n+AGAAGTTACCGTGATGTCTTCGACTGGACATGTGGCGGTTAGTACTGAACAGCTGGATTT\n+TTATAGCTGGGATAATGCTAATATGTATTATGAAGCAGTAGAAGTTTATGAAGAAACGCC\n+AGATATTAAAGTATGGCGTCAAGTAACAAAACTTTATTAAAGCCCTTCGGGGCTTTTGTT\n+GTCTATAAATATAGTAAACTATAGAGGACTTTTTATGATCGAATTAAATGAAGTCTTCGA\n+TGAAGGGAAAGAACGTCTAGCAGTTACGAACCTTTATCCGAAGCTCAAGATTCCACAAAT\n+TTTTGCAATAGACAACACTAAAGTAGCTTATCGTATGTGCTCATATACTGGTGGTGGAGA\n+TGCAAATAAAAACATCAAACCCGGTGATAAAATGATGCATGTCATTGCATTAGGAGTTAC\n+TGATAAAGGCCTTGGTCAACTTAAGACCTTAGGTGATAATCCAATTGCTGTTATTGATAC\n+AATCTTTAACCACGTAATGGGTATCATGAAGTTTTATCGTTTTGACGCTGCTTTATTTCG\n+TGTTAAAAAGAATAAAACTGGTGGAGCAGGTCGCCAGATGCAAGTTATTGTTGATCGTCT\n+AATCAAGAAGAAAGGCGGTGGCAAATTCGTTATGCTTAAAGAGTTGTATGATTTTGATAA\n+GAAATACAACTACATTTTAGTATACAAGAAGAATGCTGATCTTGTCAATATCCCTGGAAT\n+GACTGAGATCATGGACTCAATTTATAAGAAAGTAGACACTGATGTAGGTGATGCTTATAT\n+CAACGTTGAGACCGGCAAACAAGTATCTAAGCTTGAAGCTATCGCGGGTTCAATCGCAGC\n+AGAAAATGATAAACGCTCAGACCAGGCGGTTGCGTCTCGAGCTAAAATATCTCGTCGTGC\n+TTTAATGGCTTCTCAATATTCAATCCAAGTGGGATTTGATACTCGTAAAGATGCGGTAGA\n+ACATGATAAGCGATTAGATGTAATTAACTCTAAACCTCCGGTTTATTTGACAGATAAGTC\n+TTCTGACCAAGTATCGAATATTCAAATGGCTATTGATAATTTCAGAAATGATTCTCAATC\n+AATTGCTAAAACCGGCGAAGCGTTTAAGACATTTGACCCGTCATGGAAAATGGATGATGA\n+TCGTCATTCTACTGGTACAATGAAAGCCCAAGAACTTGTTCTAAGGCTCACTAATATATT\n+AACCAGTGGAACAGTAGACGATTTCAGTCAACATCCTACTGATAGAAGAGAAGCATTTAA\n+AACATTAGCGGTCAGAGACATTTATCGTATTGGTGAAGCCTGGTCTAAATTAGAGCCTAA\n+TGACTATTATGGTGCTATTAAAGAACTTACTCGAGTCGCAATGGAAGACAAAGAATGGTC\n+TTCTGATGCAAATCGTGAATACGCAGTAAAAGAGATTGTAGAATTAATTTCTAAACAGTT\n+CTCTGATTTAGCAGCTAGCATGTACAAAAATACATCAGATGTGGATCGTTATACTCCGGT\n+ACAATTGTCAGGTTTACATGCTTACGTCGGTTCATCTTATAAGTACATCAACGACTATCT\n+TTTAGGCCTTGATGATTATGGCAAAGAAACTGTTGAAAAATGGATTGAGTCTATCGATTC\n+TGCGTTTGAAAATGGTGTTCGTCTTCCGAAGGGAACTAAGCTATTTCGAGGTCAACATAC\n+TAAGCGCGAAGCTATTGAAGTTAGTTTAGAAAACAAGCACTTCTATTTCAAGAATTATGT\n+GTCAACTTCAATGGCTCCTATTATCTTTGGTGGATATGGACGAGCATATGATGCAATGGA\n+CCCCGCTGCATTGAACACAGATACATCGACTCCTAAAGAAGTGCTTGACTCTGTTTCAAC\n+TGTTCGGCCTGATAGTATTACTAACTCTGAAATGGGTGAATTGCGTTTAGCGTTCGTTAT\n+TTCTGGCGCAGAGAAAATAAAGACTATCGTAACCAATGCTGGAATCTCAGGATTGTCATT\n+TGAAGCTGAAGTTATTCTTCCTCGTGGTACTGTTCTTAGAATTGATAAAATGTATGGAAC\n+AGCTCAGAAACTTCAAGCTAATGACTACACAGCATCAAAGAGTGTTCTTATGGAATGCAC\n+TGTAGTATCTCCAGAACAATTATCTGAAACTACAATTTATGATGGCGATAAATTGTTAGA\n+AGGTGAATTGGTTGAATCTGATTATTCGTTCAGTTCTTTTATTGGTCAATTAAATGAAGC\n+TAAAGTTGAAACACCAGATTGGTTAGGTGAAGCTCTAGCATCATTTGTTGACATAAATAA\n+TTTACCAGAACGATTCATAAATTAATATTTTCACATGGACGTGAATTCAGAGAGGGCTTT\n+ATGGAAATTTTAAACGAAGTACTAGACGAAAGTAAACTGGATTTACCAGTTACGAACCTT\n+TATCCAAAGACGAAAATTCCACAAATTTTTGCTATTCAAACTAACTCCGAGGGTTCACTG\n+CCAGCATTCAGGATGTGTTCATATACATCTGGCGGTGATACCAATAAGAACGTTAAACCT\n+GGCGACAAAATGATTCATGTTGTTATGCTATCATTGAGCGAAAAAGGATCATTAGTTAAG\n+CTTAAAAACTTAGGCGGCGATCCAATTGGTGTTATCTCTACTACGTTCAATATCGTTTAT\n+TCAACGATGAAGCAGTATAAAATGGACGCATGCTTGTTCCGAATGGCCAAAAGCAAAATC\n+GGTGGACAAGCTCGTCAGATGCAGGTTATTATGGACCGACTCGTACGTTCTCGTACTGGT\n+GGTAAATTTGTTATCCTGAAAGAACTCTGGGATTATGATAAGAAGTACGCATATATTCTT\n+ATTCATCGTAAAAATGTTGATCTCTCAACCATCCCTGGCGTCCCAGAGATTGATACTGGA\n+CTGTTCACTGCAGTTGAAACTAAAGTTGGTGAAGTTTATGTTGAAAAGAAATCAGGTCAA\n+CAAGTAACTAAAGCCCAAGCCGTTGCTGCTTCTATTGCAGTCGAAAACGATAAGCGTTCA\n+GATCAAAACGTTATTTCTCGTGCTAAGATAAATCGTCGTCAAGCTATTGCTGCTCAGTAT\n+TCTGTTGATGCATCTAGCATCCAAGGCGATGATCGTGCTGCTGAAGAATTTAAACGCTTA\n+GAAGCTAAAGTTCCAGTTAAAAGCTCTAAAGGCGCTGAGTCATCAGACATGGTAGCAAAA\n+GTTAATACCATCGCTGACCGTCAAGGAAATGAGTATATCGGCAAAGTACTAAACTTCATC\n+ACTAATCCTGAAACATCTCAGGACACAGATGGTAAAGCATTGACTGCACGAATAGGTCAA\n+TTGCGCCAGTTATCTAAAATGCCTAAAGGTGCCATGTTATCAGGTGGATTTGAAACTGGT\n+GGTATGAAGTACTACATGGAAAACCAAAAAGAAATGTACAATGAAGTTCGTTCATTTGCT\n+CGATTGATAGCTGGGGTGAATACAACTAACTCCTTTCAGACGATGAAAGATTTAGTTAAA\n+ATGGCTTCAGCTGGAACTAGACCTGAAGATCGTGAACAGTTAATTGCAAATTTAATTGGA\n+TTAGCTTATAAAGAAATAAGTGCAATCATCAGAGATTCATACCAAACTGCAGCAAGTTTA\n+TCTAAAGAGAATGATCATTATTCTAAAGATGAAAAACAAGCTATCAGTGAATACTGCGCA\n+AACGCTTTCGAATACGTGAATATGTTCTTAATCGGTAAGCCGGAAGAAGGGTATTCAACT\n+TCTGATTCTCTCGAGATCATCGATAATATGGACTCTGCGTTTGAAAAAGGAACTCGTTTA\n+GACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACA\n' |
| b |
| diff -r 000000000000 -r 2c9e5136b416 test-data/merlin.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merlin.gff Mon May 04 17:21:38 2015 -0400 |
| b |
| b'@@ -0,0 +1,1231 @@\n+##gff-version 3\n+##sequence-region Merlin 1 172788\n+Merlin\tannotation\tremark\t1\t172788\t.\t.\t.\tgff-version=3;sequence-region=%28%27Merlin%27%2C 0%2C 172788%29\n+Merlin\tGeneMark.hmm\tgene\t2\t691\t-856.563659\t+\t.\tID=Merlin_1;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t2\t691\t.\t+\t.\tID=Merlin_1_mRNA;Parent=Merlin_1;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t2\t691\t.\t+\t.\tID=Merlin_1_exon;Parent=Merlin_1_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t2\t691\t.\t+\t0\tID=Merlin_1_CDS;Parent=Merlin_1_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t752\t1039\t-339.046618\t+\t.\tID=Merlin_2;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t752\t1039\t.\t+\t.\tID=Merlin_2_mRNA;Parent=Merlin_2;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t752\t1039\t.\t+\t.\tID=Merlin_2_exon;Parent=Merlin_2_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t752\t1039\t.\t+\t0\tID=Merlin_2_CDS;Parent=Merlin_2_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t1067\t2011\t-1229.683915\t-\t.\tID=Merlin_3;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t1067\t2011\t.\t-\t.\tID=Merlin_3_mRNA;Parent=Merlin_3;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t1067\t2011\t.\t-\t.\tID=Merlin_3_exon;Parent=Merlin_3_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t1067\t2011\t.\t-\t0\tID=Merlin_3_CDS;Parent=Merlin_3_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t2011\t3066\t-1335.034872\t-\t.\tID=Merlin_4;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t2011\t3066\t.\t-\t.\tID=Merlin_4_mRNA;Parent=Merlin_4;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t2011\t3066\t.\t-\t.\tID=Merlin_4_exon;Parent=Merlin_4_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t2011\t3066\t.\t-\t0\tID=Merlin_4_CDS;Parent=Merlin_4_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t3066\t4796\t-2177.374893\t-\t.\tID=Merlin_5;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t3066\t4796\t.\t-\t.\tID=Merlin_5_mRNA;Parent=Merlin_5;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t3066\t4796\t.\t-\t.\tID=Merlin_5_exon;Parent=Merlin_5_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t3066\t4796\t.\t-\t0\tID=Merlin_5_CDS;Parent=Merlin_5_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t4793\t5317\t-682.565030\t-\t.\tID=Merlin_6;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t4793\t5317\t.\t-\t.\tID=Merlin_6_mRNA;Parent=Merlin_6;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t4793\t5317\t.\t-\t.\tID=Merlin_6_exon;Parent=Merlin_6_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t4793\t5317\t.\t-\t0\tID=Merlin_6_CDS;Parent=Merlin_6_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t5289\t6431\t-1457.525863\t-\t.\tID=Merlin_7;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t5289\t6431\t.\t-\t.\tID=Merlin_7_mRNA;Parent=Merlin_7;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t5289\t6431\t.\t-\t.\tID=Merlin_7_exon;Parent=Merlin_7_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t5289\t6431\t.\t-\t0\tID=Merlin_7_CDS;Parent=Merlin_7_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t6428\t7180\t-968.015933\t-\t.\tID=Merlin_8;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t6428\t7180\t.\t-\t.\tID=Merlin_8_mRNA;Parent=Merlin_8;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t6428\t7180\t.\t-\t.\tID=Merlin_8_exon;Parent=Merlin_8_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t6428\t7180\t.\t-\t0\tID=Merlin_8_CDS;Parent=Merlin_8_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t7228\t7857\t-809.330137\t+\t.\tID=Merlin_9;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t7228\t7857\t.\t+\t.\tID=Merlin_9_mRNA;Parent=Merlin_9;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t7228\t7857\t.\t+\t.\tID=Merlin_9_exon;Parent=Merlin_9_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t7228\t7857\t.\t+\t0\tID=Merlin_9_CDS;Parent=Merlin_9_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t7857\t8252\t-515.006678\t+\t.\tID=Merlin_10;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t7857\t8252\t.\t+\t.\tID=Merlin_10_mRNA;Parent=Merlin_10;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t7857\t8252\t.\t+\t.\tID=Merlin_10_exon;Parent=Merlin_10_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t7857\t8252\t.\t+\t0\tID=Merlin_10_CDS;Parent=Merlin_10_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t8340\t8753\t-522.529341\t+\t.\tID=Merlin_11;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t8340\t8753\t.\t+\t.\tID=Merlin_11_mRNA;Parent=Merlin_11;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t8340\t8753\t.\t+\t.\tID=Merlin_11_exon;Parent=Merlin_11_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t8340\t8753\t.\t+\t0\tID=Merlin_11_CDS;Parent=Merlin_11_exon'..b'rlin\n+Merlin\tGeneMark.hmm\texon\t164715\t165071\t.\t+\t.\tID=Merlin_297_exon;Parent=Merlin_297_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t164715\t165071\t.\t+\t0\tID=Merlin_297_CDS;Parent=Merlin_297_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t165107\t165601\t-618.360781\t+\t.\tID=Merlin_298;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t165107\t165601\t.\t+\t.\tID=Merlin_298_mRNA;Parent=Merlin_298;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t165107\t165601\t.\t+\t.\tID=Merlin_298_exon;Parent=Merlin_298_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t165107\t165601\t.\t+\t0\tID=Merlin_298_CDS;Parent=Merlin_298_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t165612\t165773\t-191.091430\t+\t.\tID=Merlin_299;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t165612\t165773\t.\t+\t.\tID=Merlin_299_mRNA;Parent=Merlin_299;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t165612\t165773\t.\t+\t.\tID=Merlin_299_exon;Parent=Merlin_299_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t165612\t165773\t.\t+\t0\tID=Merlin_299_CDS;Parent=Merlin_299_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t165770\t166000\t-285.030914\t+\t.\tID=Merlin_300;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t165770\t166000\t.\t+\t.\tID=Merlin_300_mRNA;Parent=Merlin_300;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t165770\t166000\t.\t+\t.\tID=Merlin_300_exon;Parent=Merlin_300_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t165770\t166000\t.\t+\t0\tID=Merlin_300_CDS;Parent=Merlin_300_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t165997\t166191\t-241.609251\t+\t.\tID=Merlin_301;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t165997\t166191\t.\t+\t.\tID=Merlin_301_mRNA;Parent=Merlin_301;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t165997\t166191\t.\t+\t.\tID=Merlin_301_exon;Parent=Merlin_301_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t165997\t166191\t.\t+\t0\tID=Merlin_301_CDS;Parent=Merlin_301_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t166352\t167200\t-1091.167753\t+\t.\tID=Merlin_302;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t166352\t167200\t.\t+\t.\tID=Merlin_302_mRNA;Parent=Merlin_302;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t166352\t167200\t.\t+\t.\tID=Merlin_302_exon;Parent=Merlin_302_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t166352\t167200\t.\t+\t0\tID=Merlin_302_CDS;Parent=Merlin_302_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t167197\t167433\t-294.645060\t+\t.\tID=Merlin_303;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t167197\t167433\t.\t+\t.\tID=Merlin_303_mRNA;Parent=Merlin_303;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t167197\t167433\t.\t+\t.\tID=Merlin_303_exon;Parent=Merlin_303_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t167197\t167433\t.\t+\t0\tID=Merlin_303_CDS;Parent=Merlin_303_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t167487\t168944\t-1811.170385\t+\t.\tID=Merlin_304;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t167487\t168944\t.\t+\t.\tID=Merlin_304_mRNA;Parent=Merlin_304;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t167487\t168944\t.\t+\t.\tID=Merlin_304_exon;Parent=Merlin_304_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t167487\t168944\t.\t+\t0\tID=Merlin_304_CDS;Parent=Merlin_304_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t168941\t169120\t-220.159549\t+\t.\tID=Merlin_305;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t168941\t169120\t.\t+\t.\tID=Merlin_305_mRNA;Parent=Merlin_305;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t168941\t169120\t.\t+\t.\tID=Merlin_305_exon;Parent=Merlin_305_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t168941\t169120\t.\t+\t0\tID=Merlin_305_CDS;Parent=Merlin_305_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t169175\t171265\t-2617.092758\t+\t.\tID=Merlin_306;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t169175\t171265\t.\t+\t.\tID=Merlin_306_mRNA;Parent=Merlin_306;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t169175\t171265\t.\t+\t.\tID=Merlin_306_exon;Parent=Merlin_306_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t169175\t171265\t.\t+\t0\tID=Merlin_306_CDS;Parent=Merlin_306_exon;seqid=Merlin\n+Merlin\tGeneMark.hmm\tgene\t171301\t172788\t-1876.322043\t+\t.\tID=Merlin_307;seqid=Merlin\n+Merlin\tGeneMark.hmm\tmRNA\t171301\t172788\t.\t+\t.\tID=Merlin_307_mRNA;Parent=Merlin_307;seqid=Merlin\n+Merlin\tGeneMark.hmm\texon\t171301\t172788\t.\t+\t.\tID=Merlin_307_exon;Parent=Merlin_307_mRNA;seqid=Merlin\n+Merlin\tGeneMark.hmm\tCDS\t171301\t172788\t.\t+\t0\tID=Merlin_307_CDS;Parent=Merlin_307_exon;seqid=Merlin\n' |
| b |
| diff -r 000000000000 -r 2c9e5136b416 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 04 17:21:38 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="jbrowse" version="1.11.6"> + <repository changeset_revision="d5ab749c9e97" name="package_jbrowse_1_11_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |