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Changeset 0:d723eb657f1d (2016-01-25)

Next changeset 1:6bbce76c78c1 (2016-12-15)

Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty

added:
test-data/Extract_Genomic_DNA.bed
test-data/translated_bed_seqs.bed
test-data/translated_bed_seqs.fa
test-data/translated_bed_sequences.bed
test-data/translated_bed_sequences.fa
tool_dependencies.xml
translate_bed_sequences.py
translate_bed_sequences.xml

diff -r 000000000000 -r d723eb657f1d test-data/Extract_Genomic_DNA.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Extract_Genomic_DNA.bed Mon Jan 25 12:21:21 2016 -0500

b'@@ -0,0 +1,7 @@\n+15\t40902459\t40907576\tJUNC00019210\t1\t+\t40902459\t40907576\t255,0,0\t2\t36,38\t0,5079\tCTCATATGAAAATAGTGAGAAAGTCAGAAATGGAAGGTAAGTATGTTACTATAATTCCTGCTAAATCTGCTTTTTAAAAAATTTTACTGTAGCTATCTAACCAGACAACTAATATAACTTATTGTCTATCTTATTGCTTAAAAAATATATGATGGGCCATGCATAGTGGTTCACACCTGTGATCCCGACACTTTGGCAGTCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCAAGACCAACCTGGATAGCATAGTGAGATTCTGTCTCTACAAAAAATAAAAAATTAGCCAGGTGTGGGGGTGCATTCCTGTAGCCCCAGCTACTCAGGAGGCTGAGGTGAGAGGATCACTTGAGTCCAGAAGATTGAGACTGCAGTGATTGCACCAGTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCAAAAACAAAAAAAGTATACCTTGAGTCTTGGGAGTAGAGAGTAGAGTGGATAGTAAGTAAATTTATTTATTTATTTATTTTGAGACGGATTTTCACTGTTGTTCCCCAGGCTGCAGTGCAATGGTGCCATCTCAGCTGCAACTTCTGCCTCCTGGGTTTAAGCGATTCTCCTGCCTCAGCCTCCCAGGTAGCCGGGATTACAGGCATGCACCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATATTGGCCAGGCTGGTCTCGAACCCCTGGCCTCAAGTGATCCGCCTGCCTTGGCCTCAAAATGCTAGGATTACAGGCGTGAGCCACCACGTCCAGCAGTTAATAATTTTTTTAAATGTTGTTAATGTCCTTAAGTAATTTTTTAAAAATTTTATTGTATTTTTTTTTTTTTTGAGACAGAGTCTTGCTTGCCCTGTCGCCCAGGCTAGAGTGCAGTGGTGCGATCTCGGCTAACTGCAATCTCTGCCTCCCAGGTTCAAGCAATTCTCCTACCTCAGCCTCCTGAGTAGCTGGGATTACATGTGCACGCCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTGGTCAGGTTGATCTCGAACTCCTGACCTCGTGGTCCACCCGTCTCGGCCTCCCAAAGTTCTGGGATTACAGGCATGAGCCACCGGGCCCAGCTGTCCTTAAGTAATTTTTCTAATGCTTTATCAGTGTATCCTTGGACAAATTTAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATCTTCTTTTGATACAGTAAGTAATATTCAAATTATATTTAAAAAGTTATAAATTAATATTATTTTTATTTCTTATTTTTGTGTTCCTTTTGTGGAATACTTAGGATTAATTCAGAAAACCAGTTATTTGCAGAATTTAGTATACTGCTATATCTGATTAATATGGCCATTGTACTGTTTATAGTTTTAATAGTGATGAAACAATATAATATATAAACCTTTATATTTATTAACTAATATAAAACAATAGATAGCAAGTCTTTAGTTTTTTTATTAAATTAATCTTTCTTATAATATTATTACATAGAAAGGCAAATACCAGTAGCTCTTCAACAAATGAAAAGATGGTTATCTTTATTCATCATAAGAGAAGTACAGATTTGATTATATTGAGATATTTTTGGCTGGACGTGGTGGCTCATGCCTGTAATCCGAGCACTTTGGGAGGCCGAGGCTGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGATGAAACCCCATCTCTACTAAAAAAATACAAAAAATTGGCCGGGCACAGTGGCTTACGCCTGTAAACCAAGCACTTAGGGAGGCTGAGGCGGGTAGATCACGAGGTCAGGAGATCGAGACCATCCTGGCCAACGTGGTGAAACCCCATCTCTACTAAGAATACAAAAATTAGCCAGGTGTTGTGGTGGGCGCCTGTAGTCCCAGCTACTCAGGAGGTTGAGGTAGGAGAATCACTTGAATCTGGGAGGTAGAGGTTGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAACAAAAAAAACCCCAAAAAATTAGCCAGGTATGGTGGCACTGTGCCTGTAATCCCAGCTACTCAGGAGGCCAAGGCACGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATCATGCCCCTGCACTCCAACCTGGGCAGCAGAGCGAGACTCTGTCTCCAAAAAAGAGGTTTTTTTGCTGTTGTTGTTGTTTGTTTGTTGTTTAGACGGCATCTTCCTCTGTCGCCAGGCTGGAGTGCAATGGTACGATCTTGGCTCTCTGCAACCTCCGCCTCCTGGGTTCAAGTGATTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCACGCCTGGCTAATTTTGTTGTATTTTTAGTAGACACGGGGTTTCACCATGTTGGCCAGAATTGTCTTGGTCTCTTGACCTCGTGATCCGCCCACTTTGGCCTCCTAAAGTGCTGGGATTACAGGCGTGAGCCACTGTGCCTGGCCTAAAAAAGAGATATTTTTATCCAGTCAGTTAAGGAAATAGGTAAAAAGTCACTCCGTGCTAGTGGGAGTATAATTTGTAGAAGGCAACTTGGTAATATCGTTCAGAATTTTAAATGCACATGCCCTTTGACTTCAGTTTTATGTCTGGAAATTATCTCACCAATATACGTGTAAATGTTTGAAATGATGAATAGATAAGGTTATTCACAGCAGCGTTTATTATAATAGTAAACGTTGTGAAAGGTCCTGAAGGTCCATCAGTAAGGGCCTGGTTAAATAAATTGTACATTTTCCATATAATTGACTATGCAGCCGGAAAAAAAATTTTATGCTAAATAGAGAAATCTCTAAGCTATATTACTTAAGATAAAAAGCAAGACGCAAAACAAAGTATATCATGTATTACCACTTGGGTAAAACAGGGAAGAAGAAAAGCGTGTGTGTGTGTGTGTATCTTCTCGTGTGTGTACATGTATAATGTATGTATATGTAGTGACTTATGCATATATATGCATAATATCTCTGGAAGAAACTAGTAAGATTGCCTACAGAGAAAAGAACCTTGCTATAGGTTACATGTTGGCTTTGTGGTTTATTAATTTAAAACCATATGAAAGTATTACCTATTACATTCTTAAAATTGTTGAAACGAAGAAATGGAAGTAATAGTAGTCATGGTTTAGAAAAGGTACAGAATCAACTCCAACAGAACTTAAAGGAAAAATAATTTTTTAAATAAAAAGGTACAGAAGTATATACATTGAAAAGTAAAAATTATTCCCTCTTTCCCTCTTCTTTCTTTTTTGTGAGACGGGGTTTCGCTCTTGTTGGCCAGACTGGAGTATAATGGCATGATCTTGGCTCACTGCAACCTCAGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTAGGACTACAGGTGTGCACCACTACACCTGGCTAATTTATTTTATTTTTATTATTTTATTTTATTTTATTTTATTTTGAGATAGAGTCTCGCTCCGTCACCCAGGCTGGAGTGCAGTGGCGCCATCTCGGCCCACTGCAAGCTCCGCCTCCTGGTTTCACGCCATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGCGCCTGCCACCACGCCTGGCTCATTTTTTTGTATTTTTAGTAGAGACAGGGTTTCACTGTGTTAGCCAGGATGGTCTCAATTTCCTGACCTTGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGCCCCCCTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTGTGCAGGCTGGAGTGCAGTGGCCTAATC'..b'ATTTATAGTAATTTCTTAGTATCTAATAGCCAGTCCATATTCAAACTTCCCGAATTGAGGAATTTATTTTTAATTAAGATGGTATTAAATAATTACACTTGGTGAGATAATTCTTTCTTGATGTTTTTCTCCCTGACCTTCTTTCTTAAAATTGAAGCCTACAGACAAGATGAACACAATAAACATTCATATATTTTTCAACTTGATAACCCAAAAGGTGGCTGATTTGCCACCTTTTTCTTTTTCTTGGATATACCATTTGAAAGTAGATTGTAGATAAAAGTCCTATTTTAATGCTATTTTTATAAGTGACAAACAGTACAGAAGACAGGCCACATGGTAATGCTCATAGATATTCTAAGTAGATATACCTATTTTTCAAAAAGGAAGACACATTTATTTGAGGAAATGCTGATGAGTTGGCAGCATTCCCTATAATAATTCTTAGAAGACTATGCTCCATCAGAGCAAGAGCTGTGTATCTCTCTTTTCATTATTTTATTCCAGTGCCTGATTGTCTATTGACCTGAATCATTATTTGTTAATAAAAGGTCATGGGGCAGGAAGAATGCCTAAGGATAACTGTCAGCTGGGACTTGGGGACTCGGTTCAACATCCAAGTTCAAGTACTAGGGTCCTAATCATGTTAGACATATACCTCACCACCTGTGACAAATTTAGAGACTTATTTGAGAAGTATAGGGACAAACTGTAAAAATATTTATTTATATGGTGTAGTTTTAAAGTAGAAAAATTAAATATATAGTATTATCTTCTTTAAAAAAATTAAATATATAGTATTATCTTCTTTAAAAAAGAAATCAAGCCAATAATAGTTTCCCATTTCTATCACCAAGCTGAAAAAGTTAAAACATTTCCAAATAAAACAATGTTAACTTTAATCTCATTAAAGTCAAAACGAGTTTATTCAAGTCAAAAGATAAAACAGATTTGTCATCTACCTCTTGAGTTGCTATTTTACGATTTAGTTCAGCTACTTTGGAAGAAGAATTTTCTACTGCATTTTGGCAAAGGAGTTTCTCTATTTCTCTCTGATGAGATGCTTTGAGGGATGCAATGTGTGCTGCAGTATCTTCCTTGACCCTACAGAGCAAATGAAAGAAAACCACACATAAAAGTGGCTCTTCAACCTCTAATTCAGAGTTAGCACAAAAACAGTAGAAGAAACCTGGGAATTAAGCAAGGGGAAAATGGGCACCAATATTAACTGCACTGTGTTAGGTGCTTTATACATTACTACTGCCTATGAGTTCTTATGACCAATCCATGAGCTACTATTTACTGAATTTTATAAGGGCAAACTTGAGGAAATAGTGATATATCTCTACTTTACCCCAACCTGAGGCTACACTTTCTGAGGGAATCTAGGGTTCCAAAAGCAAAGCACTTGACATTTGATCTTTTAAGATAAACTCAGATTTCTTGCCCAGATGCTTCTTTGGAAAATCACAGCTGTTCCCTTTAGAATCTCCAATGCCTTGTAGGCAGCATTAACCAATTTTCAACCCATGCATGAGACTCCAGGGCTAGTTGCATATTGTGAGAATGAGACAATCTTTATGGTAATTCTCAGGACATATTATGCTTGTAATATGCAATTAATTAATTGGACTGTAAGTGTGAAAGACTATTCATTTGTCTCTGTGATAAAATTTATTCAGAGGCAGTTCAGTAAATGGTTAAAATTATAAATAAAGATTTGGTATATTTCCTACAGATAAACATTTTCTCTCTTATTGGAAAGACTTTGAAAATAACAGCATTTAACTTAAAGCATGTATTTTAGTAAACTGCTGTTGCTATATATTAATATGGTGCTTCCCAACTATAGACAAATTTATCCATTGCTTATTTCACCATATGAATATTTCTCCATGGAAACAGTGTGAGTAGGGTCCTAGAAAAAGCATAAAAACCTAAATTAAAGCACATATAACTGAATGATAGTAAAAAGTCTAAATATTGGACTAGAAAAGTTTATTCTTCACTTCTCAGGCCCAGACTTATCTAAGAAACAGATTGACAATATTAACAAATTTTAAATGATGTACAGGAAAATTAATTGGAAAACCTGAATTTTAAATTCTTTCCTGGAAAAAATGTGATTCTTCTTAAAGAGCTTCATGCTACTGTCATAATATTCAGGACTTAAGAAACAAGCTTTCCATTTGGTAGCAATATGACTGCCATATGGTAACAACATGACTCACTCACTGCCATGGCTGCCAGTCAATAAGCATTTGTTGGGTGTTTCCCATGCTCATTCTCCTCCTACAGCACATTGCTGTGGGGATGCAAAAGCAGCATAATCTTACACCAGTTCTCAAGGAACTACAAGGCTGTGTATGATTAATCCTTTCTTGGTACATATTAGTAAGTTATGTAGGAGTTGGGGGTAGGAGAAGGCAATTTCCTGGGAAGTTCCACGAAATGTTTTGTGAAGGTAGTACTTATAACAAGAATGAGGAAAAGGCATGAGGAAATGTGACAGATTAGGTAAGTAGAGTAGTATTAGAATAGTGATGAGACTTGAGATGCTAGGCAGAGAAATTTAGTCTTGATATTTAAGGAAGTTGAGAGTCACCGGAGAGCAGAGTGACCCAGGTATATGAGTATTTAAAGAATATTAATGATTTTTAAGCAAGATGACTGGGGAAGGTTAAAAAAAAGGAAGATTGGAGTGGGAAAATTGTATAATGGCAGCACTGGTTTATAAAAGTAAGGAAGACTGGAAAATGGGAAACATTTATACCCAAGGAATAACAGAGATAAAGCTGGGCTGGTAATTAAAATAAATATAGACAGGGAAGGGGAGCTTGGGAAGGGGAACTAATTTACAGGTAAAAAAAGGAAACTTGAGGTATTAGTGATTCCAAGAGAAGCAATCCAATAAATAGTTCTAGGTTTCACATCTGAACTCAGCAAAGAGAACAAGACTTTAAAAGTAAATCTAGAAGTCATGGTTCACAGAAACCGTAAGAATGGGTAAGTTTAGCAACAGAGAAAGAACAGAGAATAAACAGAAAACTAAGAGCTGAATGCTGGTAGAAAGCCAGATTTTTGGGGATGGAGAAGGAAGAAGGGTCAGAATTCAGTAAAAGAAACAGAAAAGGAGTTTTGGTCAGAGCAGCCAAGCCACAGAGGTTAAGGGGAGAAGCCATTTCAGGAAAAGTAGTGTGGTCAACATTGTTGAAGAAAATGAGGAAGGAGAAAATGCCCCTGGACTGGGAAAGCTCATTATTGAGACCAGGTTTAAAAAGGGTGATGATGAGAGCCATATTTAAGAGGAAGTGAGATAGAAATAAAAGAAAATACTATTTGTGAAAAACGGGTGCTAAAAGACAGGATTGGATTGGAACCTGATCAGGTGAAAAAAAGATCTGAGGATGTCAAAAGACTCAGAGGAAAGAGACAGTGGATAGCAAATGGAGATAGTGAGAAGGAAATGGATGAGTATAAAGTTCCTTAAGGCATGAATGGATGTGATCACAAGGTCAATTTGAAGAGTTATTTTTGAAAAGAGGACCTTTTCCTTTTAGACTGCCAACTAGCTTTAACAATAACTGTTTTCTGAAAGCAATCTGTCTATAGCAATAATAAACTATGACATTCCTTTGCTAGAAGAGCCCAAAGAGTCAGCTTATTAATACCATTTGGGTACATGCCAAAAGGCAAGACTGGCGAGCCCAAGGACACAATTTGGGTTGACACAGATGTTCAGGTACATCAGAATTTGGGCCACCAGCAGGTAGAAGACCCTATCCTGAAACAGACACATGCTCAGCAATATAATATAATTTATTAATATTCACTTATGAATTCAGTTCGGGGTCAAACTAATTATCTGGAGGAAATATATCGTATAATTTTTCTATTTTTATCTTTTTATTTTTACAAATATTTATAAATAATTTAACATTTTACCTTCTCATGGAGTTTTCAAATTGATTCATCACTGCTTCAGATTTCATCTTCAG\n'

diff -r 000000000000 -r d723eb657f1d test-data/translated_bed_seqs.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/translated_bed_seqs.bed Mon Jan 25 12:21:21 2016 -0500

@@ -0,0 +1,14 @@
+track name="novel_junctioni_translations" description="test"
+15 40902460 40907575 JUNC00019210_2 1 + 40902460 40907575 255,0,0 2 35,37 0,5078 SYENSEKVRNGRNKKLEDNYCEIT
+15 40902461 40907549 JUNC00019210_3 1 + 40902461 40907549 255,0,0 2 34,11 0,5077 HMKIVRKSEMEGIRN
+9 17406 18053 JUNC00000003_1 1 - 17406 18053 255,0,0 2 73,26 0,621 APWTSGPCRYKKYVFLDPLAGAVTKTHVMLGAE
+9 17438 18052 JUNC00000003_2 1 - 17438 18052 255,0,0 2 41,25 0,589 PPGRAGPAGTRSMSSWTPWLVL
+9 17404 18051 JUNC00000003_3 1 - 17404 18051 255,0,0 2 75,24 0,623 PLDERALQVQEVCLPGPPGWCCNKDPCDAGGRD
+8 27369376 27370079 JUNC00000874_2 1 + 27369376 27370079 255,0,0 2 51,48 0,655 PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA
+7 99077597 99079392 JUNC00001897_1 1 + 99077597 99079392 255,0,0 2 64,35 0,1760 HLLSLFFQLGVHICIPNFRNNSVSHCTQLRVLL
+7 99077598 99079360 JUNC00001897_2 1 + 99077598 99079360 255,0,0 2 63,3 0,1759 IYCLYFSNLVCISVYPTSEITV
+7 148909514 148910831 JUNC00002152_1 1 + 148909514 148910831 255,0,0 2 60,39 0,1278 DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS
+7 148909515 148910811 JUNC00002152_2 1 + 148909515 148910811 255,0,0 2 59,19 0,1277 ISRIWQTEIFPRIPIQVRTRVSHLST
+6 41766614 41767580 JUNC00002625_1 1 - 41766614 41767580 255,0,0 2 53,13 0,953 LKDSGGLAVIIERRLGSMSSLT
+6 41766612 41767578 JUNC00002625_3 1 - 41766612 41767578 255,0,0 2 55,11 0,955 KRFRWSGRNHREKIGVHVVFDQ
+6 84856497 84862316 JUNC00002772_1 1 - 84856497 84862316 255,0,0 2 7,53 0,5766 LKMKSEAVMNQFENSMRRYL

diff -r 000000000000 -r d723eb657f1d test-data/translated_bed_seqs.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/translated_bed_seqs.fa Mon Jan 25 12:21:21 2016 -0500

@@ -0,0 +1,26 @@
+>JUNC00019210_2 pep:novel chromosome:GRCh37:15:40902460:40907575:1 depth:1
+SYENSEKVRNGRNKKLEDNYCEIT
+>JUNC00019210_3 pep:novel chromosome:GRCh37:15:40902461:40907549:1 depth:1
+HMKIVRKSEMEGIRN
+>JUNC00000003_1 pep:novel chromosome:GRCh37:9:17406:18053:-1 depth:1
+APWTSGPCRYKKYVFLDPLAGAVTKTHVMLGAE
+>JUNC00000003_2 pep:novel chromosome:GRCh37:9:17438:18052:-1 depth:1
+PPGRAGPAGTRSMSSWTPWLVL
+>JUNC00000003_3 pep:novel chromosome:GRCh37:9:17404:18051:-1 depth:1
+PLDERALQVQEVCLPGPPGWCCNKDPCDAGGRD
+>JUNC00000874_2 pep:novel chromosome:GRCh37:8:27369376:27370079:1 depth:1
+PTSCNPSDMSHGYVTVKGYHKAKATHRGPWLVA
+>JUNC00001897_1 pep:novel chromosome:GRCh37:7:99077597:99079392:1 depth:1
+HLLSLFFQLGVHICIPNFRNNSVSHCTQLRVLL
+>JUNC00001897_2 pep:novel chromosome:GRCh37:7:99077598:99079360:1 depth:1
+IYCLYFSNLVCISVYPTSEITV
+>JUNC00002152_1 pep:novel chromosome:GRCh37:7:148909514:148910831:1 depth:1
+DQQDLADRDIPTDPNSGENKSLSSQHMTFCHGS
+>JUNC00002152_2 pep:novel chromosome:GRCh37:7:148909515:148910811:1 depth:1
+ISRIWQTEIFPRIPIQVRTRVSHLST
+>JUNC00002625_1 pep:novel chromosome:GRCh37:6:41766614:41767580:-1 depth:1
+LKDSGGLAVIIERRLGSMSSLT
+>JUNC00002625_3 pep:novel chromosome:GRCh37:6:41766612:41767578:-1 depth:1
+KRFRWSGRNHREKIGVHVVFDQ
+>JUNC00002772_1 pep:novel chromosome:GRCh37:6:84856497:84862316:-1 depth:1
+LKMKSEAVMNQFENSMRRYL

diff -r 000000000000 -r d723eb657f1d test-data/translated_bed_sequences.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/translated_bed_sequences.bed Mon Jan 25 12:21:21 2016 -0500

diff -r 000000000000 -r d723eb657f1d test-data/translated_bed_sequences.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/translated_bed_sequences.fa Mon Jan 25 12:21:21 2016 -0500

diff -r 000000000000 -r d723eb657f1d tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jan 25 12:21:21 2016 -0500

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="biopython" version="1.62">
+        <repository changeset_revision="f06c96348778" name="package_biopython_1_62" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>

diff -r 000000000000 -r d723eb657f1d translate_bed_sequences.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/translate_bed_sequences.py Mon Jan 25 12:21:21 2016 -0500

[

b'@@ -0,0 +1,375 @@\n+#!/usr/bin/env python\n+"""\n+#\n+#------------------------------------------------------------------------------\n+# University of Minnesota\n+# Copyright 2014, Regents of the University of Minnesota\n+#------------------------------------------------------------------------------\n+# Author:\n+#\n+# James E Johnson\n+#\n+#------------------------------------------------------------------------------\n+"""\n+\n+"""\n+Input: BED file (12 column) + 13th sequence column appended by extract_genomic_dna\n+Output: Fasta of 3-frame translations of the spliced sequence\n+ \n+"""\n+\n+import sys,re,os.path\n+import tempfile\n+import optparse\n+from optparse import OptionParser\n+from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate\n+\n+class BedEntry( object ):\n+ def __init__(self, line):\n+ self.line = line\n+ try:\n+ fields = line.rstrip(\'\\r\\n\').split(\'\\t\')\n+ (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12]\n+ seq = fields[12] if len(fields) > 12 else None\n+ self.chrom = chrom\n+ self.chromStart = int(chromStart)\n+ self.chromEnd = int(chromEnd)\n+ self.name = name\n+ self.score = int(score)\n+ self.strand = strand\n+ self.thickStart = int(thickStart)\n+ self.thickEnd = int(thickEnd)\n+ self.itemRgb = itemRgb\n+ self.blockCount = int(blockCount)\n+ self.blockSizes = [int(x) for x in blockSizes.split(\',\')]\n+ self.blockStarts = [int(x) for x in blockStarts.split(\',\')]\n+ self.seq = seq\n+ except Exception, e:\n+ print >> sys.stderr, "Unable to read Bed entry" % e\n+ exit(1)\n+ def __str__(self):\n+ return \'%s\\t%d\\t%d\\t%s\\t%d\\t%s\\t%d\\t%d\\t%s\\t%d\\t%s\\t%s%s\' % (\n+ self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, \n+ \',\'.join([str(x) for x in self.blockSizes]), \n+ \',\'.join([str(x) for x in self.blockStarts]), \n+ \'\\t%s\' % self.seq if self.seq else \'\')\n+ def get_splice_junctions(self): \n+ splice_juncs = []\n+ for i in range(self.blockCount - 1):\n+ splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])\n+ splice_juncs.append(splice_junc)\n+ return splice_juncs\n+ def get_exon_seqs(self):\n+ exons = []\n+ for i in range(self.blockCount):\n+ # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])\n+ exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])\n+ if self.strand == \'-\': #reverse complement\n+ exons.reverse()\n+ for i,s in enumerate(exons):\n+ exons[i] = reverse_complement(s)\n+ return exons\n+ def get_spliced_seq(self):\n+ seq = \'\'.join(self.get_exon_seqs())\n+ return seq\n+ def get_translation(self,sequence=None):\n+ translation = None\n+ seq = sequence if sequence else self.get_spliced_seq()\n+ if seq:\n+ seqlen = len(seq) / 3 * 3;\n+ if seqlen >= 3:\n+ translation = translate(seq[:seqlen])\n+ return translation\n+ def get_translations(self):\n+ translations = []\n+ seq = self.get_spliced_seq()\n+ if seq:\n+ for i in range(3):\n+ translation = self.get_translation(sequence=seq[i:])\n+ if translation:\n+ translations.append(translation)\n+ return translations\n+ ## (start,end)\n+ def get_subrange(self,tstart,tstop):\n+ chromStart = self.chromStart\n+ chromEnd = self.chromEnd\n+ r = range(self.blockCount)\n+ if self.strand == \'-\':\n+ r.reverse()\n+ bStart = 0\n+ for x in r:\n+ bEnd = bStart + self.blockSizes[x]\n+ if bStart <= tstart < bEnd:\n+ if self.strand == \'+\':\n+ chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)\n+ else:\n+ chromEnd = self.chromStart + self.blockStarts[x] + ('..b' >> sys.stderr, "%s" % splice_sites\n+ for i,translation in enumerate(translations):\n+ print >> sys.stderr, "frame %d: %s" % (i+1,translation)\n+ print >> sys.stderr, "splice: %s" % (\'\'.join([\'^\' if (((j*3)+i)/3) in splice_sites else \'-\' for j in range(len(translation))]))\n+ print >> sys.stderr, ""\n+ if options.bed_format:\n+ tx_entry = "%s\\t%s\\n" % (line.rstrip(\'\\r\\n\'),\'\\t\'.join(translations))\n+ outFile.write(tx_entry)\n+ else:\n+ translations = entry.get_filterd_translations(untrimmed=options.untrimmed,filtering=options.filtering,ignore_left_bp=leading_bp,ignore_right_bp=trailing_bp,debug=options.debug)\n+ for i,tx in enumerate(translations):\n+ if tx:\n+ (chromStart,chromEnd,translation,blockCount,blockSizes,blockStarts) = tx\n+ if options.min_length != None and len(translation) < options.min_length:\n+ continue\n+ if options.max_stop_codons != None and translation.count(\'*\') > options.max_stop_codons:\n+ continue\n+ frame_name = \'_%s\' % (i + 1)\n+ pep_id = "%s%s%s" % (options.id_prefix,entry.name,frame_name)\n+ if bed_fh:\n+ bed_fh.write(\'%s\\t%d\\t%d\\t%s\\t%d\\t%s\\t%d\\t%d\\t%s\\t%d\\t%s\\t%s\\t%s\\n\' % (str(entry.chrom),chromStart,chromEnd,pep_id,entry.score,entry.strand,chromStart,chromEnd,entry.itemRgb,blockCount,\',\'.join([str(x) for x in blockSizes]),\',\'.join([str(x) for x in blockStarts]),translation))\n+ location = "chromosome:%s:%s:%s:%s:%s" % (options.reference,entry.chrom,chromStart,chromEnd,strand)\n+ score = " %s:%s" % (options.score_name,entry.score) if options.score_name else \'\'\n+ seq_description = "%s %s%s" % (options.seqtype, location, score)\n+ seq_id = "%s " % pep_id\n+ if options.fa_db:\n+ seq_id = "%s%s%s%s" % (options.fa_db,options.fa_sep,pep_id,options.fa_sep)\n+ fa_id = "%s%s" % (seq_id,seq_description)\n+ fa_entry = ">%s\\n%s\\n" % (fa_id,translation)\n+ outFile.write(fa_entry)\n+ if gff_fh:\n+ if gff_fa:\n+ gff_fa.write(fa_entry)\n+ gff_fh.write("##sequence-region %s %d %d\\n" % (entry.chrom,chromStart + 1,chromEnd - 1))\n+ gff_fh.write("%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%d\\tID=%s\\n" % (entry.chrom,\'splice_junc\',\'gene\',chromStart + 1,chromEnd - 1,entry.score,entry.strand,0,pep_id))\n+ for x in range(blockCount):\n+ start = chromStart+blockStarts[x] + 1\n+ end = start + blockSizes[x] - 1\n+ phase = (3 - sum(blockSizes[:x]) % 3) % 3\n+ gff_fh.write("%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%d\\tParent=%s;ID=%s_%d\\n" % (entry.chrom,\'splice_junc\',\'CDS\',start,end,entry.score,entry.strand,phase,pep_id,pep_id,x))\n+ """\n+ ##gff-version 3\n+ ##sequence-region 19 1 287484\n+ 19 MassSpec peptide 282299 287484 10.0 - 0 ID=TEARLSFYSGHSSFGMYCMVFLALYVQ\n+ 19 MassSpec CDS 287474 287484 . - 0 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812\n+ 19 MassSpec CDS 282752 282809 . - 1 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812\n+ 19 MassSpec CDS 282299 282310 . - 0 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812\n+ """\n+ if bed_fh:\n+ bed_fh.close()\n+ if gff_fh:\n+ if gff_fa:\n+ gff_fa.close()\n+ else:\n+ outFile.close()\n+ gff_fa = open(gff_fa_file,\'r\')\n+ gff_fh.write("##FASTA\\n")\n+ for i, line in enumerate(gff_fa):\n+ gff_fh.write(line)\n+ gff_fh.close() \n+ except Exception, e:\n+ print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else \'stdin\',e)\n+\n+if __name__ == "__main__" : __main__()\n+\n'

diff -r 000000000000 -r d723eb657f1d translate_bed_sequences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/translate_bed_sequences.xml Mon Jan 25 12:21:21 2016 -0500

[

@@ -0,0 +1,128 @@
+<?xml version="1.0"?>
+<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0">
+  <description>3 frame translation of BED augmented with a sequence column</description>
+  <requirements>
+    <requirement type="package" version="1.62">biopython</requirement>
+    <requirement type="python-module">Bio</requirement>
+  </requirements>
+  <command interpreter="python">
+  translate_bed_sequences.py  --input "$input"
+  #if $fa_db:
+   --fa_db='$fa_db'
+  #end if
+  #if $fa_sep:
+   --fa_sep='$fa_sep'
+  #end if
+  #if $id_prefix:
+   --id_prefix='$id_prefix'
+  #end if
+  #if $reference:
+   --reference $reference
+  #else:
+   --reference ${input.metadata.dbkey}
+  #end if
+  #if $refsource:
+   --refsource $refsource
+  #end if
+  #if $seqtype:
+    --seqtype $seqtype
+  #end if
+  #if $score_name:
+    --score_name $score_name
+  #end if
+  #if $filter.filterseqs == 'yes':
+    #if $filter.leading_bp:
+      --leading_bp $filter.leading_bp
+    #end if
+    #if $filter.trailing_bp:
+      --trailing_bp $filter.trailing_bp
+    #end if
+  #else:
+    --unfiltered
+  #end if
+  #if $trim.trimseqs == 'no':
+    --untrimmed
+    #if str($trim.max_stop_codons) != '':
+      --max_stop_codons $trim.max_stop_codons
+    #end if
+  #end if
+  #if str($min_length) != '':
+   --min_length $min_length
+  #end if
+  --bed $translated_bed
+  --output "$output"
+  </command>
+  <inputs>
+    <param name="input" type="data" format="bed" label="BED file with added sequence column"
+           help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/>
+    <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
+           help="Any Compomics application such as PeptideShaker, requires a source">
+    </param>
+    <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"
+           help="Only used when a fasta ID source is given, defaults to the pipe character">
+    </param>
+    <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
+           help="Can be used to distinguish samples">
+        <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
+    </param>
+    <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
+           help=""/>
+    <param name="reference" type="text" value="" optional="true" label="Genome reference name"
+           help="By default, the database metadata will be used."/>
+    <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
+           help="For example:  pep:splice"/>
+    <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
+           help="For example:  with the tag name 'depth' and bed score 12:   depth:12"/>
+    <conditional name="filter">
+      <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
+        <option value="yes" selected="true">Yes</option>
+        <option value="no">No</option>
+      </param>
+      <when value="yes">
+        <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs"
+               help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
+        <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs"
+               help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
+      </when>
+      <when value="no"/>
+    </conditional>
+    <conditional name="trim">
+      <param name="trimseqs" type="select" label="Trim translations to stop codons">
+        <option value="yes" selected="true">Yes</option>
+        <option value="no">No</option>
+      </param>
+      <when value="no">
+        <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/>
+      </when>
+    </conditional>
+    <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
+  </inputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <outputs>
+    <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed">
+    </data>
+    <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
+      <param name="reference" value="GRCh37"/>
+      <param name="seqtype" value="pep:novel"/>
+      <param name="score_name" value="depth"/>
+      <output name="output" file="translated_bed_sequences.fa"/>
+    </test>
+  </tests>
+  <help>
+**Translate BED Sequences**
+
+This tool takes a BED input file that has been processed
+by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
+
+It generates a peptide fasta file with the 3-frame translations of the spliced sequence
+defined by each entry in the input BED file.
+
+  </help>
+</tool>