Mercurial > repos > galaxyp > translate_bed_sequences
changeset 0:d723eb657f1d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
| author | galaxyp |
|---|---|
| date | Mon, 25 Jan 2016 12:21:21 -0500 |
| parents | |
| children | 6bbce76c78c1 |
| files | 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 |
| diffstat | 8 files changed, 596 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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 @@ -0,0 +1,7 @@ +15 40902459 40907576 JUNC00019210 1 + 40902459 40907576 255,0,0 2 36,38 0,5079 CTCATATGAAAATAGTGAGAAAGTCAGAAATGGAAGGTAAGTATGTTACTATAATTCCTGCTAAATCTGCTTTTTAAAAAATTTTACTGTAGCTATCTAACCAGACAACTAATATAACTTATTGTCTATCTTATTGCTTAAAAAATATATGATGGGCCATGCATAGTGGTTCACACCTGTGATCCCGACACTTTGGCAGTCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCAAGACCAACCTGGATAGCATAGTGAGATTCTGTCTCTACAAAAAATAAAAAATTAGCCAGGTGTGGGGGTGCATTCCTGTAGCCCCAGCTACTCAGGAGGCTGAGGTGAGAGGATCACTTGAGTCCAGAAGATTGAGACTGCAGTGATTGCACCAGTGCACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCAAAAACAAAAAAAGTATACCTTGAGTCTTGGGAGTAGAGAGTAGAGTGGATAGTAAGTAAATTTATTTATTTATTTATTTTGAGACGGATTTTCACTGTTGTTCCCCAGGCTGCAGTGCAATGGTGCCATCTCAGCTGCAACTTCTGCCTCCTGGGTTTAAGCGATTCTCCTGCCTCAGCCTCCCAGGTAGCCGGGATTACAGGCATGCACCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATATTGGCCAGGCTGGTCTCGAACCCCTGGCCTCAAGTGATCCGCCTGCCTTGGCCTCAAAATGCTAGGATTACAGGCGTGAGCCACCACGTCCAGCAGTTAATAATTTTTTTAAATGTTGTTAATGTCCTTAAGTAATTTTTTAAAAATTTTATTGTATTTTTTTTTTTTTTGAGACAGAGTCTTGCTTGCCCTGTCGCCCAGGCTAGAGTGCAGTGGTGCGATCTCGGCTAACTGCAATCTCTGCCTCCCAGGTTCAAGCAATTCTCCTACCTCAGCCTCCTGAGTAGCTGGGATTACATGTGCACGCCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTGGTCAGGTTGATCTCGAACTCCTGACCTCGTGGTCCACCCGTCTCGGCCTCCCAAAGTTCTGGGATTACAGGCATGAGCCACCGGGCCCAGCTGTCCTTAAGTAATTTTTCTAATGCTTTATCAGTGTATCCTTGGACAAATTTAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATCTTCTTTTGATACAGTAAGTAATATTCAAATTATATTTAAAAAGTTATAAATTAATATTATTTTTATTTCTTATTTTTGTGTTCCTTTTGTGGAATACTTAGGATTAATTCAGAAAACCAGTTATTTGCAGAATTTAGTATACTGCTATATCTGATTAATATGGCCATTGTACTGTTTATAGTTTTAATAGTGATGAAACAATATAATATATAAACCTTTATATTTATTAACTAATATAAAACAATAGATAGCAAGTCTTTAGTTTTTTTATTAAATTAATCTTTCTTATAATATTATTACATAGAAAGGCAAATACCAGTAGCTCTTCAACAAATGAAAAGATGGTTATCTTTATTCATCATAAGAGAAGTACAGATTTGATTATATTGAGATATTTTTGGCTGGACGTGGTGGCTCATGCCTGTAATCCGAGCACTTTGGGAGGCCGAGGCTGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGATGAAACCCCATCTCTACTAAAAAAATACAAAAAATTGGCCGGGCACAGTGGCTTACGCCTGTAAACCAAGCACTTAGGGAGGCTGAGGCGGGTAGATCACGAGGTCAGGAGATCGAGACCATCCTGGCCAACGTGGTGAAACCCCATCTCTACTAAGAATACAAAAATTAGCCAGGTGTTGTGGTGGGCGCCTGTAGTCCCAGCTACTCAGGAGGTTGAGGTAGGAGAATCACTTGAATCTGGGAGGTAGAGGTTGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAACAAAAAAAACCCCAAAAAATTAGCCAGGTATGGTGGCACTGTGCCTGTAATCCCAGCTACTCAGGAGGCCAAGGCACGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATCATGCCCCTGCACTCCAACCTGGGCAGCAGAGCGAGACTCTGTCTCCAAAAAAGAGGTTTTTTTGCTGTTGTTGTTGTTTGTTTGTTGTTTAGACGGCATCTTCCTCTGTCGCCAGGCTGGAGTGCAATGGTACGATCTTGGCTCTCTGCAACCTCCGCCTCCTGGGTTCAAGTGATTCTCCTGCTTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCACGCCTGGCTAATTTTGTTGTATTTTTAGTAGACACGGGGTTTCACCATGTTGGCCAGAATTGTCTTGGTCTCTTGACCTCGTGATCCGCCCACTTTGGCCTCCTAAAGTGCTGGGATTACAGGCGTGAGCCACTGTGCCTGGCCTAAAAAAGAGATATTTTTATCCAGTCAGTTAAGGAAATAGGTAAAAAGTCACTCCGTGCTAGTGGGAGTATAATTTGTAGAAGGCAACTTGGTAATATCGTTCAGAATTTTAAATGCACATGCCCTTTGACTTCAGTTTTATGTCTGGAAATTATCTCACCAATATACGTGTAAATGTTTGAAATGATGAATAGATAAGGTTATTCACAGCAGCGTTTATTATAATAGTAAACGTTGTGAAAGGTCCTGAAGGTCCATCAGTAAGGGCCTGGTTAAATAAATTGTACATTTTCCATATAATTGACTATGCAGCCGGAAAAAAAATTTTATGCTAAATAGAGAAATCTCTAAGCTATATTACTTAAGATAAAAAGCAAGACGCAAAACAAAGTATATCATGTATTACCACTTGGGTAAAACAGGGAAGAAGAAAAGCGTGTGTGTGTGTGTGTATCTTCTCGTGTGTGTACATGTATAATGTATGTATATGTAGTGACTTATGCATATATATGCATAATATCTCTGGAAGAAACTAGTAAGATTGCCTACAGAGAAAAGAACCTTGCTATAGGTTACATGTTGGCTTTGTGGTTTATTAATTTAAAACCATATGAAAGTATTACCTATTACATTCTTAAAATTGTTGAAACGAAGAAATGGAAGTAATAGTAGTCATGGTTTAGAAAAGGTACAGAATCAACTCCAACAGAACTTAAAGGAAAAATAATTTTTTAAATAAAAAGGTACAGAAGTATATACATTGAAAAGTAAAAATTATTCCCTCTTTCCCTCTTCTTTCTTTTTTGTGAGACGGGGTTTCGCTCTTGTTGGCCAGACTGGAGTATAATGGCATGATCTTGGCTCACTGCAACCTCAGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTAGGACTACAGGTGTGCACCACTACACCTGGCTAATTTATTTTATTTTTATTATTTTATTTTATTTTATTTTATTTTGAGATAGAGTCTCGCTCCGTCACCCAGGCTGGAGTGCAGTGGCGCCATCTCGGCCCACTGCAAGCTCCGCCTCCTGGTTTCACGCCATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGCGCCTGCCACCACGCCTGGCTCATTTTTTTGTATTTTTAGTAGAGACAGGGTTTCACTGTGTTAGCCAGGATGGTCTCAATTTCCTGACCTTGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGCCCCCCTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTGTGCAGGCTGGAGTGCAGTGGCCTAATCTTGGCTCACTGCAACCTCCGCCTCATGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTACCTGGGACTACAGGTGCACACCACCACGCCCAGCCAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCACGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGTTTATCTGCCTGCCTTGGCTTCCCAAAGTGCTGGGATTTTAGGCATGAGCCACCACACCCGGCCTAATTTTGTATTTTTAGTAGAAGCGGTGTTTCACCATGTCGGCCAAGCTAGTCTCAAACTCCTGACCTCGGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGATGGGATTACAGACGTGAGCCACCACACCCAGCCTATTCCCTCTTCTTCAGGTGACTCACTCCTTACAGATAACCACTGTTGACAATTTTTGGTGTACTTGCAGAAATTTTTTTTGTATGTCCAAGTGCATGTTTAGCTTTTATTTTTTTAAACAAGACAAAAATGGGATTGCCTAGTAATATGTCTTATAGCACTTTCTATGTTATTACATAAAGATTTACCTCAGTCTGTTACAATCTCTTGTATGGCTGCACCAACATTTAGTGAACTCCCTATTGATGGACACTTGAGTGGTTTCTTTCATGTACTTTTTGTTTTAAGGCTCAAGTTTTAGAAAAGGAATTGCTTTATAGGTCATTTTTTGAAAAAATAAGCAAGCAGTATATATTAAGCATATTTTTCTAGTTTATTTTTTTGAGATGGGGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGACATGATTATAGTTCATTGCAGCCCTGGACTTCAGGTCTCAAGTGATCCTCCCACTTCACGCTCCCAAAGTGTTGGGATTACAGATGTGAGCCACCACGGCTGGCTGATAATATTCTTGAAATTAGCAAACCATTAAGACCAATCTGAAAAGTATCCTTTAGTTGCCTTGTAATTCCTTCAGCCAGTATTAGATGAGTCTTTTTTTAAAAAGATGTCTTTATAATTTTCTGCATTAGATGAGTCTTTTTTAAAAAGATGTCTTTATAATTTTCTGCTAGTCATTCTATGAAAGTCTTTCACCTTCTGTACTCTTTCAGCTGTTATTGAAAGATTCTTGGTAATTGTTTGGGGTATAGATTATAAAAATACTTTTTAATTTTTAGGAATAAGAAATTAGAAGATAATTACTGTGAAATTACTG +9 17404 18053 JUNC00000003 1 - 17404 18053 255,0,0 2 75,26 0,623 GTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTGTACCTACGGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGTGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCCAGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTATATGCGCGGCCAGCAGACCTGCAGGGCCCGCTCGTCCAGGGGGC +8 27369375 27370080 JUNC00000874 1 + 27369375 27370080 255,0,0 2 52,49 0,656 GCCGACCTCTTGCAATCCAAGTGACATGAGCCATGGGTACGTGACAGTAAAGGTGAGTCAGTTTTGTCTCTCAGTCGGCTAAGTGCTCTCCCACCAGGTCACCTAAAACGACCAGCAGAGACACCCAAGAGGCTGAGCTGTGAGGATCACCTGAACCTGAGCCTGGGAAGTGGAGGTTGCAGTGAGCTGTGATCACACCACTGTGCTCCAGCCTGGGCAACGGAGTGAAACCCTGTCTCAAGAAAAAAAAAAAAAAAAAAGGACCAGCAGTGACATTTGTTAAATATCGAGGGTGGTTGAACATCCACTATTTATAAGGAAATGTTATTTCCCACAAATCTCATTCCTCAGAAATCAGTGAAAGACAGACCCTGTCTCGGATTCTATAAAGCAGTGTGACTGATGTGGCCAAACCCCCATAGAACAGCAGGCTAGGGAGCTTGGGCAGCCTGGGAGGCTAAAGCATGCACACAGCTGGCCTGTGTTGGAGGAGAGCATGTTTTCATTCAACAGGCATTTATCGAACACTTCCTCTGTGTCAGGCACAGGCCAGATACAAGGGGTGCAGTGACGATCAAGACAGACCTGTCCTCAAGGAGCCCACATTGAGGGCAAAGAGAGGGAAAGGTCATTAAAATGTTCTTTTTGTTTTAAAGGGTTATCATAAAGCCAAGGCCACACACAGAGGGCCCTGGCTCGTGGCCT +7 99077597 99079394 JUNC00001897 1 + 99077597 99079394 255,0,0 2 64,37 0,1760 CATTTATTGTCTTTATTTTTCCAACTTGGTGTGCATATCTGTATACCCAACTTCAGAAATAACAGTGTAGGCCAGGTGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGATTCCGAGGCGGGTGGATCACATGAGGTCAGTAGTTTGAGACCAGCCTGGCCAATATGGTGAAACCCAGCTCTACTTAAGATGCGAAAATTAGCCTGGTGTGGTGGTGCACGCTTGTAGTCCCAGTTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCAGAGGTTGCATTGAGCCGAGATCATGCCGCTGCATTCCAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAACAAAACAAAACAACAACAAAAATAACAGTGTATTTGAGGGCACCACTCCAAACCCTACTGGGGATGATACGTTATGTAAAATATTTACACCAGGTCACCTTTCTGAAATGGGAAAAATTCTGACTCCTGAAACACATCTGGTCCTAAGGGTTTCACATAAGGGACTGGGGACAGTGAATAGTCGTGTTGTGTTAGGGCTCAGACCGAGACACTTCATGCATTCTTCACTCTCACCTCGTGTTCCTCATCTGTAAGACCTCCAGGAGTTGAGAATTATGGTAGATTTACATTCCAAAGGCTCACTTCTTATGCTCTTGAAAGTCTTTTTCTTTCTTTTCTCTGGAAATGGGTAACTTCTTGGTGTGTAACATTAGTGGGTGCTCAGGAAATGATTTTCAACCAACTTCATTTCTGAACCTTCACTGCTTCCATTCTTTTCAGGAGCCTACCCTGTCCTAGTCCACTGTAGTCTCCCACTGTGGGAGTTGCCTTGCTAAATAGTTTTCTTTCCGGGGTCACATGTTTAACCCTTGCACTGACACTCTTAGCACAGAGTCTTGACCACCTCTGTGGGACTGTCCACCCACCTCTGGATTTTTATAATTTTAATTTTCCCTTTAAAAGCATTACAGGAGCATACATAAGTACATGGAAGGCATAGAAAAGGAGGAGAAGAGGAAAGTGTTCATGGGTAACACTGTTAATATTTTGGAAGGTTTCCTGCCAGTCTTTTTTTCCTATGCCTTTACAAAAGTAGCTGAGCATATTCTATGTGCAATCCTGTAATCTGTTTTAAATGTAACATTATTGTATCAGCATTTCCCCACATAATCAGTAAACGAGCATAATATAATTCCATTGTGTGGTCCATAAAAATATTTCATTGTTTTCCCATGTGGGGACATTGAGCTTGCCTTTGTTTGTTCGTTGGTTTGCTTGTGTATTTATAATGTTTGAATAGATGTTTGAGTATAAATCTTTGCATGAATTTTTGATCATTTCCCAAGATACTTTCCCAAAATCAGAATTTTGAAGTTAAATGAGATGGCACTTTAATCTTTATTGATTACTGAATGATTCTTCAACAAACTTTGTACTGTTTTGCATATCCAATAGTAACATTTTAGAGTGCTTCTTTTTTTTTTTGAGACAGAGTTTCGCTCTTGTTGCCCAGGCAGGAGTACAATGGCAGGATCTCAGCTCACCACAACCTCTGCCTCCCCGGTTCAAGTGATTCTCCTGCCTCAGACTCCTGAGTAGCTGGGATTACAGGCATGTGCCACCACACCTAGCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTCAGGCTGGTCTCAAACTCCCGATCTCGGGTGACCCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCAGCTGAGAGTGCTTCTTTA +7 148909514 148910833 JUNC00002152 1 + 148909514 148910833 255,0,0 2 60,41 0,1278 GATCAGCAGGATTTGGCAGACAGAGATATTCCCACGGATCCCAATTCAGGTGAGAACAAGGTCAGAATGAATCTTGAGGGCAACAAGTGTTTTTCAAAAGGAATCATTAAATTAATAATTTATTGTGTTTATGCAGCTGATACTAAAATTACTTCAGCACTGATTTTTTGTTCTTTGAGACGGAGTCTTGCTCTGTTGTTCAGGCTGGAGTGCAGTGGTGTGATCTCAGCTCACCGCAACCTCCGTTTCCCGGGTTTAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGAGATTACAGGCATGTGCCACCACACCTGGCTCATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGTCAGGCTGCTTCTGAACTCCTGGCCTCAAATGATCTGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACGGGCATGAGCCACCGCGTCCGGCCATTCAGCACTGATTTTTGAACAATAAAAACAACCAAAAAGCATCTAAAAGCTGCATATATTTCTGTGTCAGAAAATTATTTACATTTTCTGGAATTTCTCTTGAGTGAATACTAGTTAGAAGTTTCCCAAGAAACTTGTAGGGAGGGTCTAGGCATTCAGGGAGGCATAAAAGAACAATGGAAGCCCCACCTGCCCACGACCTATGTGTGTGTCCATGTGATTGCAGAGCTGAGAAGTCCAGTGTCATTGCCTGGTAGTTAGGACACAAGTCTCATCCTACCCACCATACCAGGGAGAGAGGATGAGAAGTTGAATCTAGGATTCCTTGTACTTTGTCAACTTCACCACAGAGAAATTGAGGGGACCCAGGGCAGAGGGAAAGCGGGGCCTTCCTGCTTCACTGTGGTTCTTATCAATGACCTCTGGTTGCAGCCTCTGCCATCGCTGGTTTCTAAATCATACCTGTTAGCCATGGCCCTGAGGGCCGTTATCTGGGGCTTTCTTCTGGCCTGTCCTGGCCCCATGGGTTCCTCTGGGGCTAAGTGGCAGAGCTGGGAGATCTGGGTTTTAATCCCGGCCCTGCCACTGCACAGACCTTGGGCTAAGCCTCCTTCTGGCCAACTTGAAATGCATCGAGCAGTGAGAGTCCATTTAGGAAGGGGCTTATGAGGGTAAGGAGGATGGCCTGGAAATGCAACACCGATACCAAAACATGCCCTGCAGGTTGCAGCCACCGCATGGGATGGTTTTCAAACCTTTGATGGGAGGCCGAGTAGAACTGAACAAAATCTAAGACTGCCTTCTTTCCATGACAACAGAGTCTCTCATCTCAGCACATGACATTTTGTCATGGATCAAG +6 41766612 41767580 JUNC00002625 1 - 41766612 41767580 255,0,0 2 55,13 0,955 CTGGTCAAAGACGACATGGACCCCAATCTTCTCTCGATGATTACGGCCAGACCACCTAGAACATGGATATAAGCTTGTTACTAGTAAAAACTGGCATATATAATCGTAGGTAGAGGTAGGTATTAATAAAACAGGAAACTGAGAAAATTTAACCTTCTGGTTTTGGTTTTCCCATCAATAAAATGGTGGTAATCAATGTTCACACTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTCAGACAGGGTCTCACTCTGTTGCCCAGGCTGCAGTGCAGTGGTGTGATTGATAAAGGCTCACTGCAGCTTCAACCTTCCCGAGCTCAGGTGATCCCCCCACCTCAGCCTCCCGAGTAGGTGGGACTATAGGTGCACACCACCATGCCTGGCTAATTTTTGCATTTTTTGTAGAGACAGGGTTTTAACCATGTTGCCGAGGCTGGTCTCAAACTCCTGAGCTCAAGCAATCTGCCTACCTTGGCCTCCCAAAGTTCTAGGGTTACAGTCATGAGCCACTGCGCCTGGCCCATTTATTTGCTGTTAATGTTCCATGAAGTACTCTAAACCTAGAGATCCCTAAACAAGCAATTCAAGCAACAGTCTTTTTGTAGTTTCCTGCCTGTGCTTCTTTTGCAGATTATTTTATACTTCATCCTGAAGATGAATCTACATAAGTCCAAGCCAGGCTAGAAAATCTTTAAGCACAGACACCCAGTGCAGGCTGGATAATTAATTACACAGGAGCATGAGAGCAAAAGCCCAGTCCTGCTGGGCTCCCACATCAATTTGCCTTAGTGGATGTGAACAGTTTAATCTCCATGGAAAACACGAGGTCTCAAGTGAACAGGCTTCCCCTCCCAACACCATAGAAGACATTTGCCCTCACCAAAGCCTTTGGAGCAGCTATTCCCACAGCTCTCACCCAGCTGGGACTCCCACAGCAAGCTCACCTGAATCTTTTAA +6 84856456 84862316 JUNC00002772 1 - 84856456 84862316 255,0,0 2 48,53 0,5807 TTTACTCTGCAGCTCATTAACTTGACTTTGGAAATGTCTTATAAGTACCTAGGAAATTGTTAGAAGTGCTGAGTTAATAAAGCTCCTCCTTGAACACTATCTGAAAAATATAAGAAAGCCAACTCACAAAAGGGAACTCTTATATACTGTTGGTGGGAATGTAAGTAAGCACAGCTACTATGGAAAAAAATTATAGAGATTTCTCAAAAAACTAAAAATAGAATTACCGTATTATCTAGCAATCCCACTACTGGGTATCTATCCAAAGGAAAAGAAATTTGTATATCAAACGGACACCTGGCACTTGCATGTTTATTGCAGCACTATTCACAATAGCAAAGATATGGAATCAATCTAAGTTCCCATCAACAGACGAAAAGAAATGTGATATATATACCCAATGGAATACAATTCAGCCTTAAATAAGAGGGAAATAATGTCATACGCAGTTAAATGGATGGAACTGAAGGTCATTATGTTAAGTGAAGTAAGCTAGGCACAGAAAAATACTGCATGTTCTCACTCATGTATGAGAGCTAAAAAACTTGATCTCATGAACACAGAGAATAGAACAATAGATACCAGAGATGGGAGTGGGGGGTTGGGAAGGATGAAGAGAGGTTGGTTATGGGTACAAACATACATACAGTTAGATAGATGAAATAAGTTCTAATGTTTAATAGCAGACCAGGGTGACTGTACTTGGCAACAATATTATGTGTATTTCACGGTAACTAGAAGAGAGAGTTTGAAGTGATACCAAGACATAAAAATGATGAACACTCAAGGTGACAGAAATCCCAATTACCCTGACTTGATTATTACACATTCTTTGCATGTAGCAAACACTCACATGTATCCTATAAATATCTAAATCATTATATATCAATAAAAGGGGGGGAAAATAAATATGAACATTTTTCATGACTAGAAAAAGTCCTTTTAAAATAAAGCTCTATAAAGTCTACACATTTGGAAAAAGGTAGACAATATTATCTTTATACTCTGTGGTTAAGTATGATAGTTTTTATTTAAGAACTATGGCTTAAATATAACATAAGCCTCATAATATCTGTGAAATAAATGTCAGTCTCATATCTTTAGGTAAACTGAAATATATGAACAGATACTTCCATCAAGAAACTAAGAGAAATTGGGAAAAATTTATCTTATCTCTAATGCTGTATTTTTAATGATCAGACTATGCTGATTTCTCTTTAACTCAATTTTACAATATTACATTTATAACGCTGGGAAAATAACATTTATGGCACTATGGCATCATGATACTACTTTTCCTACCTCTTCCAGACTATTCCTTAATACAAAATCACTTGATAGAATGCTTATAGTTGCCCTCTGACACCCTATTCCTATGGAGGATAAGGCCAGAGAGGTTCTCTGTAAGGCTGTATGGATTGTTACTTACGAAAGGCACTTTAAGTATTTTTCATTAACGTAGTCAAATAGTCCTTTTTTTTCTCAGCGATCTGAAGTTAAGTTACAGACTTCATTACATTTTGCCCCTAAATACTTCAAATGCCACTTTGGGAGGTCAAAGTGGGTGGATCACTTGAGGTCAGAAGTTCGAGACCAACCTGGCCAACATGGTGAAACCCCATCTCTACCAAAAATATAAAAATTAGTCAGGCATGGTGGCGTGCACCTGTAATCCCAGCTACTTGGAAGGCTGAGACAGAAGAATCGCTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCTGAGACAGCCTGGGTGACAGAAGGAGACTGTCTCAAAGAAACAAAACCTTCAGATGCTTCAACATACATCTCTTTAGAATAAGGGCATTTCTCACAAAACCATAACATTTTATACCTAAGAAAATTTATAGTAATTTCTTAGTATCTAATAGCCAGTCCATATTCAAACTTCCCGAATTGAGGAATTTATTTTTAATTAAGATGGTATTAAATAATTACACTTGGTGAGATAATTCTTTCTTGATGTTTTTCTCCCTGACCTTCTTTCTTAAAATTGAAGCCTACAGACAAGATGAACACAATAAACATTCATATATTTTTCAACTTGATAACCCAAAAGGTGGCTGATTTGCCACCTTTTTCTTTTTCTTGGATATACCATTTGAAAGTAGATTGTAGATAAAAGTCCTATTTTAATGCTATTTTTATAAGTGACAAACAGTACAGAAGACAGGCCACATGGTAATGCTCATAGATATTCTAAGTAGATATACCTATTTTTCAAAAAGGAAGACACATTTATTTGAGGAAATGCTGATGAGTTGGCAGCATTCCCTATAATAATTCTTAGAAGACTATGCTCCATCAGAGCAAGAGCTGTGTATCTCTCTTTTCATTATTTTATTCCAGTGCCTGATTGTCTATTGACCTGAATCATTATTTGTTAATAAAAGGTCATGGGGCAGGAAGAATGCCTAAGGATAACTGTCAGCTGGGACTTGGGGACTCGGTTCAACATCCAAGTTCAAGTACTAGGGTCCTAATCATGTTAGACATATACCTCACCACCTGTGACAAATTTAGAGACTTATTTGAGAAGTATAGGGACAAACTGTAAAAATATTTATTTATATGGTGTAGTTTTAAAGTAGAAAAATTAAATATATAGTATTATCTTCTTTAAAAAAATTAAATATATAGTATTATCTTCTTTAAAAAAGAAATCAAGCCAATAATAGTTTCCCATTTCTATCACCAAGCTGAAAAAGTTAAAACATTTCCAAATAAAACAATGTTAACTTTAATCTCATTAAAGTCAAAACGAGTTTATTCAAGTCAAAAGATAAAACAGATTTGTCATCTACCTCTTGAGTTGCTATTTTACGATTTAGTTCAGCTACTTTGGAAGAAGAATTTTCTACTGCATTTTGGCAAAGGAGTTTCTCTATTTCTCTCTGATGAGATGCTTTGAGGGATGCAATGTGTGCTGCAGTATCTTCCTTGACCCTACAGAGCAAATGAAAGAAAACCACACATAAAAGTGGCTCTTCAACCTCTAATTCAGAGTTAGCACAAAAACAGTAGAAGAAACCTGGGAATTAAGCAAGGGGAAAATGGGCACCAATATTAACTGCACTGTGTTAGGTGCTTTATACATTACTACTGCCTATGAGTTCTTATGACCAATCCATGAGCTACTATTTACTGAATTTTATAAGGGCAAACTTGAGGAAATAGTGATATATCTCTACTTTACCCCAACCTGAGGCTACACTTTCTGAGGGAATCTAGGGTTCCAAAAGCAAAGCACTTGACATTTGATCTTTTAAGATAAACTCAGATTTCTTGCCCAGATGCTTCTTTGGAAAATCACAGCTGTTCCCTTTAGAATCTCCAATGCCTTGTAGGCAGCATTAACCAATTTTCAACCCATGCATGAGACTCCAGGGCTAGTTGCATATTGTGAGAATGAGACAATCTTTATGGTAATTCTCAGGACATATTATGCTTGTAATATGCAATTAATTAATTGGACTGTAAGTGTGAAAGACTATTCATTTGTCTCTGTGATAAAATTTATTCAGAGGCAGTTCAGTAAATGGTTAAAATTATAAATAAAGATTTGGTATATTTCCTACAGATAAACATTTTCTCTCTTATTGGAAAGACTTTGAAAATAACAGCATTTAACTTAAAGCATGTATTTTAGTAAACTGCTGTTGCTATATATTAATATGGTGCTTCCCAACTATAGACAAATTTATCCATTGCTTATTTCACCATATGAATATTTCTCCATGGAAACAGTGTGAGTAGGGTCCTAGAAAAAGCATAAAAACCTAAATTAAAGCACATATAACTGAATGATAGTAAAAAGTCTAAATATTGGACTAGAAAAGTTTATTCTTCACTTCTCAGGCCCAGACTTATCTAAGAAACAGATTGACAATATTAACAAATTTTAAATGATGTACAGGAAAATTAATTGGAAAACCTGAATTTTAAATTCTTTCCTGGAAAAAATGTGATTCTTCTTAAAGAGCTTCATGCTACTGTCATAATATTCAGGACTTAAGAAACAAGCTTTCCATTTGGTAGCAATATGACTGCCATATGGTAACAACATGACTCACTCACTGCCATGGCTGCCAGTCAATAAGCATTTGTTGGGTGTTTCCCATGCTCATTCTCCTCCTACAGCACATTGCTGTGGGGATGCAAAAGCAGCATAATCTTACACCAGTTCTCAAGGAACTACAAGGCTGTGTATGATTAATCCTTTCTTGGTACATATTAGTAAGTTATGTAGGAGTTGGGGGTAGGAGAAGGCAATTTCCTGGGAAGTTCCACGAAATGTTTTGTGAAGGTAGTACTTATAACAAGAATGAGGAAAAGGCATGAGGAAATGTGACAGATTAGGTAAGTAGAGTAGTATTAGAATAGTGATGAGACTTGAGATGCTAGGCAGAGAAATTTAGTCTTGATATTTAAGGAAGTTGAGAGTCACCGGAGAGCAGAGTGACCCAGGTATATGAGTATTTAAAGAATATTAATGATTTTTAAGCAAGATGACTGGGGAAGGTTAAAAAAAAGGAAGATTGGAGTGGGAAAATTGTATAATGGCAGCACTGGTTTATAAAAGTAAGGAAGACTGGAAAATGGGAAACATTTATACCCAAGGAATAACAGAGATAAAGCTGGGCTGGTAATTAAAATAAATATAGACAGGGAAGGGGAGCTTGGGAAGGGGAACTAATTTACAGGTAAAAAAAGGAAACTTGAGGTATTAGTGATTCCAAGAGAAGCAATCCAATAAATAGTTCTAGGTTTCACATCTGAACTCAGCAAAGAGAACAAGACTTTAAAAGTAAATCTAGAAGTCATGGTTCACAGAAACCGTAAGAATGGGTAAGTTTAGCAACAGAGAAAGAACAGAGAATAAACAGAAAACTAAGAGCTGAATGCTGGTAGAAAGCCAGATTTTTGGGGATGGAGAAGGAAGAAGGGTCAGAATTCAGTAAAAGAAACAGAAAAGGAGTTTTGGTCAGAGCAGCCAAGCCACAGAGGTTAAGGGGAGAAGCCATTTCAGGAAAAGTAGTGTGGTCAACATTGTTGAAGAAAATGAGGAAGGAGAAAATGCCCCTGGACTGGGAAAGCTCATTATTGAGACCAGGTTTAAAAAGGGTGATGATGAGAGCCATATTTAAGAGGAAGTGAGATAGAAATAAAAGAAAATACTATTTGTGAAAAACGGGTGCTAAAAGACAGGATTGGATTGGAACCTGATCAGGTGAAAAAAAGATCTGAGGATGTCAAAAGACTCAGAGGAAAGAGACAGTGGATAGCAAATGGAGATAGTGAGAAGGAAATGGATGAGTATAAAGTTCCTTAAGGCATGAATGGATGTGATCACAAGGTCAATTTGAAGAGTTATTTTTGAAAAGAGGACCTTTTCCTTTTAGACTGCCAACTAGCTTTAACAATAACTGTTTTCTGAAAGCAATCTGTCTATAGCAATAATAAACTATGACATTCCTTTGCTAGAAGAGCCCAAAGAGTCAGCTTATTAATACCATTTGGGTACATGCCAAAAGGCAAGACTGGCGAGCCCAAGGACACAATTTGGGTTGACACAGATGTTCAGGTACATCAGAATTTGGGCCACCAGCAGGTAGAAGACCCTATCCTGAAACAGACACATGCTCAGCAATATAATATAATTTATTAATATTCACTTATGAATTCAGTTCGGGGTCAAACTAATTATCTGGAGGAAATATATCGTATAATTTTTCTATTTTTATCTTTTTATTTTTACAAATATTTATAAATAATTTAACATTTTACCTTCTCATGGAGTTTTCAAATTGATTCATCACTGCTTCAGATTTCATCTTCAG
--- /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
--- /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
--- /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 @@ -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
--- /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 @@ -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
--- /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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/translate_bed_sequences.py Mon Jan 25 12:21:21 2016 -0500 @@ -0,0 +1,375 @@ +#!/usr/bin/env python +""" +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2014, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# James E Johnson +# +#------------------------------------------------------------------------------ +""" + +""" +Input: BED file (12 column) + 13th sequence column appended by extract_genomic_dna +Output: Fasta of 3-frame translations of the spliced sequence + +""" + +import sys,re,os.path +import tempfile +import optparse +from optparse import OptionParser +from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate + +class BedEntry( object ): + def __init__(self, line): + self.line = line + try: + fields = line.rstrip('\r\n').split('\t') + (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12] + seq = fields[12] if len(fields) > 12 else None + self.chrom = chrom + self.chromStart = int(chromStart) + self.chromEnd = int(chromEnd) + self.name = name + self.score = int(score) + self.strand = strand + self.thickStart = int(thickStart) + self.thickEnd = int(thickEnd) + self.itemRgb = itemRgb + self.blockCount = int(blockCount) + self.blockSizes = [int(x) for x in blockSizes.split(',')] + self.blockStarts = [int(x) for x in blockStarts.split(',')] + self.seq = seq + except Exception, e: + print >> sys.stderr, "Unable to read Bed entry" % e + exit(1) + def __str__(self): + 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' % ( + self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, + ','.join([str(x) for x in self.blockSizes]), + ','.join([str(x) for x in self.blockStarts]), + '\t%s' % self.seq if self.seq else '') + def get_splice_junctions(self): + splice_juncs = [] + for i in range(self.blockCount - 1): + splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1]) + splice_juncs.append(splice_junc) + return splice_juncs + def get_exon_seqs(self): + exons = [] + for i in range(self.blockCount): + # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1]) + exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]]) + if self.strand == '-': #reverse complement + exons.reverse() + for i,s in enumerate(exons): + exons[i] = reverse_complement(s) + return exons + def get_spliced_seq(self): + seq = ''.join(self.get_exon_seqs()) + return seq + def get_translation(self,sequence=None): + translation = None + seq = sequence if sequence else self.get_spliced_seq() + if seq: + seqlen = len(seq) / 3 * 3; + if seqlen >= 3: + translation = translate(seq[:seqlen]) + return translation + def get_translations(self): + translations = [] + seq = self.get_spliced_seq() + if seq: + for i in range(3): + translation = self.get_translation(sequence=seq[i:]) + if translation: + translations.append(translation) + return translations + ## (start,end) + def get_subrange(self,tstart,tstop): + chromStart = self.chromStart + chromEnd = self.chromEnd + r = range(self.blockCount) + if self.strand == '-': + r.reverse() + bStart = 0 + for x in r: + bEnd = bStart + self.blockSizes[x] + if bStart <= tstart < bEnd: + if self.strand == '+': + chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart) + else: + chromEnd = self.chromStart + self.blockStarts[x] + (tstart - bStart) + if bStart <= tstop < bEnd: + if self.strand == '+': + chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart) + else: + chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart) + bStart += self.blockSizes[x] + return(chromStart,chromEnd) + #get the blocks for sub range + def get_blocks(self,chromStart,chromEnd): + tblockCount = 0 + tblockSizes = [] + tblockStarts = [] + for x in range(self.blockCount): + bStart = self.chromStart + self.blockStarts[x] + bEnd = bStart + self.blockSizes[x] + if bStart > chromEnd: + break + if bEnd < chromStart: + continue + cStart = max(chromStart,bStart) + tblockStarts.append(cStart - chromStart) + tblockSizes.append(min(chromEnd,bEnd) - cStart) + tblockCount += 1 + ## print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes) + return (tblockCount,tblockSizes,tblockStarts) + ## [(start,end,seq,blockCount,blockSizes,blockStarts),(start,end,seq,blockCount,blockSizes,blockStarts),(start,end,seq,blockCount,blockSizes,blockStarts)] + ## filter: ignore translation if stop codon in first exon after ignore_left_bp + def get_filterd_translations(self,untrimmed=False,filtering=True,ignore_left_bp=0,ignore_right_bp=0,debug=False): + translations = [None,None,None,None,None,None] + seq = self.get_spliced_seq() + ignore = (ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3 + block_sum = sum(self.blockSizes) + exon_sizes = [x for x in self.blockSizes] + if self.strand == '-': + exon_sizes.reverse() + splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))] + if debug: + print >> sys.stderr, "splice_sites: %s" % splice_sites + junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0] + if seq: + for i in range(3): + translation = self.get_translation(sequence=seq[i:]) + if translation: + tstart = 0 + tstop = len(translation) + offset = (block_sum - i) % 3 + if debug: + print >> sys.stderr, "frame: %d\ttstart: %d tstop: %d offset: %d\t%s" % (i,tstart,tstop,offset,translation) + if not untrimmed: + tstart = translation.rfind('*',0,junc) + 1 + stop = translation.find('*',junc) + tstop = stop if stop >= 0 else len(translation) + offset = (block_sum - i) % 3 + trimmed = translation[tstart:tstop] + if debug: + print >> sys.stderr, "frame: %d\ttstart: %d tstop: %d offset: %d\t%s" % (i,tstart,tstop,offset,trimmed) + if filtering and tstart > ignore: + continue + #get genomic locations for start and end + if self.strand == '+': + chromStart = self.chromStart + i + (tstart * 3) + chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3 + else: + chromStart = self.chromStart + offset + (len(translation) - tstop) * 3 + chromEnd = self.chromEnd - i - (tstart * 3) + #get the blocks for this translation + (tblockCount,tblockSizes,tblockStarts) = self.get_blocks(chromStart,chromEnd) + translations[i] = (chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts) + if debug: + print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes) + # translations[i] = (chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts) + return translations + def get_seq_id(self,seqtype='unk:unk',reference='',frame=None): + ## Ensembl fasta ID format + # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT + # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding + frame_name = '' + chromStart = self.chromStart + chromEnd = self.chromEnd + strand = 1 if self.strand == '+' else -1 + if frame != None: + block_sum = sum(self.blockSizes) + offset = (block_sum - frame) % 3 + frame_name = '_' + str(frame + 1) + if self.strand == '+': + chromStart += frame + chromEnd -= offset + else: + chromStart += offset + chromEnd -= frame + location = "chromosome:%s:%s:%s:%s:%s" % (reference,self.chrom,chromStart,chromEnd,strand) + seq_id = "%s%s %s %s" % (self.name,frame_name,seqtype,location) + return seq_id + def get_line(self, start_offset = 0, end_offset = 0): + if start_offset or end_offset: + s_offset = start_offset if start_offset else 0 + e_offset = end_offset if end_offset else 0 + if s_offset > self.chromStart: + s_offset = self.chromStart + chrStart = self.chromStart - s_offset + chrEnd = self.chromEnd + e_offset + blkSizes = self.blockSizes + blkSizes[0] += s_offset + blkSizes[-1] += e_offset + blkStarts = self.blockStarts + for i in range(1,self.blockCount): + blkStarts[i] += s_offset + items = [str(x) for x in [self.chrom,chrStart,chrEnd,self.name,self.score,self.strand,self.thickStart,self.thickEnd,self.itemRgb,self.blockCount,','.join([str(x) for x in blkSizes]),','.join([str(x) for x in blkStarts])]] + return '\t'.join(items) + '\n' + return self.line + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-i', '--input', dest='input', help='BED file (tophat junctions.bed) with sequence column added' ) + parser.add_option( '-o', '--output', dest='output', help='Translations of spliced sequence') + parser.add_option( '-b', '--bed_format', dest='bed_format', action='store_true', default=False, help='Append translations to bed file instead of fasta' ) + parser.add_option( '-D', '--fa_db', dest='fa_db', default=None, help='Prefix DB identifier for fasta ID line, e.g. generic' ) + parser.add_option( '-s', '--fa_sep', dest='fa_sep', default='|', help='fasta ID separator defaults to pipe char, e.g. generic|ProtID|description' ) + parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation' ) + parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file' ) + parser.add_option( '-S', '--seqtype', dest='seqtype', default='pep:splice', help='SEQTYPE:STATUS for fasta ID line' ) + parser.add_option( '-P', '--id_prefix', dest='id_prefix', default='', help='prefix for the sequence ID' ) + parser.add_option( '-R', '--reference', dest='reference', default=None, help='Genome Reference Name for fasta ID location ' ) + parser.add_option( '-r', '--refsource', dest='refsource', default=None, help='Source for Genome Reference, e.g. Ensembl, UCSC, or NCBI' ) + parser.add_option( '-Q', '--score_name', dest='score_name', default=None, help='include in the fasta ID line score_name:score ' ) + parser.add_option( '-l', '--leading_bp', dest='leading_bp', type='int', default=None, help='leading number of base pairs to ignore when filtering' ) + parser.add_option( '-t', '--trailing_bp', dest='trailing_bp', type='int', default=None, help='trailing number of base pairs to ignore when filtering' ) + parser.add_option( '-U', '--unfiltered', dest='filtering', action='store_false', default=True, help='Do NOT filterout translation with stop codon in the first exon' ) + parser.add_option( '-u', '--untrimmed', dest='untrimmed', action='store_true', default=False, help='Do NOT trim from splice site to stop codon' ) + parser.add_option( '-L', '--min_length', dest='min_length', type='int', default=None, help='Minimun length (to first stop codon)' ) + parser.add_option( '-M', '--max_stop_codons', dest='max_stop_codons', type='int', default=None, help='Filter out translations with more than max_stop_codons' ) + parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' ) + (options, args) = parser.parse_args() + # Input files + if options.input != None: + try: + inputPath = os.path.abspath(options.input) + inputFile = open(inputPath, 'r') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(2) + else: + inputFile = sys.stdin + # Output files + bed_fh = None + gff_fh = None + gff_fa_file = None + gff_fa = None + outFile = None + if options.output == None: + #write to stdout + outFile = sys.stdout + if options.gff: + gff_fa_file = tempfile.NamedTemporaryFile(prefix='gff_fasta_',suffix=".fa",dir=os.getcwd()).name + gff_fa = open(gff_fa_file,'w') + else: + try: + outPath = os.path.abspath(options.output) + outFile = open(outPath, 'w') + except Exception, e: + print >> sys.stderr, "failed: %s" % e + exit(3) + if options.gff: + gff_fa_file = outPath + if options.bed: + bed_fh = open(options.bed,'w') + bed_fh.write('track name="%s" description="%s" \n' % ('novel_junctioni_translations','test')) + if options.gff: + gff_fh = open(options.gff,'w') + gff_fh.write("##gff-version 3.2.1\n") + if options.reference: + gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference)) + leading_bp = 0 + trailing_bp = 0 + if options.leading_bp: + if options.leading_bp >= 0: + leading_bp = options.leading_bp + else: + print >> sys.stderr, "failed: leading_bp must be positive" + exit(5) + if options.trailing_bp: + if options.trailing_bp >= 0: + trailing_bp = options.trailing_bp + else: + print >> sys.stderr, "failed: trailing_bp must be positive" + exit(5) + # Scan bed file + try: + for i, line in enumerate( inputFile ): + if line.startswith('track'): + if outFile and options.bed_format: + outFile.write(line) + continue + entry = BedEntry(line) + strand = 1 if entry.strand == '+' else -1 + translations = entry.get_translations() + if options.debug: + exon_seqs = entry.get_exon_seqs() + exon_sizes = [len(seq) for seq in exon_seqs] + splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))] + print >> sys.stderr, entry.name + print >> sys.stderr, line.rstrip('\r\n') + print >> sys.stderr, "exons: %s" % exon_seqs + print >> sys.stderr, "%s" % splice_sites + for i,translation in enumerate(translations): + print >> sys.stderr, "frame %d: %s" % (i+1,translation) + print >> sys.stderr, "splice: %s" % (''.join(['^' if (((j*3)+i)/3) in splice_sites else '-' for j in range(len(translation))])) + print >> sys.stderr, "" + if options.bed_format: + tx_entry = "%s\t%s\n" % (line.rstrip('\r\n'),'\t'.join(translations)) + outFile.write(tx_entry) + else: + translations = entry.get_filterd_translations(untrimmed=options.untrimmed,filtering=options.filtering,ignore_left_bp=leading_bp,ignore_right_bp=trailing_bp,debug=options.debug) + for i,tx in enumerate(translations): + if tx: + (chromStart,chromEnd,translation,blockCount,blockSizes,blockStarts) = tx + if options.min_length != None and len(translation) < options.min_length: + continue + if options.max_stop_codons != None and translation.count('*') > options.max_stop_codons: + continue + frame_name = '_%s' % (i + 1) + pep_id = "%s%s%s" % (options.id_prefix,entry.name,frame_name) + if bed_fh: + 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)) + location = "chromosome:%s:%s:%s:%s:%s" % (options.reference,entry.chrom,chromStart,chromEnd,strand) + score = " %s:%s" % (options.score_name,entry.score) if options.score_name else '' + seq_description = "%s %s%s" % (options.seqtype, location, score) + seq_id = "%s " % pep_id + if options.fa_db: + seq_id = "%s%s%s%s" % (options.fa_db,options.fa_sep,pep_id,options.fa_sep) + fa_id = "%s%s" % (seq_id,seq_description) + fa_entry = ">%s\n%s\n" % (fa_id,translation) + outFile.write(fa_entry) + if gff_fh: + if gff_fa: + gff_fa.write(fa_entry) + gff_fh.write("##sequence-region %s %d %d\n" % (entry.chrom,chromStart + 1,chromEnd - 1)) + 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)) + for x in range(blockCount): + start = chromStart+blockStarts[x] + 1 + end = start + blockSizes[x] - 1 + phase = (3 - sum(blockSizes[:x]) % 3) % 3 + 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)) + """ + ##gff-version 3 + ##sequence-region 19 1 287484 + 19 MassSpec peptide 282299 287484 10.0 - 0 ID=TEARLSFYSGHSSFGMYCMVFLALYVQ + 19 MassSpec CDS 287474 287484 . - 0 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812 + 19 MassSpec CDS 282752 282809 . - 1 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812 + 19 MassSpec CDS 282299 282310 . - 0 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812 + """ + if bed_fh: + bed_fh.close() + if gff_fh: + if gff_fa: + gff_fa.close() + else: + outFile.close() + gff_fa = open(gff_fa_file,'r') + gff_fh.write("##FASTA\n") + for i, line in enumerate(gff_fa): + gff_fh.write(line) + gff_fh.close() + except Exception, e: + print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e) + +if __name__ == "__main__" : __main__() +
--- /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>