Mercurial > repos > rdvelazquez > bioext_bam2msa

diff test-data/bam2msa-out1.fa @ 0:72b7678b5b09 draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
author rdvelazquez
date Wed, 14 Mar 2018 14:46:48 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam2msa-out1.fa	Wed Mar 14 14:46:48 2018 -0400
@@ -0,0 +1,196 @@
+>Z|JP|K03455|2036|DUPLICATE
+CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
+GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
+AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
+CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGGTATTAATAGGACCTACA
+CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC
+ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAGGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG
+GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT
+GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
+AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA
+AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT
+AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG
+ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG
+GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC
+CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA
+ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT
+CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC
+CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
+GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCARCTGTGTAAA
+CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
+GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGRGTATATTATGATCCA
+TTAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT
+TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC
+ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
+ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
+------------------------------------------------------------
+---------------------------------------------------------
+>Z|JP|K03455|2036|DUPLICATE
+CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
+GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
+AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
+CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGGTATTAGTAGGACCTACA
+CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC
+ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCGAAAGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG
+GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT
+GCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
+AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAA
+AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT
+AAAGACTTCCGGAAGTATACTGCATTCACTATACCTAGTACAAACAATGAGACACCAGGG
+ATTAGATATCAATACAATGTGCTACCACAGGGCTGGAAAGGATCACCAGCAATATTTCAG
+GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC
+CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA
+ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT
+CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC
+CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
+GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA
+CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
+GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA
+TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT
+TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC
+ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
+ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
+------------------------------------------------------------
+---------------------------------------------------------
+>Z|JP|K03455|2036|DUPLICATE
+CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
+GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAYCAGGG
+AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
+CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGATATTAATAGGACCTACA
+CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC
+ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCGAAAGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG
+GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT
+GCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
+AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAA
+AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCTTTAGAT
+AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG
+ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG
+GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC
+CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA
+ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT
+CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC
+CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
+GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA
+CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
+GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA
+TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT
+TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC
+ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
+ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
+------------------------------------------------------------
+---------------------------------------------------------
+>Z|JP|K03455|2036|DUPLICATE
+CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
+GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
+AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAGACAATATGAT
+CAGATACTTATAGAAATTTGTGGGAAAAAGGCTGTAGGTACAGTGTTAGTAGGACCTACA
+CCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGGTGTACTTTAAATCTTCCA
+ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAGGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG
+GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT
+GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
+AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA
+AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT
+AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG
+ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG
+GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC
+CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA
+ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT
+CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC
+CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
+GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA
+CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
+GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA
+TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGAC------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------
+>Z|JP|K03455|2036|DUPLICATE
+CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
+GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
+AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT
+CAGATACTTATAGAAATTTGTGGGAAAAAGGCTGTAGGTACAGTGTTAGTAGGACCTACA
+CCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGGTGTACTTTAAATTTTCCA
+ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAGGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG
+GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT
+GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
+AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA
+AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT
+AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG
+ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG
+GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC
+CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA
+ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT
+CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC
+CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
+GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA
+CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
+GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA
+TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT
+TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC
+ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
+ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
+------------------------------------------------------------
+---------------------------------------------------------
+>Z|JP|K03455|2036|DUPLICATE
+CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
+GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
+AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
+CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
+CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCC
+ATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATG
+GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT
+GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
+AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAA
+AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT
+GAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGG
+ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAA
+AGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTAT
+CAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAA
+ATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACAT
+CAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTA
+CAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTG
+GGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAA
+CTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTA
+GAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCA
+TCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATT
+TATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCAC
+ACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTA
+ATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGG
+TGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCC
+TTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC
+>Z|JP|K03455|2036
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------AAATATGTTGACTCAGATTGGTTGTACTTTAAATTTTCCA
+ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAGGGTT
+AAACAATGGCCATTGACAGAAGAAAAAATAAAGGCGTTAACAGAAATTTGTACAGAAATG
+GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAATATTT
+GCCATAAAGAAAAAAGATAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTCAAT
+AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCGGGATTAAAA
+AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT
+AAAGACTTTAGAAAGCATACTGCATTCACTATACCTAGTGTAAATAATGAAACACCGGGG
+ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG
+GCTAGCATGACAAAAATCTTAGAACCCTTTAGAACAAACAATCCAGAGATGGTGATTTAC
+CAATATATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGACAGCATAGAGAAAAA
+ATACAGGAGTTGAGAGAACATCTACTGAAATGGGGATTTACCACACCAGATAAAAAA---
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------