From 76581a006ada8bb6842fa6e46c3c58569298eb5d Mon Sep 17 00:00:00 2001 From: Dave B Date: Wed, 6 Jun 2018 14:09:20 -0400 Subject: [PATCH 01/11] Add tn93. --- tools/tn93/.shed.yml | 11 ++ tools/tn93/test-data/tn93-in1.fa | 224 +++++++++++++++++++++++++ tools/tn93/test-data/tn93-in2-alpha.fa | 112 +++++++++++++ tools/tn93/test-data/tn93-in2-beta.fa | 112 +++++++++++++ tools/tn93/test-data/tn93-out1.csv | 29 ++++ tools/tn93/test-data/tn93-out2.csv | 17 ++ tools/tn93/tn93-out1.csv | 29 ++++ tools/tn93/tn93.xml | 107 ++++++++++++ 8 files changed, 641 insertions(+) create mode 100644 tools/tn93/.shed.yml create mode 100644 tools/tn93/test-data/tn93-in1.fa create mode 100644 tools/tn93/test-data/tn93-in2-alpha.fa create mode 100644 tools/tn93/test-data/tn93-in2-beta.fa create mode 100644 tools/tn93/test-data/tn93-out1.csv create mode 100644 tools/tn93/test-data/tn93-out2.csv create mode 100644 tools/tn93/tn93-out1.csv create mode 100644 tools/tn93/tn93.xml diff --git a/tools/tn93/.shed.yml b/tools/tn93/.shed.yml new file mode 100644 index 00000000000..5d194d1693a --- /dev/null +++ b/tools/tn93/.shed.yml @@ -0,0 +1,11 @@ +name: tn93 +owner: iuc +description: Compute distances between sequences +long_description: | + This is a simple program meant to compute pairwise distances between aligned + nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ +homepage_url: https://github.com/veg/tn93/ +type: unrestricted +categories: + - Next Gen Mappers diff --git a/tools/tn93/test-data/tn93-in1.fa b/tools/tn93/test-data/tn93-in1.fa new file mode 100644 index 00000000000..093f666672b --- /dev/null +++ b/tools/tn93/test-data/tn93-in1.fa @@ -0,0 +1,224 @@ +>B_FR_83_HXB2_ACC_K03455_5 +CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC +AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA +GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACCTTC +>B_US_83_RF_ACC_M17451 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT +TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA +AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA +CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT +CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC +GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG +CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA +TAATAGGAGCAGAAACTTTC +>B_US_86_JRFL_ACC_U63632 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA +AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA +ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG +GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC +>B_US_90_WEAU160_ACC_U21135 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC +AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA +AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA +GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG +CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC +>D_CD_83_ELI_ACC_K03454_7 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA +AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC +AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG +AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC +ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA +ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG +GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_CD_83_NDK_ACC_M27323 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC +AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA +CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC +AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC +AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG +ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA +ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_CD_84_84ZR085_ACC_U88822 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA +AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC +AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA +AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC +AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG +GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_UG_94_94UG114_ACC_U88824 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA +TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC +TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC +AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA +GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA +CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC +AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA +GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC +AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA +ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG +GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT +CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA +TAGTAGGAGCAGAAACTTTC diff --git a/tools/tn93/test-data/tn93-in2-alpha.fa b/tools/tn93/test-data/tn93-in2-alpha.fa new file mode 100644 index 00000000000..e8252b6c779 --- /dev/null +++ b/tools/tn93/test-data/tn93-in2-alpha.fa @@ -0,0 +1,112 @@ +>B_FR_83_HXB2_ACC_K03455_5 +CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC +AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA +GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACCTTC +>B_US_83_RF_ACC_M17451 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT +TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA +AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA +CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT +CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC +GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG +CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA +TAATAGGAGCAGAAACTTTC +>B_US_86_JRFL_ACC_U63632 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA +AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA +ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG +GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC +>B_US_90_WEAU160_ACC_U21135 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC +AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA +AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA +GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG +CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC \ No newline at end of file diff --git a/tools/tn93/test-data/tn93-in2-beta.fa b/tools/tn93/test-data/tn93-in2-beta.fa new file mode 100644 index 00000000000..70c28bf5c0b --- /dev/null +++ b/tools/tn93/test-data/tn93-in2-beta.fa @@ -0,0 +1,112 @@ +>D_CD_83_ELI_ACC_K03454_7 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA +AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC +AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG +AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC +ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA +ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG +GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_CD_83_NDK_ACC_M27323 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC +AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA +CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC +AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC +AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG +ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA +ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_CD_84_84ZR085_ACC_U88822 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA +AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC +AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA +AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC +AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG +GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_UG_94_94UG114_ACC_U88824 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA +TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC +TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC +AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA +GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA +CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC +AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA +GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC +AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA +ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG +GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT +CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA +TAGTAGGAGCAGAAACTTTC diff --git a/tools/tn93/test-data/tn93-out1.csv b/tools/tn93/test-data/tn93-out1.csv new file mode 100644 index 00000000000..9981b245286 --- /dev/null +++ b/tools/tn93/test-data/tn93-out1.csv @@ -0,0 +1,29 @@ +B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 +B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 +B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586 +B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619 +B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988 +B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 +B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908 +B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759 +B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066 +B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146 +B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213 +B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 +B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797 +B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044 +B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011 +B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054 +B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856 +B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097 +B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203 +B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019 +D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 +D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948 +D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033 +D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 +D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626 +D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088 +ID1,ID2,Distance diff --git a/tools/tn93/test-data/tn93-out2.csv b/tools/tn93/test-data/tn93-out2.csv new file mode 100644 index 00000000000..3459c62c219 --- /dev/null +++ b/tools/tn93/test-data/tn93-out2.csv @@ -0,0 +1,17 @@ +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586 +B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619 +B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988 +B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759 +B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066 +B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146 +B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213 +B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797 +B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044 +B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011 +B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054 +B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856 +B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097 +B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203 +B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019 +ID1,ID2,Distance diff --git a/tools/tn93/tn93-out1.csv b/tools/tn93/tn93-out1.csv new file mode 100644 index 00000000000..a8fef1214f6 --- /dev/null +++ b/tools/tn93/tn93-out1.csv @@ -0,0 +1,29 @@ +#ID1,ID2,Distance +B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 +B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 +B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586 +B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619 +B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988 +B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 +B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908 +B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759 +B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066 +B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146 +B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213 +B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 +B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797 +B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044 +B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011 +B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054 +B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856 +B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097 +B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203 +B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019 +D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 +D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948 +D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033 +D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 +D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626 +D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088 diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml new file mode 100644 index 00000000000..e956ad9953c --- /dev/null +++ b/tools/tn93/tn93.xml @@ -0,0 +1,107 @@ + + + compute distances between aligned sequences + + tn93 + + + + + + 0: + -d $options.counts_in_name + #end if + #end if + #if $second_fasta: + -s '$second_fasta' + #end if + '$input_fasta' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + seqname:10 + +':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers +only affect histogram and mean calculations. +]]> + + + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + + + From 44ce2b6c4be891319a01d488390dffd955aa0711 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 11 Jun 2018 21:38:44 +0200 Subject: [PATCH 02/11] Update tn93.xml --- tools/tn93/tn93.xml | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index e956ad9953c..675f6ce06de 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -1,20 +1,20 @@ - - + compute distances between aligned sequences tn93 - - - 0: - -d $options.counts_in_name + -d '$options.counts_in_name' #end if #end if #if $second_fasta: @@ -23,8 +23,9 @@ '$input_fasta' ]]> - - + + @@ -45,9 +46,12 @@ - - - + + + From 968b5caa8b9c7887f17700ada069017ccae5ec4e Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 18 Jun 2018 12:54:24 -0400 Subject: [PATCH 03/11] Fix output formats. --- tools/tn93/tn93.xml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index 675f6ce06de..0883e8d7b17 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -56,12 +56,7 @@ - - - - - - + From b6834a53ca0cb462695b110b042172c9475f6024 Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 14 Jan 2019 12:10:48 -0500 Subject: [PATCH 04/11] Clean up formats and tests. --- tools/tn93/tn93-out1.csv | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 tools/tn93/tn93-out1.csv diff --git a/tools/tn93/tn93-out1.csv b/tools/tn93/tn93-out1.csv deleted file mode 100644 index a8fef1214f6..00000000000 --- a/tools/tn93/tn93-out1.csv +++ /dev/null @@ -1,29 +0,0 @@ -#ID1,ID2,Distance -B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 -B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 -B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566 -B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206 -B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586 -B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619 -B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988 -B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 -B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908 -B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759 -B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066 -B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146 -B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213 -B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 -B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797 -B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044 -B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011 -B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054 -B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856 -B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097 -B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203 -B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019 -D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 -D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948 -D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033 -D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 -D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626 -D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088 From db8b33a0925256026979594372c0840b265335a3 Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 14 Jan 2019 16:18:17 -0500 Subject: [PATCH 05/11] Remove nonexistent output formats. --- tools/tn93/tn93.xml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index 0883e8d7b17..326ae8550b9 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -11,7 +11,7 @@ -t $options.threshold -a $options.ambigs -g $options.fraction - -f $format + -f csv -l $options.overlap #if len(str($options.counts_in_name)) > 0: -d '$options.counts_in_name' @@ -26,11 +26,6 @@ - - - - - @@ -60,14 +55,12 @@ - - From a0fc59dfec89b6660b160296d2d7efdbb02f3188 Mon Sep 17 00:00:00 2001 From: Dave B Date: Thu, 17 Jan 2019 15:16:12 -0500 Subject: [PATCH 06/11] Fix category in .shed.yml --- tools/tn93/.shed.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/tn93/.shed.yml b/tools/tn93/.shed.yml index 5d194d1693a..1db6ccc89f6 100644 --- a/tools/tn93/.shed.yml +++ b/tools/tn93/.shed.yml @@ -8,4 +8,4 @@ remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/to homepage_url: https://github.com/veg/tn93/ type: unrestricted categories: - - Next Gen Mappers + - Sequence Analysis From 5c1418d1933ade897b72eb841ebe131a2c4f4c0e Mon Sep 17 00:00:00 2001 From: Dave B Date: Thu, 17 Jan 2019 15:31:49 -0500 Subject: [PATCH 07/11] Fix optional parameter to actually be optional. --- tools/tn93/tn93.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index 326ae8550b9..935aa87cf14 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -13,7 +13,7 @@ -g $options.fraction -f csv -l $options.overlap - #if len(str($options.counts_in_name)) > 0: + #if $options.counts_in_name: -d '$options.counts_in_name' #end if #end if @@ -46,7 +46,7 @@ + optional="true" label="Sequence name component immediately preceding a copy number" /> From 123e28e1386a4c86fabe55879e2c413722ea4a4d Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 19 Mar 2019 10:19:52 -0400 Subject: [PATCH 08/11] Add a wrapper for the `readreduce` command. --- tools/tn93/readreduce.xml | 75 ++++++++ tools/tn93/test-data/readreduce-in1.fa | 224 ++++++++++++++++++++++++ tools/tn93/test-data/readreduce-in2.fa | 112 ++++++++++++ tools/tn93/test-data/readreduce-out1.fa | 0 tools/tn93/test-data/readreduce-out2.fa | 0 5 files changed, 411 insertions(+) create mode 100644 tools/tn93/readreduce.xml create mode 100644 tools/tn93/test-data/readreduce-in1.fa create mode 100644 tools/tn93/test-data/readreduce-in2.fa create mode 100644 tools/tn93/test-data/readreduce-out1.fa create mode 100644 tools/tn93/test-data/readreduce-out2.fa diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml new file mode 100644 index 00000000000..297d82400a5 --- /dev/null +++ b/tools/tn93/readreduce.xml @@ -0,0 +1,75 @@ + + into clusters with TN-93 + + tn93 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + + + diff --git a/tools/tn93/test-data/readreduce-in1.fa b/tools/tn93/test-data/readreduce-in1.fa new file mode 100644 index 00000000000..093f666672b --- /dev/null +++ b/tools/tn93/test-data/readreduce-in1.fa @@ -0,0 +1,224 @@ +>B_FR_83_HXB2_ACC_K03455_5 +CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC +AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA +GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACCTTC +>B_US_83_RF_ACC_M17451 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT +TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA +AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA +CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT +CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC +GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG +CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA +TAATAGGAGCAGAAACTTTC +>B_US_86_JRFL_ACC_U63632 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA +AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA +ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG +GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC +>B_US_90_WEAU160_ACC_U21135 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC +AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA +AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA +GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG +CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC +>D_CD_83_ELI_ACC_K03454_7 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA +AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC +AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG +AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC +ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA +ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG +GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_CD_83_NDK_ACC_M27323 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC +AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA +CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC +AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC +AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG +ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA +ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_CD_84_84ZR085_ACC_U88822 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT +TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT +GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA +AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC +AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT +CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA +AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC +AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG +GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT +CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA +TAATAGGAGCAGAAACTTTC +>D_UG_94_94UG114_ACC_U88824 +CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA +TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC +TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA +CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC +AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA +GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA +CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC +AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA +AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA +GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA +TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC +AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA +ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG +GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT +CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA +TAGTAGGAGCAGAAACTTTC diff --git a/tools/tn93/test-data/readreduce-in2.fa b/tools/tn93/test-data/readreduce-in2.fa new file mode 100644 index 00000000000..e8252b6c779 --- /dev/null +++ b/tools/tn93/test-data/readreduce-in2.fa @@ -0,0 +1,112 @@ +>B_FR_83_HXB2_ACC_K03455_5 +CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC +AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA +GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACCTTC +>B_US_83_RF_ACC_M17451 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT +TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA +AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA +GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA +CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT +CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA +AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC +GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG +CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC +AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA +ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA +TAATAGGAGCAGAAACTTTC +>B_US_86_JRFL_ACC_U63632 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA +AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA +GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA +AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC +AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC +AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA +GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG +CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA +ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG +GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC +>B_US_90_WEAU160_ACC_U21135 +CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA +TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT +TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT +GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA +CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA +CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA +AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC +AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA +GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA +CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT +ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA +TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA +AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC +AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC +TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA +AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC +AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA +GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG +CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT +GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC +AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA +ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG +GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA +TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT +CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA +TAGTAGGAGCAGAAACTTTC \ No newline at end of file diff --git a/tools/tn93/test-data/readreduce-out1.fa b/tools/tn93/test-data/readreduce-out1.fa new file mode 100644 index 00000000000..e69de29bb2d diff --git a/tools/tn93/test-data/readreduce-out2.fa b/tools/tn93/test-data/readreduce-out2.fa new file mode 100644 index 00000000000..e69de29bb2d From f009487e8fec49f10396185ffd2fc4fe65bf4f29 Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 19 Mar 2019 10:32:17 -0400 Subject: [PATCH 09/11] Note to self: change tool ID before commit. --- tools/tn93/readreduce.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml index 297d82400a5..ae7afee6a17 100644 --- a/tools/tn93/readreduce.xml +++ b/tools/tn93/readreduce.xml @@ -1,4 +1,4 @@ - + into clusters with TN-93 tn93 From 9a6adfe0c2af44657cd0c6227350b9cd18173c69 Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 9 Jul 2019 09:44:51 -0400 Subject: [PATCH 10/11] Update per reviews - Fix indentation - Rename readreduce - Add suite --- tools/tn93/.shed.yml | 8 ++++++++ tools/tn93/readreduce.xml | 22 +++++++++++----------- tools/tn93/tn93.xml | 30 +++++++++++++++--------------- 3 files changed, 34 insertions(+), 26 deletions(-) diff --git a/tools/tn93/.shed.yml b/tools/tn93/.shed.yml index 1db6ccc89f6..029becaf122 100644 --- a/tools/tn93/.shed.yml +++ b/tools/tn93/.shed.yml @@ -9,3 +9,11 @@ homepage_url: https://github.com/veg/tn93/ type: unrestricted categories: - Sequence Analysis +auto_tool_repositories: + name_template: "{{ tool_id }}" + description_template: "Wrapper for the TN-93 tool: {{ tool_name }}" +suite: + name: "suite_tn93" + description: "TN-93 – Transmission Analysis by Distance Clustering" + long_description: | + TN-93 uses the 1993 Tamura-Nei model to deduce pathogen transmission by genetic distance estimation. diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml index ae7afee6a17..92effcd846e 100644 --- a/tools/tn93/readreduce.xml +++ b/tools/tn93/readreduce.xml @@ -1,4 +1,4 @@ - + into clusters with TN-93 tn93 @@ -7,17 +7,17 @@ + -s '$size' + #end if + '$input' + ]]> diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index 935aa87cf14..6280c37f790 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -6,22 +6,22 @@ + #end if + #if $second_fasta: + -s '$second_fasta' + #end if + '$input_fasta' + ]]> Date: Wed, 17 Jul 2019 11:23:47 -0400 Subject: [PATCH 11/11] Put dependency version and citation in a macro. --- tools/tn93/macros.xml | 17 +++++++++++++++++ tools/tn93/readreduce.xml | 18 ++++++------------ tools/tn93/tn93.xml | 20 ++++++++------------ 3 files changed, 31 insertions(+), 24 deletions(-) create mode 100644 tools/tn93/macros.xml diff --git a/tools/tn93/macros.xml b/tools/tn93/macros.xml new file mode 100644 index 00000000000..050c77a80a0 --- /dev/null +++ b/tools/tn93/macros.xml @@ -0,0 +1,17 @@ + + + 1.0.4 + + + + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + + + + + \ No newline at end of file diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml index 92effcd846e..3da05d5b6f8 100644 --- a/tools/tn93/readreduce.xml +++ b/tools/tn93/readreduce.xml @@ -1,7 +1,10 @@ - + into clusters with TN-93 + + macros.xml + - tn93 + tn93 - - - @UNPUBLISHED{spond, - author = "Sergei Kosakovsky Pond", - title = "HyPhy: Hypothesis Testing using Phylogenies", - year = "2000", - note = "http://hyphy.org/", - url = "http://hyphy.org/"} - - + diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index 6280c37f790..3fe93a854c0 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -1,7 +1,10 @@ - + compute distances between aligned sequences + + macros.xml + - tn93 + tn93 - - - @UNPUBLISHED{spond, - author = "Sergei Kosakovsky Pond", - title = "HyPhy: Hypothesis Testing using Phylogenies", - year = "2000", - note = "http://hyphy.org/", - url = "http://hyphy.org/"} - - + + 10.1093/oxfordjournals.molbev.a040023 +