| Next changeset 1:7db5615f4621 (2017-12-21) |
|
Commit message:
Initial upload |
|
added:
test-data/contigs.fa test-data/test-contigs.fa test-data/test_reads.fa tool_dependencies.xml velvet.xml velvetoptimiser.xml |
| b |
| diff -r 000000000000 -r d81360ea69d8 test-data/contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fa Tue Jun 28 17:30:32 2016 -0400 |
| b |
| b'@@ -0,0 +1,1771 @@\n+>NODE_1_length_2499_cov_8.185675\n+AAGTGATTTCAGTTCACGCTGCTGGATGTGGTGAGACCTAGTGCGAGTGTTACGGTGCGC\n+TAACCGCGAAGGTCACCGCTCAAGGGGAAACTACCCTGTTTGGGTGAAACTCCTATGGTG\n+GACGCGAACTAACGGAAGAATACATCTCTGTCGCATTAAATAACGTCGCGGCGTCCCCTA\n+TGGGTGCTGCTCCAGTTACAGTCATTCAAAATTGCGATCGACAGCGCAGTAAGGACCGCC\n+GGACAGACCCTCGTTTGCTAAACGGCATTCAGTATAGTCTCACTAATGCGGCGTAACATA\n+CTGCAGCGCGGGGTGGTCACTTGGGGGTGGAACGCCAGAGAGAGCGCATCCTAACTGTGC\n+CGCTCGACAATAGAGTGTAGCCCCCGAACTCTCGGGAGAATTACTGCGGCATGCAATCAA\n+ACTCTCATAATTTTATCCCTGCGCGTCCACCAGCCCGCAGCTCCGGATTCTGGCTAAACA\n+CGATTGAGTAACTGGCAGATTTCCCACCAGGCAGAAAAGAAGCTATAACCAAACCCGGTG\n+ACAATAAACGACCCCCACGCGGCTTGACATAAAAAAACACTATACAGCCAGAGTTCCTTC\n+TTCTTCTTGTCGTAGAAACCATCGGAATATATGCGCTGACCCTCCGCCGTTTGACCCCAC\n+ACAGGGTCAATGCGTTAAATTTGGATTCCTGCAGATATACTTTCGGAGGACGATAATTCA\n+GTCTCCGCCGGAGCCATCGGGAAGTAGGTTGCGAATCGAGCTTTAATAGCGACGGCGATC\n+TGGCGTATCAGGTCCACAATGGTTACAGCATAGCCAACTGGCACGGCAGCTATTATAACG\n+AAGGGAGGCGATTCCGTGGCACGTAGTCGATTCCCTCACTGGGCTTTGGCTGTCCTTAAG\n+CTCGCGCGGGCAAAGTTCCCTCTGGCCGCGAGCCAGTCCGAGGAGAAGGCTCGTTCAATC\n+GTAAAAGTGTCGGAGAAGGGAGTGCGTCTGGCCGCCTACCTGTCGCGTAACAGCGTTGAG\n+ATAGCCTACACCTAGCGAAGCGGTTATGGTCTGCCAGAAACGCAGTCAAGGCAAATCTCT\n+TGGCTTCGAGGCATCGGGTGACTAGATTTCGGTCATACCATTCTGGGACCTCGGGAGCTG\n+GGAGTACTGGACCCCTATTCAGGGCATTGGCAAGGTGTTACTGGATCAGCCGTAAAATAG\n+GCTGTCGGCCGGAACATGCCTGTTGATTTTCCCAAAGGGTTCCTCGTCCAGATGTCGTAC\n+GGTTGTAACGTATCTCTGGATACGGATATAGGGCCAACCCAACTCAACGGCCTGTCTTGG\n+TAACCGCCTGGTTTTATTCCGTTCCGGACATAATCCCTGCCAAATTCGTGACCTGTCATT\n+CGTCGCTTACACGCGCATATCAATTGGATCTAATCGAACAGGCATTCTGCTACTTAGCCC\n+GACGTGATTGTCACCTAGGTACTCCGGTTTACTCATTAGGGGTGTACTTAGTCCAGTGCG\n+CCACGAAGAGATAACTATTTTCGATTTGCACTGCAACAGCGTATTGGTCCTATCAGATAG\n+ACCGGCGTCCCTACGTTCGAGCACTCTTAACACGGATCTAGAAGGGCCTTGGCGTATTTA\n+TCAATTATAATGATAGGCACAGTCATCAGCACGACCTGATGACGTCCCGCTTTGATCGTT\n+TTACAGGTATTGTAAGGCAAGTTCCACTGAGCATGACATCTGTGTTCCCCCTACCCCGAT\n+GTAGGGGTGGAGATATGCATGGTGTAAAGATATTTCCCATTACATGTGTACGGAACAACG\n+CATATGGATGTTTCTGTGAGGGAAGCCTCGCGGATCGCCGTCCGGACCGCTCTACGCTCG\n+CGCATACCCTTAAATGAATTCGACGCTTAAGGGTGCTTTAGGAGTTATTTGCGGGAACAA\n+CGGTCACAAAAGGACCACCTCTATGGTGTTGACCAGCCGCCGATTCCTGGGTCTGTCGCC\n+CACTCCCGGAATGATCCAATGTTTGCTTTAACAGACTCAGCACAAACCAGAGCTGTCCGA\n+CTCGCCTATTGATAATAGACACTCACACGGGACTGGCCTACCAACCAGTATTCGAGAATG\n+GCGACAGGGCGTTGTATTGGACCCACTACTGAACACCGTTACGTAGTTCGGCTTTTCGTG\n+CGGGTGTACTACAGAAATAGCGTCCGAGCACGGTACGACTTCATAAAATAGCGGGTAGGC\n+GTAAGACAATTTATTATTCTTTACCGAGAGTTCTTAACAAAAAATTCTGGGCCGGTAGCA\n+CATGATGAATAATAAGTCCCTTGCCAACTCGACCGCACCAAGATGCCGGTTGGGTAGTCC\n+ATCCCATCCAGCGGACTCTGAGATATTTGAAGAGTCGGGTTAACTAGGCCAGAACATATC\n+AATAGTCACATAATGTTAGAGGGGTTGGTGAAGTAAGGAAGTAGGGGCTACCGATCTCAT\n+TATCTTCGCCGTAGGGCATAACCGCAAACATCAGGTGACTCTTGGCATCATCCATGATGC\n+TGGTACT\n+>NODE_2_length_1616_cov_8.225247\n+AAGGGACCTCGGGAGTTACCGCTCTTCGGCTCCCAAATGCTCTGACGCGTCAGTTAATGA\n+TGCAAAGTAACAAGTGGGTCACCCGTGTTTTGCAGATCCTTGACTAGCCCTTGCGGTGAA\n+CGAAAAGAGGGCTTGCGACGGCATGAGGACAACTCACTCATGGCACAACTCGTTCTTACT\n+AAGACCGAATGCCAAATAGGTCCTTACATCATGAGACGGGCCAAATCAAACACACTAATA\n+GTACTTGGAACACAGTGCTAGAGGTATACATCTCGAGCCTGACCCCTGGGCTCCGGTGAT\n+ACGTGAGGGACAGACTGCAGATAGGTCTGGCAGCAACCACGCGGCAGTACCGAAAGCGCC\n+TTAGTGTTTGGTTGAGTACCAACCTCATGCACACGTGAATTAGAGTACAATGCAATGGGC\n+CGGAGCGGCAAGCTTAGACCGTCCCCAACTGATCGTTCCGGCGCATGACGAACTCAAAGA\n+TACTCACATAAAAGGTCTAAAATAGAGTACGTTCCAACAGTCCCAGGCGTAACGCTAAAA\n+CCCGAATGCGACAGGTTTAGCGGGCAGTGGGGACGCGACTGCTAGGGCCCTGACTCCTCT\n+CATGGCTGGAACGACCAACGCGTGTTACCATGCCGATTCACTTATATCTGTGGTCCCTCG\n+GCTCGTGGCCCAAGACCAGATTACGCTGCTGATAGTCAAACGTGATGAAGTGAGCTATTA\n+AGCTGGGCGCAGCTTTGTCGCAAAGGATGAGATTAATAAATAGCATGACACACCAGTTCC\n+AGAGTTTGAACCTGTACCGAGTATGAACGGCCGAGAGTAGATGGACCAGGATCTGAGGTA\n+TAGCGTTTGCACGAATTTAGAAAAATACGTCCCTCGAGGAGTATACGAGTCATATGACAC\n+CCTGGTTATGTGGTAAGTGCTAAATCGTTGCGTTGCTAAATTGGAACATCAGAGGACTCC\n+GCTCACAGAAGCTCATAATCACTAAGGAATCCCCACATTTCAATATTTTCCTACCACTGT\n+CAATAACCGGGCAAAATCCTATGATCCCCCGGTACGCGGAGCATAGGTACCATAGCATTG\n+CCAAGGTAACTGACAAGAGTCACCTGGCCCCATGACCGACACGTTTGGGCCTATTGAATA\n+CTTCAGAACGGCGGAAAAAGAGAGGGGTGTATGCCTACCTATACGTACACGCTCTTTGGG\n+ATGGATGAACTGCAAATGGGGAGTGAAACGACGGATGACCTGCAAGCATGTGCCGCGC'..b'GGCTGTAGCCCCGAACGT\n+GCAAAACTAGCTGGTCTTGGATGAAACAGAGCCTGAAGCATTTCGTGAGGTTGCGAGACA\n+TGGATTGTGGCGATGGAAAGTCAGTCGCCGCGTGGTATCACCTCGCCCAGCAGGTCAAAG\n+GGTTCGCACTATTCTAATTTTGCAGGACCCGTACCCACTCAGTGAAAATAGGAGTACGGC\n+CCCGATCGCCCCCTGTATGAATGTAAGTCATGAGCGCTATTGGCGGCAGGCAGCACTCTG\n+ACACACCCTCAGTTTCTGGCTTTCGTCAACCGATTGCTACCAGCTAGCTTCCAATCGTGG\n+AGGGCTCTCTGTACGCCTTCGCGGCTTTGTTGAGACCCACGCAGTTCTAGGTTGTCATTA\n+TCCGATATGTATCCATGTACGTTCGT\n+>NODE_46_length_647_cov_7.907264\n+ACCCGCACTAAGCCGTAGGCGCGACAACTAGTTTAACTAAGTTGAAAGTCGCTCTTCTGT\n+CGGGGAAACAATGTCCAGTCCAGTATACGACGTCCCTTTCCCCCGGCGCGTCAGGGAATT\n+ATACCGGCCCTAGGTACGGTGAGCCGGCTTGGCGTTAAGATAACCCCCTGCAGTGAGGGC\n+CTGCCGCTACACGGATCGTGTCGCCTCAAGGTGTACCTTTGCAGCCTGGGACTGAAGGGA\n+AGTACACGACGTTTGGGCCAGCCTACCCCTCTAGGTATTACGAAACACGATGATCGTCTG\n+TGAACGTTCATACTTTGACTTTCCTTGCGACGACCCAGAAGTAGATCGACGCACGCACTT\n+TAAGAGCTTATAGCAGGTTTCAGGAAGACGGATCCATATGCGTAGCGGCTAGTCTTGTCA\n+GATTGAAATCTATCCTTGCGTTGTGACCAACTGGGCAGAGCCGTGGCAGGTAAGCATAAA\n+GGAACTAGATTGGTCCTTAGCCGAGATGGCACAATTGCGGATAATCCCCGTAGGATCCGA\n+CTGACCAAATCTTGTGTGCATAATAGACAGCAGAAAAAGCTGTAGAAGGAAAACGGCGTT\n+TCTCTTCTAACGTGATGTGCAGCCTTTCGCTGCATTGCCCAGGTAACAGTTGGCCCCCCT\n+TTGCCCCAATTCCCC\n+>NODE_47_length_407_cov_8.117936\n+AAGAAAAGCAGGGTTATACAATAGAGAGCGCCTTCTTCCCCTTAGGACGGGTCGCCAGTC\n+AAGTTAGGCTTTGGTACTGTCAGGGATTGGAGGTGCTAAAATTGGGTTGCGTCCGTCCGT\n+ATCGGTACAACATCGCTCACGTCTATTCACAAACTGCTTCTCCGGTACCATTTATTTGAT\n+TAAAGTGTGGACTCTCATGCACCTCATAGTACAACGTACCGCGCGCGGCAACGCATCTAT\n+TAATAGCTGGAATGCCTTTATTCCAGCCCCAACCTCTAACGACCGGGCCGGACTGGCTTT\n+AATCCTGATGCGGGTAAGCCATCCTTTAGTTGTTTAGCACTCTCTTCTCTACGCGCCGGT\n+CCGAACAGTAAGCTAAGCTTATATATACCGCGATGAAGTTGTGTGGTCTGAACCTCATTC\n+GATGTCGTTCTCACA\n+>NODE_48_length_215_cov_7.604651\n+CGGCAGAGCCCCGACGGGATCTGGAGTCACACAGGTCTCGATTGTAACTAAATGGTCGCC\n+TCGTAAGCTATATGGGTTTGTTGTGAGTGTAGCGCCGAGGACGTTACGTAATTGGCTAAC\n+AATCGCGCCATCCCAACCTCCTAAGGGCGGGGTGTCTCGACCCGGCTAGGCTCCTTTCAC\n+ATATCTAACTAGACCTGATAGATTCGTAATCAGCTTCTTGGTATACGGCCGTCCTGAGGA\n+CTA\n+>NODE_49_length_184_cov_7.711957\n+CAGACTGGTTCCTTTGGTATCGGCTGACTGCGGGTTTTACTGCAATCGGGCTGTCCGCTA\n+TGTGGTGGTCTGCCTGCGAGTCCAATCGCAAATTTAAAGAACTGAACGGTATAGGGCACA\n+ACATGGCTACACAGCCCCCTGGACACAATTTCGCCGGTGGACTGCTACGGGACTAACAAG\n+CCTTTCTTTAGCAAGTACTCCGTACTTGTGGC\n+>NODE_50_length_328_cov_8.512196\n+CCCGAAGTCGACAGTGAATAGCGCGCGCTTTACATCACAGTATTGTGGTCTGTCTCGCGC\n+CCGGCCTGGTACTTACGGTGAGATATAGATACAGTGTGACCAGATGCGCCACTAATTAGT\n+TGCAAAGTTGAAGGCCAGTCTTGTTGGGTAGGGTGGTACGGCTATAGAGCCGCACAGTTC\n+ACAGAGCTTGGCACGTCATTCCCGCGTTGGCGTCATTCGGAAAACGTGGTGTATGCGCAA\n+TCGGGGCGATAAAAACGTAAGGAGCGTTTATGCCAAACGAAGAATAGCTGGGAGACAACT\n+AACCGCCGGTGGGGTCGCGCTATTGAAGACCAGGCATTGCGAAAGTCAAACTACGT\n+>NODE_51_length_716_cov_7.587989\n+ACCAGGCATTGCGAAAGTCAAACTACGTCGCCATCGCGGCCAGAAGAGCGGCGTAGAGCC\n+CTGCGTTTGCATCTTCCATTGCAAACGCTAGATCCCAAAGCCGGACTCCGATTCTAGGCC\n+GTGCATGCAGTCTCATTTCAGCACGTCACGGTGAAGTGTTCTCAACATACAGGAACTCCC\n+ATAGTCATTAGATTCTACTCGTTATTCGCTTCGATGCTCATTCGTGGTTCACAACTTTCA\n+GCCACAGGATGTTTGGCACACGCCGTACGCGAGTATATCAGATCTCTCCCCGTTTCGTGA\n+CAATAATATAAGATTACTCGAGCTCAATAGTCTTATATTTATCAGCATACGAATTCTTCT\n+CAAAACTAAGTACCCAGCTGTCGTACAAACTCGAGGCCGCACGCGTCAACGTGAGTCTTC\n+AGTGGCATGGCGATAGGCTGGCGCGAATTTCACAGACTTTCAGCTGACTTAGAGTGGTGG\n+GTGTTATATTTCTCGTTGATCACGGAACTGTCCCAACAACTAGGCACCTGAAGCGCCTGA\n+CCCTGCTTCAAAAGTCTAGGGGGCTCGAAAACCCATTAGAATCACACAAAGTGCAGGGGG\n+GTTTAAGTAAAATCACCCCCCAAACAGTGACATATAACTAGTACAAGCGATTATTCACAG\n+GCTCCGCGACGGATTCTGGCGCCGCATCGTTAAGCCCTTCAGTACGCAAAGGCTAGTTTC\n+GTCGCTAGGTTGCGGGCATCACAC\n+>NODE_52_length_131_cov_7.816794\n+ACAATAAGTTAAAGGAGCCAGAGAGATAGCGGTGTGGTACGACGGTGCAACGATGGTCGC\n+TATGGGAACAGTCTGTTAATACGAAAGTGAACAATGGTTATCTAACATGATGGCTGCCGT\n+GGAGGTCCGACGCAGCGGCATAGCCCTGTCGCAGTGGAT\n+>NODE_53_length_219_cov_7.424657\n+GTGATGATTCATTGCTCTGCTACTTCCGAATTTCTGATCTACGAAATCTCGGGTCCCTTC\n+TGAGATAAGCTTGGTGGGACTGACGCTTAGATCCCCACCTGAGCGCTATTGGGGAATTTA\n+CTTGACTCGAACCGGTTCAGCGATAATTTGTCCTTGATTGTTTACCAATAGAGGTGTGCG\n+ACTCATTAGGGCCGGGTGGGGAGATCGGTTATAACATAACTTGACATAGCTAGCACTGTG\n+GTGGTTT\n+>NODE_54_length_60_cov_6.783333\n+ACCCGATGCCTGGCACGTTCCTGGGAACAGCCTGGGGCATGAGACGGACCCGATATACAA\n+TCCTAACGCCGACAATGGTATAGATTTT\n' |
| b |
| diff -r 000000000000 -r d81360ea69d8 test-data/test-contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-contigs.fa Tue Jun 28 17:30:32 2016 -0400 |
| b |
| b'@@ -0,0 +1,1668 @@\n+>NODE_1_length_99973_cov_15.958339\n+ATTTATGCCGTTGGCCACGAATTCAGAATCATATTAGCCTAATGTATTCCACATTCCTCA\n+CCACATGTATGAACTTGGGTAGCAGACTTTAAAAGCTAATTGATATGGCCCCTGGCGTCG\n+GCGTCAAAAATAGTTGGGAATGCGATATTCCCGTATAATAAGATGACAGGACAGTACTTA\n+AAGGAGCATAATTCGCCACTGGAGATGCTGGTGAGGGTGCATCTATACTCACTATTTGCG\n+ATGGTACCTTTTGAGGTGTTATATTATTGACGTTAGTCTTCGGTGCGGTCCTCCTACGTT\n+GCCCAGTATGTACCATGGCGTGCAAACCGACACGCGAAGATCAAGATCGCTGTAGTCTCT\n+AGACACTCGCCCGCCCGAGACCGCCCAGACGATGGATCCCTGGCTTGCAAGCCAGTCTCG\n+ATGACAACGCGCTCGGACAACGGTGAGATTGATAAACACTCAAACGGCTGGCAAATAGTA\n+CCAACACGAGCCGCCTATCTGTAGTACTGATACTATTCCTATAGACGACTATGACCCTAT\n+TATCTAATCCGCATACAGCCCCATGGATCAGAAGCAGCTTTCCTACACTGGATTTCCTAG\n+TTGACAATCTGAATACAAGTGATGTGTACAGCTCCACCTGACTACTCCTTCGAAATTTAA\n+TGCGTGGATCTTTGAACCCACGGCTGAGGAGCTAAGGGTGAGCTACTCTACATACGGCAA\n+GGGCGGTCAGTAAATAGGCCTTCGTGACTAGCGAGCGGGGACTCCGCTCTAAGCGCTGGT\n+GAAAATCGCTCCAAGGGACTTGTCTCGTTAGCCGGCCTAGTCATCGCTGTTCCGGAAATT\n+CCCGATTCGTACAACCGGCCCAGGGCTGCGGGATAAGACATCGACTCACGCTGTCCAATG\n+TCATACTGCATAGCATAGTCAAATAGAAGTGCCTACATACATCGAGCAACCACGTCATGG\n+TAAATACTACAAAGGAATAAAGAGAATATCGGGGGCTACTCCTGTCGTATTCCATCAGCT\n+ATGGGATCAAAGGTACAGCACACGAATATAATAGCGGATTCTCTGCAGTCGCGATGATTT\n+TTGTCTCTAAGCTTACAATAGGCAGAGGTCGTAAGCAACAATCATCCTCCTTTATCCGTA\n+TCTAGGCGGGGGGTGCAAACCACAAACCGAGGGCGATTGCGAAATGCTGCATCCTGGATA\n+CCGTTATGACAGCAGAGTTCATAGCAATATTCCGAAGTGGAGACGGCCCAGGAGACGAAT\n+TTAACCAAATGCCTGACACTATCACCCACCTACTCGACGCACGGAAGCATACGCCTGTTT\n+AGACGCAGGGTTTCCTGTCGGCTATCTCATCACCGTGGGAACTATATCTATCGTCCACGA\n+ATACAGCGATTCAGCTTAAGCAATTCATGGTGGTAGGCCGAATAGAACCAAGAACTCCGA\n+TCGCCGATTCCTCCATCACGACACCCAGGTGGACTCTTATAGGCTGCAGGTTTTAACAGT\n+TCCAGCCCAGACATGTCTTACGTAGTATTTGTAATGCATCGAGGTCCAACAGTTGCGTAG\n+GTCGTAAAATCTTACGCTTCATTTTGCCCCTTAACTACTCACAACCGGACTACTAACCCG\n+GCCTCGGGTGTTTTTAAGGCTCCAACACGGTCTAAAGGGCACCTAATCGCGGTTGTCTCT\n+CAAACAATTTCTAGTCGGGCAATTTCGAATACAACCCGAACCTCTGGGCATCAGAATGAA\n+GACGCTTGCTGGCCTAAGGCGCGTTGTTATTGAAACTTTATCGAGGAGATTGACCATATA\n+AGGAGTCGGAGCCCCTTGGTCCCCTTCGTAGTGCTCAATGACACGCCCTTAAAGGTCTGA\n+AAAGCTTCAGAAAAGGCTACGACGGTGTTAATAACGTCTTTTATTGGCCGGTGTCCTTAG\n+TACAAGGATCTTCTGACACGGTCCTTGGGGAGTCGTTATTCTGGGATACAGTAAATTGCC\n+CCTAGCTCCTATGGCATAAACTTCTAAGGCTTGTTAATCGGGCAAGATTCTAATCTTCCC\n+GACATAAATCGCTTCACGTATTATGCGCGTGATTATAATTGCCCAGCCACGTAGGGAATG\n+TCTTCTGCACAGGCTGACTAGCAGAGAATTGGACCCCTGCATTGAGAATACCCCTCTTCG\n+GACTCGAGGTTGGGCGCCTACAGTCCAACGTTGAGTGTGAGCTAAAGCCCCTCTGGCGTG\n+AGCGGAGATACCCACCATGCCAAGTGCACAGCGAAAAGATGCATCCCCATTCTTATGCTT\n+CGATGATGGTCACCAGGCAGATAAGATACGTGAACGAAATTCTAGTTAATTCGTCATACA\n+GAGTATCCTGAGTTTGTGGTCCATACTTCATACCTCAAGTGGGGGCACTGAAACTAGGAA\n+TTAACTCCTACGGTAAAACTGGTGTGTCATCTGCTTACCACGGTCGACGCAATTTGCGAC\n+CCCTTATTCATGGCGTTGACTAGTTCCATCCATGTGTGCAGCTAGCTGTTTGTCCGGTGC\n+AACTGCCCTTGGACGGGGACCATCCCTAAGCAGTAAACGTAACACATTGTATTTACAACA\n+GGCACCACGGCTGGTTGGGAGGACGAGGATTGGAGTCTCTCGGAAGTTAGTGATAGAGCA\n+GATAACTCAAAGGTGTCCGCTCAACAGCGTCATAATGAAGACATAGGCAAGTCGTGGGTC\n+CCCCCGATGCGGGGCGCTTCTCACAATGGTTTACACTCCCGTTACCGGACTAGACGAACG\n+TACTCGCATGCCCCCGGTCGAAGGATCAAGGTGATAGAACGGGTTTCCGGTGTGATCCAC\n+TGCGGAGAAGCGATCTGGAACAGAGTTTATCAGGGAGACGGGATGCGATTCATTACGAAT\n+TCTCTCGCCTTTCTGTACAAACATACATCAGAGCGCGATTTGGAGCAGGAGGCTCCACAC\n+CGCTTTCCTAAGGTTAATTGTCAAACCAGGCTATTAGACGAGAGCTTCGGTCTTCAATAG\n+CGCCCACTATCACGTGCGTAAGCTCTTCGATTGAATCGGCCAGGGCATTTTTCCGGAGTG\n+GGCAGCTTTCCACTGTAGTTCGGGTAATGTCACGAAATTTCAAGTGGTCCGGTACTCCGT\n+CAAGGAGGAGGCGGTGACCCGAAGACCCGTCTTCGGCAACGGGCAGTCTAGGAGACTCGG\n+ATCAATGGAGTGCGTCAGGTTCCTTCATGTCTGGTTGCCGTAAAGAGGGAGCCTCCCCAT\n+ACGTTCGCGTTGTAGGAAAGCGAGGCTTGTGTACGAGACCTCTGCCACGCTTTTCCACAT\n+ATGCAACGAGTTTGCAAGCGTCCGAGACTAAATGCTGGGGACCAAGAAAGGTTTGTCGAC\n+GACGGGCAATGACTACGCCGTTGGGACTGGAAGCGCTACTTAAATACCCGAACGGTGATA\n+GTAACTCATTAGTATGAAAGTAGAGCAACTATGATTTCAGAACTAACAACGTCCATGATT\n+TTGCACCTGCGGCTCCTTCTAATGCTCTTCGGAATACAAACGGGCATATCTTCGCGCTCA\n+ATGATGCAGCAATTGATGAGTTCAGTGTGTAGGGGCATCTAGTTCCTATTGGTTGCGAAA\n+TAGCTCGTAAGCGCATTATGTCCGATTTAATTAGCTTTTTTCACTCAGCTAAACTCCGAC\n+GTATCCGACCAATAGGCGAGGATGGGTTATATTAGAGACTGCTCCCTTATCGTAACGAAT\n+TAGGCATTAAGGCCTGTGCTCTCCTCGGCTCCTTTATGTTGCGTTCGGATCCGGGGTCAC\n+ACGTACATATGGCAGAGAGGTTTGCGAATACTCTGCC'..b'CGCCGCTTACGGGCAGTAGCAATGCACAGTGTCTCTAAGCCATACTGCTAGTACG\n+CGTCAGATTTAGACACGCAGGTATGCCGCTATCTACGAACACAAGACACCTAATTGACAG\n+AACCACGGGGTGTTGCATGCACCAACGCGTTGTATTCCCTTCCTATAAGGGGTTGAACCG\n+AAATATTCAACACGTGGTGAGATCACCAGGTGGTGGTCATCCTTTGCCGTGAACCAGTAC\n+CTTATCGGGGCATCTTTAACTGCTTTTGGATTTGTGAGAGAGGATCTGCTACGCACAATG\n+AGGTCCGCTGTAAGATTTGCGGGATGGAGCGGAAGCGAGCGCCTTCGTAAATGGTGACGT\n+TACTCTATTGAGTGCTTTGAAGTGAGAAAGTTTCGAAGTAATGTCTGCGACGGACGGCTG\n+AGCTTTTACGACCGCTCTATACGGCTCTAAGAGTTGTGGAAGGGATCCGCAGGGCTCGGG\n+GAGAAGGTAATCGCTGAATTCACTGGGAAAGGCATCGCATGTAACTTCTGAAGGTCACCC\n+CTTGTGTGATCGTCGAACCTAGTGAGTATACATCTTTGCTGGCCTACTCGGCACAATTCG\n+AGGTTCGTATGGCATAAATCGCTTGTTCGATGTGGGTACTAACCAAGAACCTTAGCTCTG\n+GGACAGTATCTTCCACCGCGAGCTTTAGATAGGCTGTTGGAGCCTGGAATGACTTAGATT\n+TTCCACAAAGGAAACTGTAGGGTTGGAAGTTGGCTTGTTGGCGGCTGTGGGAACTGTTTG\n+GGACTTACTTTCACTGACCGTTGAAGGACCGAAGCTCCCAAACAGCGGGACGTTGACAAT\n+GGTGAACCCGGCTTCCAATTAACTATTCTTACCTTCTCTATCCGATTCTTATTCGTAGCT\n+CCCTCAAACTCCAGTCCTGAGGTCTGCTAGGCTTAAACCCAGGCAGGGCAGTGGACACAA\n+TGCTGGTGTATTGGATAGCCGTAACACCGCCCATAGCAAAATTTCAGCGTGCGGCATTCC\n+ATGAGTGTTGTTGGGTGACCTTGGGTGCGTGTGATATGTGAGGGCAGTCTAAGGGAGACA\n+ATTGATTTCGGCCAAGAGCCCGGTAAAGCCTCCGTCCGAGCGAGGAATGCATTGGATGGA\n+ACCCAAGCTGAACAGTAGGGTTCTCTTAGCAGTCTTGCACTACAATAACGGACTTTTGTC\n+AATTCGGTTGAGTCTTATACCGGTGCGCACGACCTTTCGGTTAGATGCGGGAAATGGCTG\n+GCGAGCTCGCTCAAACTGGGAAGACCTTGGCAATAGATAGCTTCTTGTCACCCTGGACCG\n+TGGTCTGCGGTTCGCCGTATACCCATTAAAGTGATTTCAGTTCACGCTGCTGGATGTGGT\n+GAGACCTAGTGCGAGTGTTACGGTGCGCTAACCGCGAAGGTCACCGCTCAAGGGGAAACT\n+ACCCTGTTTGGGTGAAACTCCTATGGTGGACGCGAACTAACGGAAGAATACATCTCTGTC\n+GCATTAAATAACGTCGCGGCGTCCCCTATGGGTGCTGCTCCAGTTACAGTCATTCAAAAT\n+TGCGATCGACAGCGCAGTAAGGACCGCCGGACAGACCCTCGTTTGCTAAACGGCATTCAG\n+TATAGTCTCACTAATGCGGCGTAACATACTGCAGCGCGGGGTGGTCACTTGGGGGTGGAA\n+CGCCAGAGAGAGCGCATCCTAACTGTGCCGCTCGACAATAGAGTGTAGCCCCCGAACTCT\n+CGGGAGAATTACTGCGGCATGCAATCAAACTCTCATAATTTTATCCCTGCGCGTCCACCA\n+GCCCGCAGCTCCGGATTCTGGCTAAACACGATTGAGTAACTGGCAGATTTCCCACCAGGC\n+AGAAAAGAAGCTATAACCAAACCCGGTGACAATAAACGACCCCCACGCGGCTTGACATAA\n+AAAAACACTATACAGCCAGAGTTCCTTCTTCTTCTTGTCGTAGAAACCATCGGAATATAT\n+GCGCTGACCCTCCGCCGTTTGACCCCACACAGGGTCAATGCGTTAAATTTGGATTCCTGC\n+AGATATACTTTCGGAGGACGATAATTCAGTCTCCGCCGGAGCCATCGGGAAGTAGGTTGC\n+GAATCGAGCTTTAATAGCGACGGCGATCTGGCGTATCAGGTCCACAATGGTTACAGCATA\n+GCCAACTGGCACGGCAGCTATTATAACGAAGGGAGGCGATTCCGTGGCACGTAGTCGATT\n+CCCTCACTGGGCTTTGGCTGTCCTTAAGCTCGCGCGGGCAAAGTTCCCTCTGGCCGCGAG\n+CCAGTCCGAGGAGAAGGCTCGTTCAATCGTAAAAGTGTCGGAGAAGGGAGTGCGTCTGGC\n+CGCCTACCTGTCGCGTAACAGCGTTGAGATAGCCTACACCTAGCGAAGCGGTTATGGTCT\n+GCCAGAAACGCAGTCAAGGCAAATCTCTTGGCTTCGAGGCATCGGGTGACTAGATTTCGG\n+TCATACCATTCTGGGACCTCGGGAGCTGGGAGTACTGGACCCCTATTCAGGGCATTGGCA\n+AGGTGTTACTGGATCAGCCGTAAAATAGGCTGTCGGCCGGAACATGCCTGTTGATTTTCC\n+CAAAGGGTTCCTCGTCCAGATGTCGTACGGTTGTAACGTATCTCTGGATACGGATATAGG\n+GCCAACCCAACTCAACGGCCTGTCTTGGTAACCGCCTGGTTTTATTCCGTTCCGGACATA\n+ATCCCTGCCAAATTCGTGACCTGTCATTCGTCGCTTACACGCGCATATCAATTGGATCTA\n+ATCGAACAGGCATTCTGCTACTTAGCCCGACGTGATTGTCACCTAGGTACTCCGGTTTAC\n+TCATTAGGGGTGTACTTAGTCCAGTGCGCCACGAAGAGATAACTATTTTCGATTTGCACT\n+GCAACAGCGTATTGGTCCTATCAGATAGACCGGCGTCCCTACGTTCGAGCACTCTTAACA\n+CGGATCTAGAAGGGCCTTGGCGTATTTATCAATTATAATGATAGGCACAGTCATCAGCAC\n+GACCTGATGACGTCCCGCTTTGATCGTTTTACAGGTATTGTAAGGCAAGTTCCACTGAGC\n+ATGACATCTGTGTTCCCCCTACCCCGATGTAGGGGTGGAGATATGCATGGTGTAAAGATA\n+TTTCCCATTACATGTGTACGGAACAACGCATATGGATGTTTCTGTGAGGGAAGCCTCGCG\n+GATCGCCGTCCGGACCGCTCTACGCTCGCGCATACCCTTAAATGAATTCGACGCTTAAGG\n+GTGCTTTAGGAGTTATTTGCGGGAACAACGGTCACAAAAGGACCACCTCTATGGTGTTGA\n+CCAGCCGCCGATTCCTGGGTCTGTCGCCCACTCCCGGAATGATCCAATGTTTGCTTTAAC\n+AGACTCAGCACAAACCAGAGCTGTCCGACTCGCCTATTGATAATAGACACTCACACGGGA\n+CTGGCCTACCAACCAGTATTCGAGAATGGCGACAGGGCGTTGTATTGGACCCACTACTGA\n+ACACCGTTACGTAGTTCGGCTTTTCGTGCGGGTGTACTACAGAAATAGCGTCCGAGCACG\n+GTACGACTTCATAAAATAGCGGGTAGGCGTAAGACAATTTATTATTCTTTACCGAGAGTT\n+CTTAACAAAAAATTCTGGGCCGGTAGCACATGATGAATAATAAGTCCCTTGCCAACTCGA\n+CCGCACCAAGATGCCGGTTGGGTAGTCCATCCCATCCAGCGGACTCTGAGATATTTGAAG\n+AGTCGGGTTAACTAGGCCAGAACATATCAATAGTCACATAATGTTAGAGGGGTTGGTGAA\n+GTAAGGAAGTAGGGGCTACCGATCTCATTATCTTCGCCGTAGGGCATAACCGCAAACATC\n+AGGTGACTCTTGGCATCATCCATGATGCTGGTACt\n' |
| b |
| diff -r 000000000000 -r d81360ea69d8 test-data/test_reads.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_reads.fa Tue Jun 28 17:30:32 2016 -0400 |
| b |
| b'@@ -0,0 +1,285716 @@\n+>SEQUENCE_0_length_35\n+GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT\n+>SEQUENCE_1_length_35\n+CGACGAATGACAGGTCACGAATTTGGCGGGGATTA\n+>SEQUENCE_2_length_35\n+CCAAATAGGTCCTTACATCATGAGACGGGCCAAAT\n+>SEQUENCE_3_length_35\n+CGAGATGTATACCTCTAACACTGTGTTCCAAGTAC\n+>SEQUENCE_4_length_35\n+AAGCTCCCGCAATGGATCTTGTGACGGGCTGCTCG\n+>SEQUENCE_5_length_35\n+GCCGGTACAAACAGGAGGCAGGCAGTTCTAGTTCC\n+>SEQUENCE_6_length_35\n+TGCAGGTCAGGGTTCGTCATGCCTAGTGCAACGCC\n+>SEQUENCE_7_length_35\n+GTTCGCTACCAGCTTGTGGACCAGGAGGGTAACCC\n+>SEQUENCE_8_length_35\n+CTTAATACCATGAGTCGAAGAAAATTAACTTGGGG\n+>SEQUENCE_9_length_35\n+CATGGAGTAAGTCCTAGTAGCCTTGTGCATGGCGT\n+>SEQUENCE_10_length_35\n+TGTCCCTGTCACTGGAGTGATCTTTTATTCTCACC\n+>SEQUENCE_11_length_35\n+CTCATGCGTAATTTTAGCCGCCACGGCTATGCGTG\n+>SEQUENCE_12_length_35\n+CTTAGTCCTACAGGTTTTGCTATCCATTAAGCTGC\n+>SEQUENCE_13_length_35\n+ATATCTCGGTGCAGGGATGTTCAACATCATCACAC\n+>SEQUENCE_14_length_35\n+CGTCCATCGCCGATGAAATCCTGCTCAGGAGTGGA\n+>SEQUENCE_15_length_35\n+ACGCGTAGTCCTCTTGCGGCTTCCGCGCCCCGGGA\n+>SEQUENCE_16_length_35\n+CTTGAGCGGTGACCTTCGCGGTTAGCGCACCGTAA\n+>SEQUENCE_17_length_35\n+AGTGGTTTCAGTTCACGCTGCTGGATGTGGTGAGA\n+>SEQUENCE_18_length_35\n+ACTAGTCAACGCCATGAATAAGGGGTCGCAAATTG\n+>SEQUENCE_19_length_35\n+AGGAATTAACTCCTACGGTGAAACTGGTGTGTCAT\n+>SEQUENCE_20_length_35\n+CGCTGAATAAGCAAAATGCGTCGGCTGGGTCGACA\n+>SEQUENCE_21_length_35\n+GGAGACACGCCTGGCACGAGCGGAGGGATAGCTGT\n+>SEQUENCE_22_length_35\n+GAACGTGAGCTTCAATGGTGCCAAAATCGATAAAG\n+>SEQUENCE_23_length_35\n+CAGCACGTGGTTACTAGTCGTAAAGCCCCAAATAG\n+>SEQUENCE_24_length_35\n+TTTCCCTCCGTAGACAAATAGAGGTTAAGGGGCGT\n+>SEQUENCE_25_length_35\n+TTCTCTTCGTGTGAGGCCCTACGCTGTAAGATCCT\n+>SEQUENCE_26_length_35\n+CGGATTGGTCTAGCGTTGGAACTTGTCCGTCATGC\n+>SEQUENCE_27_length_35\n+CGCCTCAGAGCTGTGCTGATGGGTGTCCCCAGTCT\n+>SEQUENCE_28_length_35\n+CCAAGGGGCTCCTGTCGATCCTTGAGTCATTCATC\n+>SEQUENCE_29_length_35\n+AGCTCATTTTGCCGCGCCTGTAAGTCGCATCACAA\n+>SEQUENCE_30_length_35\n+CAGTTGACGAGTTACCGCTTACCCAGACGATTACG\n+>SEQUENCE_31_length_35\n+CCGAAGCGGAGGACAAGAAATTATCCCTATCAATT\n+>SEQUENCE_32_length_35\n+AACGCATTGACCTTGTGTGGGGTCAAACGGCGGAG\n+>SEQUENCE_33_length_35\n+CAGAGTTCCTTCTTCTTCTTGTCGTAGAAACCATC\n+>SEQUENCE_34_length_35\n+GTGGCTTCCCGGTATTGTAACGGGGGGAACCACGG\n+>SEQUENCE_35_length_35\n+CAGCAAGGGGCATACAGCACATCATGTCGCAACTC\n+>SEQUENCE_36_length_35\n+CAACTCGAACGTCTTAGTACTCCACAGATAGAATG\n+>SEQUENCE_37_length_35\n+TTGCGCTCAGCTGTCTGCCGTTGACTTCCTTCAAC\n+>SEQUENCE_38_length_35\n+ACCGTTGCAACTCCACATACCACCCCAGTACCCCA\n+>SEQUENCE_39_length_35\n+CCGGGATAAACCAGAAAAAAAGGCTCGTGACTGTC\n+>SEQUENCE_40_length_35\n+TCAGTTTATCAGCCTCGAGGCCACGATCGAGCCAG\n+>SEQUENCE_41_length_35\n+GCCCACATATTACGACGATGCGGCCCCGCTCTCTA\n+>SEQUENCE_42_length_35\n+GGACTATTCTAAATAAGCGGGTACAACTTACGTAG\n+>SEQUENCE_43_length_35\n+TTCCGCGCCGTCGAGTACAAAACGTCGCAATTTAA\n+>SEQUENCE_44_length_35\n+TATACATGTAGAGACTACGATAAAATTGAAGGGGA\n+>SEQUENCE_45_length_35\n+CCGGTCTATGATCCCTAATGAAAACGTTGATTCCC\n+>SEQUENCE_46_length_35\n+TGGTTTCTCACCGCAATCGGACCTTGCGGGTATGA\n+>SEQUENCE_47_length_35\n+CGTTGCGAGAGCAATCTATCAAGAGGATAAGCGCA\n+>SEQUENCE_48_length_35\n+AGGTAAGGATAGGGGCAAACGCGCGAAGGACACCC\n+>SEQUENCE_49_length_35\n+GACATATAGTCACTTGCTGTCGAATCGTAGTGGCT\n+>SEQUENCE_50_length_35\n+ACCATATAAGGAGTCGGAGCCCCTTGGTCCCCTTC\n+>SEQUENCE_51_length_35\n+GACGTTATTAACACCGTCGTAGCCTTTTCTGAAGC\n+>SEQUENCE_52_length_35\n+GGCTGAGGCCCGCCCCGAAACTTAATAGCCAGAAC\n+>SEQUENCE_53_length_35\n+TTCATACCGAGTCATACGTCGTCTTAGAGCGCATC\n+>SEQUENCE_54_length_35\n+GCTTGCAACTGGTTGATAGTTCAGACGAATGGTCG\n+>SEQUENCE_55_length_35\n+GGAATCAATAGTCGCGTTCAGAGCGCTCACTTTTT\n+>SEQUENCE_56_length_35\n+CGGAACACTAATCACCTTCCTAGTCGGCGGTAACA\n+>SEQUENCE_57_length_35\n+AGTTGGCCACTAAAGCTTACCCTCGAATGACTTCC\n+>SEQUENCE_58_length_35\n+GGCAATTTACTGTATCCCAGAATAACGACTCCCCA\n+>SEQUENCE_59_length_35\n+AGCTTCAGAAAAGGCTACGACGGTGTTAATAACGT\n+>SEQUENCE_60_length_35\n+AGAGTAACGCTAAGCGCAACGATACTCGCCGCGTC\n+>SEQUENCE_61_length_35\n+ATATCGCCCCAGACCTGAGAGTGGCATGCCCGACC\n+>SEQUENCE_62_length_35\n+CACCTGGCCTCATGACCGACACGTTTGGGCCTATT\n+>SEQUENCE_63_length_35\n+ATTTGCAGTTCATCCATCCCAAAGAGCGTGTACGT\n+>SEQUENCE_64_length_35\n+GGTCATACCATTCTGGGACCTCGGGAGCTGGGAGT\n+>SEQUENCE_65_length_35'..b'ACCCCCAAAACGTCACCTATCCGGCCCAGGCGA\n+>SEQUENCE_142797_length_35\n+AACCGCAGAGTCCGGAGCTCCCATAAACGAGGAAT\n+>SEQUENCE_142798_length_35\n+TTCGTCAAGAGATTCCTGTAATCCACCAAAGATTC\n+>SEQUENCE_142799_length_35\n+TTAATGCTCATTGAAAGAGACAGGGGAACGCACCA\n+>SEQUENCE_142800_length_35\n+GACCAGCAATTAAACGTAAACAAACGCGTCGATGT\n+>SEQUENCE_142801_length_35\n+TCCCAAGCCTCAGGAGACCCTCCTGCGGGTCCAGG\n+>SEQUENCE_142802_length_35\n+CCACATCGAACAAGCGATTTATGCCATACGAACCT\n+>SEQUENCE_142803_length_35\n+CGCATGTAACTTCTGAAGGTCACCCGTTGTGTGAT\n+>SEQUENCE_142804_length_35\n+TCCGGGGTCAAATAGACAGCGGAGCCCTCAACCCT\n+>SEQUENCE_142805_length_35\n+ACACCCTGCCCTTGGGCTTAGACGCGTGCCCGTGG\n+>SEQUENCE_142806_length_35\n+AATGACCAGGAACAGGCAGGTTTTTATCTACCTGC\n+>SEQUENCE_142807_length_35\n+CCAGGCGAGCGTCTGCTGGAAGATAACCCTTGATC\n+>SEQUENCE_142808_length_35\n+CGGCCACCGGAGCATAAGGTCAATAGATCGGTCAA\n+>SEQUENCE_142809_length_35\n+TGAACCGTGATATCAGATGACCACCCCTAAGTCGC\n+>SEQUENCE_142810_length_35\n+CCTAGTGCTATCCTGTATCTAAGTTCATCACAGTC\n+>SEQUENCE_142811_length_35\n+TGTGCGCTGCACCTGAGAATTAGAGACAGAGGTGA\n+>SEQUENCE_142812_length_35\n+ATCACCGGTCACCTCGACTGTCCATTAACGGTCTC\n+>SEQUENCE_142813_length_35\n+TCGTCTCAATATGTAAAACATGGTAGTGTGTGAGC\n+>SEQUENCE_142814_length_35\n+GCAGTCTACCCCTGGGGTATGAGCTGCCGCCTCTG\n+>SEQUENCE_142815_length_35\n+AAGATCAGTGCCTTCTCTGTATCAACTGCTCCCTG\n+>SEQUENCE_142816_length_35\n+TCTCGGAGGGCGTAGTAAATGGTAGAATTTACGAA\n+>SEQUENCE_142817_length_35\n+GTATGTAAGTAAACTCCACGTGGCTGCTCTGAGGT\n+>SEQUENCE_142818_length_35\n+CGAACAGTGTACTGGTGCATGTGCCGGAGAGAAAC\n+>SEQUENCE_142819_length_35\n+CGGCGTGCCGCGTAGCTCGCACCCCCGAGCGTTAA\n+>SEQUENCE_142820_length_35\n+GGTGCCCGCCGATACTAATTACGGTCGCTTGACCG\n+>SEQUENCE_142821_length_35\n+GATTAAAACCATGATACCCTGTCCTTCAGACGTGG\n+>SEQUENCE_142822_length_35\n+AAAATGAACGGGCAGAATGCGAGAGCAACATCAAG\n+>SEQUENCE_142823_length_35\n+CAAGACGCGACTGACACTTAATTGATCCGACTTGT\n+>SEQUENCE_142824_length_35\n+GGTCCGTTCTTCGAAGCAGAGCGAAGCGCGCTCAC\n+>SEQUENCE_142825_length_35\n+ATCATCCATGTAGGAGAACAAGTTAGTGGTTTTTG\n+>SEQUENCE_142826_length_35\n+CAGTGCATGGGAGGTAACTGGGCGCAGAGGGCCAG\n+>SEQUENCE_142827_length_35\n+AGCCTAAGATCACGTATCCCATACAGCCCACCGGG\n+>SEQUENCE_142828_length_35\n+ATAGCGTGGTGTCCTTATTATATCTCGCAGGCTGT\n+>SEQUENCE_142829_length_35\n+CCGGGGTATTTGAAATGAGTCGCCAACCGTGGGAG\n+>SEQUENCE_142830_length_35\n+AGCAAGACCTGCAGCTACTGCCTTGGAGGTGGGTG\n+>SEQUENCE_142831_length_35\n+TCCAGTTCCTTCAAAAGGTTATCCACGTTCGTGCA\n+>SEQUENCE_142832_length_35\n+TTTCCGAATGACGCCAACGCGGGAATGACGTGCCA\n+>SEQUENCE_142833_length_35\n+TAATTAGTTGCAAAGTTGAAGGCCAGTCTTGTTGG\n+>SEQUENCE_142834_length_35\n+TGTCTACCTTCAGTTCGTTGGAAGGACAACGATCC\n+>SEQUENCE_142835_length_35\n+CAGGACTACTCGCGGAACCGACAGGATGGGGTAAG\n+>SEQUENCE_142836_length_35\n+GCGCAATGGGAAAAAATACCATGGGTGCCGGTTCA\n+>SEQUENCE_142837_length_35\n+GAGTCAGGATAGCGTCAATCCATCCGGATTTGGCA\n+>SEQUENCE_142838_length_35\n+TATCAAGCCATTGAAGTCTACTAACACCTCAGGTT\n+>SEQUENCE_142839_length_35\n+GGGCTGAGAGCCGGGCCTCTTTGTCCTTAAACGAA\n+>SEQUENCE_142840_length_35\n+ACGTATCAGAGAAAGTCCAAGCTTGATCGTAAAGG\n+>SEQUENCE_142841_length_35\n+CCATTCAACCCTTACCGCTAGACGACGGTCGCGGA\n+>SEQUENCE_142842_length_35\n+CGAAGCTTCTCTCAATCACATACGTGCAAGCGACG\n+>SEQUENCE_142843_length_35\n+TATACGCTGGTGGGATGATAAGCTCAGGGCCTTAG\n+>SEQUENCE_142844_length_35\n+TAAGATATTATAGAGGGACAGACTATGTTGTTGTC\n+>SEQUENCE_142845_length_35\n+ATATCATCAAAGACTCTTTGTGAAGTGGGGCTGTA\n+>SEQUENCE_142846_length_35\n+TGTAAGCCATTATGATTACACGATTCCTCTAACTA\n+>SEQUENCE_142847_length_35\n+CGCTGAGGCTGAATACGCGGTTAAGCAGACCCTAC\n+>SEQUENCE_142848_length_35\n+GAACACACTTAGCCTAGGGTGCACGGGTTCAATGA\n+>SEQUENCE_142849_length_35\n+ATAGAGGAGCCCGATCTTTTGAAATATGCCTCATA\n+>SEQUENCE_142850_length_35\n+GGTCGCGAACTACGGATAATGATTAACCCATTGGA\n+>SEQUENCE_142851_length_35\n+GGATCCAATCCGCGTTGTCACTACACGACGTGAGG\n+>SEQUENCE_142852_length_35\n+CTCTATTCGTCGTATGCCCGCTTTCAAAGCGTATT\n+>SEQUENCE_142853_length_35\n+AACCACTAGCTCGCCCTCCAGCTTCTTACGTTATC\n+>SEQUENCE_142854_length_35\n+GCCCCTCTGGCGTGAGCGGAGATACCCACCATGCC\n+>SEQUENCE_142855_length_35\n+GTATCTTATCTGCCTGGTGACCATCATCGAAGCAT\n+>SEQUENCE_142856_length_35\n+GAGACAGACCACAATACTGTGATGTAAAGCGCGCG\n+>SEQUENCE_142857_length_35\n+TATCTTTTATCGTTTCACAGGGGGCCAGGGGCGCG\n' |
| b |
| diff -r 000000000000 -r d81360ea69d8 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 28 17:30:32 2016 -0400 |
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| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="velvet" version="1.2.10"> + <repository changeset_revision="a6d81014257d" name="package_velvet_1_2_10" owner="simon-gladman" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="velvetoptimiser" version="2.2.5"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="shell_command">chmod ugo+x $INSTALL_DIR/bin/VelvetOptimiser.pl</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |
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| diff -r 000000000000 -r d81360ea69d8 velvet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet.xml Tue Jun 28 17:30:32 2016 -0400 |
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| @@ -0,0 +1,120 @@ +<tool id="velvet" name="velvet" version="0.1.0"> + <requirements> + <requirement type="package" version="1.2.10">velvet</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + + <command><![CDATA[ + velveth + out + $kmer + #for $i in $files: + -${i.filetype} + + #if str($i.paired_type.paired_type_selector) == "paired": + + #if $i.__index__ > 1: + -shortPaired$i.__index__ + #else + -shortPaired + #end if + + -separate $i.paired_type.input1 $i.paired_type.input2 + #end if + + #if str($i.paired_type.paired_type_selector) == "single" + + #if $i.__index__ > 1 + -short$i.__index__ + #else + -short + #end if + + $i.paired_type.input1 + #end if + + #if str($i.paired_type.paired_type_selector) == "paired_collection" + #if $i.__index__ > 1 + -shortPaired$i.__index__ + #else + -shortPaired + #end if + -separate $i.paired_type.input1.forward $i.paired_type.input1.reverse + #end if + #if str($i.paired_type.paired_type_selector) == "paired_iv" + #if $i.__index__ > 1 + -shortPaired$i.__index__ + #else + -shortPaired + #end if + $i.paired_type.input1 + #end if + #end for + + && + + velvetg out > $log + ]]></command> + <inputs> + <param name="kmer" type="integer" value="29" label="K-mer" help="The kmer value to use for velvet - must be an odd integer between 19 and 191" /> + <repeat name="files" title="Input files" min="1"> + <param name="filetype" label="Input file type" type="select" help="Input file type"> + <option value="fastq">Fastq</option> + <option value="fasta">Fasta</option> + <option value="bam">Bam</option> + </param> + <conditional name="paired_type"> + <param name="paired_type_selector" type="select" label="Single or paired end reads" help="Select between paired and single end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + <option value="paired_collection">Paired Collection</option> + <option value="paired_iv">Paired Interleaved</option> + </param> + <when value="paired"> + <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="input2" type="data" format="fastqsanger,fasta,bam" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select the reads" help="Specify dataset with the reads"/> + </when> + <when value="paired_collection"> + <param name="input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + </when> + <when value="paired_iv"> + <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select set of interleaved reads" help="Specify dataset with interleaved paired reads"/> + </when> + </conditional> + </repeat> + + </inputs> + <outputs> + <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> + <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Contig Stats" from_work_dir="out/stats.txt"/> + <data format="tabular" name="graph" label="${tool.name} on ${on_string}: Last Graph" from_work_dir="out/LastGraph"/> + <data format="tabular" name="log" label="${tool.name} on ${on_string}: log" /> + </outputs> + <tests> + <test> + <param name="kmer" value="29" /> + <param name="files_0|filetype" value="fasta" /> + <param name="files_0|paired_type|paired_type_selector" value="single" /> + <param name="files_0|paired_type|input1" value="test_reads.fa" ftype="fasta" /> + <output name="contigs" ftype="fasta" file="contigs.fa" /> + </test> + </tests> + <help><![CDATA[ + The Velvet wrapper, wraps both velveth and velvetg for single kmer value with no parameters supplied to velvetg. It is mainly for teaching how kmer size affects the assembly. + + It returns the contigs.fa file, the contig_stats.txt file, the LastGraph file and captures the screen output to the log. + + This tool is mainly wrapped for assembly teaching purposes. It should not be used for actual assemblies. Please use the Velvet Optimiser for this purpose. + + The kmer value supplied needs to be an odd integer. + ]]></help> + <citations> + <citation type="doi">10.1101/gr.074492.107</citation> + <citation type="doi">10.1371/journal.pone.0008407</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r d81360ea69d8 velvetoptimiser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvetoptimiser.xml Tue Jun 28 17:30:32 2016 -0400 |
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| b'@@ -0,0 +1,311 @@\n+<tool id="velvetoptimiser" name="VelvetOptimiser" version="1.1.0">\n+ <requirements>\n+ <requirement type="package" version="1.2.10">velvet</requirement>\n+ <requirement type="package" version="2.2.5">velvetoptimiser</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+\n+ <command><![CDATA[\n+ export OMP_NUM_THREADS=2 &&\n+ VelvetOptimiser.pl\n+ -t \\${GALAXY_SLOTS:-2}\n+ -s $start_kmer\n+ -e $end_kmer\n+ -d out\n+ -f "\n+ #for $i in $files:\n+ -${i.filetype}\n+\n+ #if str($i.paired_type.paired_type_selector) == "paired":\n+\n+ #if $i.__index__ > 1:\n+ -shortPaired$i.__index__\n+ #else\n+ -shortPaired\n+ #end if\n+\n+ -separate $i.paired_type.input1 $i.paired_type.input2\n+ #end if\n+\n+ #if str($i.paired_type.paired_type_selector) == "single"\n+\n+ #if $i.__index__ > 1\n+ -short$i.__index__\n+ #else\n+ -short\n+ #end if\n+\n+ $i.paired_type.input1\n+ #end if\n+\n+ #if str($i.paired_type.paired_type_selector) == "paired_collection"\n+ #if $i.__index__ > 1\n+ -shortPaired$i.__index__\n+ #else\n+ -shortPaired\n+ #end if\n+ -separate $i.paired_type.input1.forward $i.paired_type.input1.reverse\n+ #end if\n+ #if str($i.paired_type.paired_type_selector) == "paired_iv"\n+ #if $i.__index__ > 1\n+ -shortPaired$i.__index__\n+ #else\n+ -shortPaired\n+ #end if\n+ $i.paired_type.input1\n+ #end if\n+ #end for\n+ "\n+\n+ #if str($advanced.advanced_select) == "advanced"\n+ $advanced.verbose\n+ -k $advanced.optFuncKmer\n+ -c $advanced.optFuncCov\n+ #if str($advanced.velvetg_opts) != ""\n+ -o "$advanced.velvetg_opts"\n+ #end if\n+ -m $advanced.minCovCutoff\n+ -z $advanced.maxCovCutoff\n+ #end if\n+ ##&> $stderr\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="start_kmer" type="integer" value="31" label="Start k-mer size" help="Odd integer, Lower limit of k-mer size range to search for optimum value" />\n+ <param name="end_kmer" type="integer" value="191" label="End k-mer size" help="Odd integer, Upper limit of k-mer size range to search for optimum value" />\n+ <param name="kmer_step" type="integer" value="2" label="K-mer search step size" help="Even integer, the k-mer value step size when searching the range" />\n+\n+ <repeat name="files" title="Input files" min="1">\n+ <param name="filetype" label="Input file type" type="select" help="Input file type">\n+ <option value="fastq">Fastq</option>\n+ <option value="fasta">Fasta</option>\n+ <option value="bam">Bam</option>\n+ </param>\n+ <conditional name="paired_type">\n+ <param name="paired_type_selector" type="select" label="Single or paired end reads" help="Select between paired and single end data">\n+ <option value="paired">Paired</option>\n+ <option value="single">Single</option>\n+ <option value="paired_collection">Paired Collection</option>\n+ <option value="paired_iv">Paired Interleaved</option>\n+ </param>\n+ <when value="paired">\n+ <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select first set of reads" help="Specify dataset with forward reads"/>\n+ <param name="input2" type="data" format="fastqsanger,fasta,bam" label="Select second set of reads" help="Specify dataset with reverse reads"/>\n+ </when>\n+ <when value="single">\n+ <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select the reads" help="Specify dataset with the reads"/>\n+ </whe'..b'tigs divided by the total bases in all contigs plus the log of the number of bases in long contigs (as an example only.)\n+\n+ **Hash Length**\n+\n+ The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.\n+\n+ The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::\n+\n+ # it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.\n+ # it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits\n+ # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.\n+\n+ Now you still have quite a lot of possibilities. As is often the case, it\'s a trade- off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below). . . so there\'s a sweet spot to be found with time and experience.\n+ We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C # (L - k + 1)/L where k is your hash length, and L you read length.\n+ Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! VelvetOptimiser automates these tests for you.\n+\n+\n+ **Velvetg options**\n+\n+ -scaffolding yes|no : scaffolding of contigs used paired end information (default: on)\n+\n+ -max_branch_length integer : maximum length in base pair of bubble (default: 100)\n+\n+ max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)\n+\n+ -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)\n+\n+ -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)\n+\n+ -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)\n+\n+ -coverage_mask integer : minimum coverage required for confident regions of contigs (default: 1)\n+\n+ -long_mult_cutoff integer : minimum number of long reads required to merge contigs (default: 2)\n+\n+ -paired_exp_fraction double : remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)\n+\n+ -conserveLong yes|no : preserve sequences with long reads in them (default no)\n+\n+\n+ **Input Files**\n+\n+ Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate\n+ read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.\n+\n+ Supported file formats are::\n+\n+ fasta\n+ fastq\n+ bam\n+\n+ Read categories are::\n+\n+ short (default)\n+ shortPaired\n+ long (for Sanger, 454 or even reference sequences)\n+ longPaired\n+ reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)\n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">@UNPUBLISHED{GLADMAN2012,\n+ author = "Gladman Simon",\n+ title = "VelvetOptimiser",\n+ year = "2012",\n+ note = "https://github.com/slugger70/VelvetOptimiser"}\n+ </citation>\n+ <citation type="doi">10.1101/gr.074492.107</citation>\n+ <citation type="doi">10.1371/journal.pone.0008407</citation>\n+ </citations>\n+</tool>\n' |