| Previous changeset 3:9ba8ebb636f4 (2015-09-07) Next changeset 5:8f4500f6f2aa (2022-12-06) |
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Commit message:
v0.1.11 using BLAST+ 2.5.0 and Biopython 1.67 |
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modified:
test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rhodopsin_nucs.fasta tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.py tools/blast_rbh/blast_rbh.xml tools/blast_rbh/tool_dependencies.xml |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular --- a/test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -ENA|BC112106|BC112106.1 gi|57163782|ref|NM_001009242.1| 1213 1047 86 100 1047 92.07 1514 +ENA|BC112106|BC112106.1 gi|57163782|ref|NM_001009242.1| 1213 1047 86 100 1047 92.073 1514 |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular --- a/test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 348 348 100 100 348 96.55 701 +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 348 348 100 100 348 96.552 701 |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rbh_blastp_k12.tabular --- a/test-data/rbh_blastp_k12.tabular Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rbh_blastp_k12.tabular Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,10 +1,10 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|16127995|ref|NP_414542.1| gi|16127995|ref|NP_414542.1| 21 21 100 100 21 100.00 38.1 -gi|16127996|ref|NP_414543.1| gi|16127996|ref|NP_414543.1| 820 820 100 100 820 100.00 1687 -gi|16127997|ref|NP_414544.1| gi|16127997|ref|NP_414544.1| 310 310 100 100 310 100.00 642 -gi|16127998|ref|NP_414545.1| gi|16127998|ref|NP_414545.1| 428 428 100 100 428 100.00 882 -gi|16128000|ref|NP_414547.1| gi|16128000|ref|NP_414547.1| 258 258 100 100 258 100.00 531 -gi|16128001|ref|NP_414548.1| gi|16128001|ref|NP_414548.1| 476 476 100 100 476 100.00 959 -gi|16128002|ref|NP_414549.1| gi|16128002|ref|NP_414549.1| 317 317 100 100 317 100.00 648 -gi|16128003|ref|NP_414550.1| gi|16128003|ref|NP_414550.1| 195 195 100 100 195 100.00 397 -gi|16128004|ref|NP_414551.1| gi|16128004|ref|NP_414551.1| 188 188 100 100 188 100.00 365 +gi|16127995|ref|NP_414542.1| gi|16127995|ref|NP_414542.1| 21 21 100 100 21 100.000 38.1 +gi|16127996|ref|NP_414543.1| gi|16127996|ref|NP_414543.1| 820 820 100 100 820 100.000 1687 +gi|16127997|ref|NP_414544.1| gi|16127997|ref|NP_414544.1| 310 310 100 100 310 100.000 642 +gi|16127998|ref|NP_414545.1| gi|16127998|ref|NP_414545.1| 428 428 100 100 428 100.000 882 +gi|16128000|ref|NP_414547.1| gi|16128000|ref|NP_414547.1| 258 258 100 100 258 100.000 531 +gi|16128001|ref|NP_414548.1| gi|16128001|ref|NP_414548.1| 476 476 100 100 476 100.000 959 +gi|16128002|ref|NP_414549.1| gi|16128002|ref|NP_414549.1| 317 317 100 100 317 100.000 648 +gi|16128003|ref|NP_414550.1| gi|16128003|ref|NP_414550.1| 195 195 100 100 195 100.000 397 +gi|16128004|ref|NP_414551.1| gi|16128004|ref|NP_414551.1| 188 188 100 100 188 100.000 365 |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rbh_blastp_k12_self.tabular --- a/test-data/rbh_blastp_k12_self.tabular Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rbh_blastp_k12_self.tabular Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,5 +1,5 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|16127997|ref|NP_414544.1| NP_414544_near_copy 310 309 99 100 309 99.68 638 -NP_414544_near_copy gi|16127997|ref|NP_414544.1| 309 310 100 99 309 99.68 638 -NP_414546_near_copy_1 NP_414546_near_copy_2 99 100 99 98 98 100.00 197 -NP_414546_near_copy_2 NP_414546_near_copy_1 100 99 98 99 98 100.00 197 +gi|16127997|ref|NP_414544.1| NP_414544_near_copy 310 309 99 100 309 99.676 638 +NP_414544_near_copy gi|16127997|ref|NP_414544.1| 309 310 100 99 309 99.676 638 +NP_414546_near_copy_1 NP_414546_near_copy_2 99 100 99 98 98 100.000 197 +NP_414546_near_copy_2 NP_414546_near_copy_1 100 99 98 99 98 100.000 197 |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular --- a/test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 100 86 1047 92.07 1474 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 100 86 1047 92.073 1474 |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular --- a/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 22 19 230 97.39 559 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 22 19 230 97.391 559 |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 test-data/rhodopsin_nucs.fasta --- a/test-data/rhodopsin_nucs.fasta Mon Sep 07 04:40:51 2015 -0400 +++ b/test-data/rhodopsin_nucs.fasta Wed Apr 19 07:44:47 2017 -0400 |
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| b'@@ -1,161 +1,138 @@\n >gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA\n-ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCT\n-TCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCT\n-CATCGTGCTTGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACG\n-CCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCA\n-CCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGC\n-CACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTGAGCGGTACGTGGTGGTGTGT\n-AAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACCTGGGTCATGG\n-CACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG\n-CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTC\n-CACTTCACCATCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGG\n-CAGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCAT\n-GGTCATTGCTTTCCTGATCTGTTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGG\n-TCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCTTCGCAAAGTCCTCCTCCATCTACAACCCTG\n-TCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCC\n-ACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACCGGCCTAA\n-\n+ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCTTCGAGTACCC\n+ACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCTCATCGTGCTTGGCTTCCCCA\n+TCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCC\n+GTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCACCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCC\n+CACAGGATGCAATTTGGAGGGCTTCTTTGCCACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTG\n+AGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACC\n+TGGGTCATGGCACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG\n+CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCA\n+TCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGGCAGCCCAGCAGCAGGAGTCA\n+GCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCATGGTCATTGCTTTCCTGATCTGTTGGGTGCC\n+CTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGGTCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCT\n+TCGCAAAGTCCTCCTCCATCTACAACCCTGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACC\n+CTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACC\n+GGCCTAA\n >gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds\n-TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTA\n-CATACCCATGTCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAG\n-CCATGGCAATATTCCATTCTGTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCA\n-TGACCTTGTACGTCACCATCCAGCACAAGAAGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGC\n-CTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTGACAATGTACTCCTCAATGAACGGATACTTC\n-ATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGGTGGTGAAATCGCCCTTTGGT\n-CCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCCGATTTAGTGA\n-GAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT\n-GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCG\n-AGGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTT\n-CTTCTGCTATGGCCGCCTGGTGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACC\n-CAGAAGGCCGAGAAAGAGGTGACCAGGATGGTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCC\n-CCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGGCTCTGAGTTCGGCCCCATCTTCATGACCGT\n-CCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACATCATGCTCAACAAGCAGTTC\n-CGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCCTCCTCTGCCG\n-CCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG\n-CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGC\n-GAAGTTCCCCTTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGC\n-CCCCCCGAACCCCTTCGCTGCTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCA\n-GCGAAGGGGTTGTCATCCGGACGCGCCAAGAATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCT\n-GCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCGCACTCCGGCCGGTTCATACCTCTTATTTTT\n-TTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTCAGGTCTGGTAGTGGCGGAGA\n-TTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG\n-\n+TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCC'..b'GACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCCTGCCTAA\n-\n+ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCTTCGAGGCGCC\n+GCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCTGATCATGCTTGGCTTCCCCA\n+TCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACCCCCCTCAACTACATCCTGCTCAACCTGGCC\n+GTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCACCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCC\n+GACGGGCTGCAACCTCGAGGGCTTCTTTGCCACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCG\n+AGCGGTACGTAGTGGTGTGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACC\n+TGGGTCATGGCTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTG\n+CGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTACACTTCATCA\n+TCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTGCAGCCCAGCAGCAGGAGTCG\n+GCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCATGGTCATCGCTTTCCTCATATGCTGGCTGCC\n+CTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGATCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCT\n+TTGCCAAGACGTCTGCCGTCTATAACCCCGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACT\n+CTCTGCTGTGGCAAGAACCCCCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCC\n+TGCCTAA\n >gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds\n-CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCC\n-ACTGGTGTAGTGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTC\n-TGTCTGCCTACATGTTCTTCCTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCAT\n-CGAACATAAGAAACTGAGGACCCCACTGAACTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATG\n-GTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGCACGGCTACTTTGTCTTCGGCCCCACCGGCT\n-GCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGGTGCCTCGTTGTCCTGGCCAT\n-TGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGCCATCATGGGT\n-GTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC\n-CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTT\n-TGTGATCTACATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTG\n-GTGTGCACCGTCAAAGAGGCCGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGG\n-TCACCCGCATGGTCGTCATCATGGTCATCTCCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTG\n-GTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATCTTCATGACCATTCCATCCTTCTTTGCCAAG\n-AGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTTCCGCCATTGCATGATCACCA\n-CCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTAAAACTGAGGC\n-TTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA\n-AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACAC\n-AACCATATAGGTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTAC\n-AATATAGTCAACTTGATAGCAAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGT\n-GAAATAAATTGCAA\n+CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCCACTGGTGTAG\n+TGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTCTGTCTGCCTACATGTTCTTC\n+CTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCATCGAACATAAGAAACTGAGGACCCCACTGAA\n+CTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATGGTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGC\n+ACGGCTACTTTGTCTTCGGCCCCACCGGCTGCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGG\n+TGCCTCGTTGTCCTGGCCATTGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGC\n+CATCATGGGTGTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC\n+CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTTTGTGATCTAC\n+ATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTGGTGTGCACCGTCAAAGAGGC\n+CGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGGTCACCCGCATGGTCGTCATCATGGTCATCT\n+CCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTGGTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATC\n+TTCATGACCATTCCATCCTTCTTTGCCAAGAGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTT\n+CCGCCATTGCATGATCACCACCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTA\n+AAACTGAGGCTTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA\n+AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACACAACCATATAG\n+GTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTACAATATAGTCAACTTGATAGC\n+AAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGTGAAATAAATTGCAA\n' |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 tools/blast_rbh/README.rst --- a/tools/blast_rbh/README.rst Mon Sep 07 04:40:51 2015 -0400 +++ b/tools/blast_rbh/README.rst Wed Apr 19 07:44:47 2017 -0400 |
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| @@ -1,7 +1,7 @@ Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper ========================================================== -This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -84,7 +84,13 @@ v0.1.7 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Updated citation information with GigaScience paper. -v0.1.8 - Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install. +v0.1.8 - Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install. +v0.1.9 - Updates to the command line API for the Python script. + - PEP8 style updates to the Python script (internal change only). + - Fix parameter help text which was not being displayed. +v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. + - Update Biopython dependency. + - Tweak Python script to work under Python 2 or Python 3. ======= ====================================================================== @@ -98,17 +104,17 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_update -t testtoolshed --check_diff tools/blast_rbh/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_update -t toolshed --check_diff tools/blast_rbh/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blast_rbh/ + $ planemo shed_upload --tar_only tools/blast_rbh/ ... $ tar -tzf shed_upload.tar.gz test-data/four_human_proteins.fasta |
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| diff -r 9ba8ebb636f4 -r d8d9a9069586 tools/blast_rbh/blast_rbh.py --- a/tools/blast_rbh/blast_rbh.py Mon Sep 07 04:40:51 2015 -0400 +++ b/tools/blast_rbh/blast_rbh.py Wed Apr 19 07:44:47 2017 -0400 |
| [ |
| b'@@ -2,7 +2,7 @@\n """BLAST Reciprocal Best Hit (RBH) from two FASTA input files.\n \n Run "blast_rbh.py -h" to see the help text, or read the associated\n-README.rst file which is also available on GitHub at:\n+blast_rbh.xml and README.rst files which are available on GitHub at:\n https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh\n \n This requires Python and the NCBI BLAST+ tools to be installed\n@@ -18,60 +18,78 @@\n # results, rather than doing minimum HSP coverage in Python.\n # [Not doing this right now as would break on older BLAST+]\n \n+from __future__ import print_function\n+\n import os\n+import shutil\n import sys\n import tempfile\n-import shutil\n+\n from optparse import OptionParser\n \n-def stop_err( msg ):\n- sys.stderr.write("%s\\n" % msg)\n- sys.exit(1)\n \n def run(cmd):\n return_code = os.system(cmd)\n if return_code:\n- stop_err("Error %i from: %s" % (return_code, cmd))\n+ sys.exit("Error %i from: %s" % (return_code, cmd))\n+\n \n if "--version" in sys.argv[1:]:\n- #TODO - Capture version of BLAST+ binaries too?\n- print "BLAST RBH v0.1.6"\n+ # TODO - Capture version of BLAST+ binaries too?\n+ print("BLAST RBH v0.1.11")\n sys.exit(0)\n \n-#Parse Command Line\n+try:\n+ threads = int(os.environ.get("GALAXY_SLOTS", "1"))\n+except ValueError:\n+ threads = 1\n+assert 1 <= threads, threads\n+\n+# Parse Command Line\n usage = """Use as follows:\n \n $ python blast_rbh.py [options] A.fasta B.fasta\n+\n+Many of the options are required. Example with proteins and blastp:\n+\n+$ python blast_rbh.py -a prot -t blasp -o output.tsv protA.fasta protB.fasta\n+\n+There is additional guideance in the help text in the blast_rbh.xml file,\n+which is shown to the user via the Galaxy interface to this tool.\n """\n \n parser = OptionParser(usage=usage)\n parser.add_option("-a", "--alphabet", dest="dbtype",\n default=None,\n- help="Alphabet type (nucl or prot)")\n+ help="Alphabet type (nucl or prot; required)")\n parser.add_option("-t", "--task", dest="task",\n default=None,\n- help="BLAST task (e.g. blastp, blastn, megablast)")\n-parser.add_option("-i","--identity", dest="min_identity",\n+ help="BLAST task (e.g. blastp, blastn, megablast; required)")\n+parser.add_option("-i", "--identity", dest="min_identity",\n default="70",\n help="Minimum percentage identity (optional, default 70)")\n parser.add_option("-c", "--coverage", dest="min_coverage",\n default="50",\n help="Minimum HSP coverage (optional, default 50)")\n parser.add_option("--nr", dest="nr", default=False, action="store_true",\n- help="Preprocess FASTA files to collapse identifical "\n+ help="Preprocess FASTA files to collapse identitical "\n "entries (make sequences non-redundant)")\n parser.add_option("-o", "--output", dest="output",\n default=None, metavar="FILE",\n- help="Output filename")\n+ help="Output filename (required)")\n+parser.add_option("--threads", dest="threads",\n+ default=threads,\n+ help="Number of threads when running BLAST. Defaults to the "\n+ "$GALAXY_SLOTS environment variable if set, or 1.")\n options, args = parser.parse_args()\n \n if len(args) != 2:\n- stop_err("Expects two input FASTA filenames")\n+ sys.exit("Expects two input FASTA filenames")\n fasta_a, fasta_b = args\n if not os.path.isfile(fasta_a):\n- stop_err("Missing input file for species A: %r" % fasta_a)\n+ sys.exit("Missing input file for species A: %r" % fasta_a)\n if not os.path.isfile(fasta_b):\n- stop_err("Missing input file for species B: %r" % fasta_b)\n+ sys.exit("Missing input file for species B: %r" % fasta_b)\n if os.path.abspath(fasta_a) == os.path.abspath(fasta_b):\n self_comparison = True\n print("Doing self comparison; ignoring s'..b'op_err("Missing Biopython")\n+ sys.exit("Missing Biopython")\n for record in SeqIO.parse(input_fasta, "fasta"):\n s = str(record.seq).upper()\n try:\n@@ -259,7 +290,7 @@\n unique += 1\n del by_seq\n if duplicates:\n- #TODO - refactor as a generator with single SeqIO.write(...) call\n+ # TODO - refactor as a generator with single SeqIO.write(...) call\n with open(output_fasta, "w") as handle:\n for record in SeqIO.parse(input_fasta, "fasta"):\n if record.id in representatives:\n@@ -269,12 +300,14 @@\n elif record.id in duplicates:\n continue\n SeqIO.write(record, handle, "fasta")\n- print("%i unique entries; removed %i duplicates leaving %i representative records" % (unique, len(duplicates), len(representatives)))\n+ print("%i unique entries; removed %i duplicates leaving %i representative records"\n+ % (unique, len(duplicates), len(representatives)))\n else:\n os.symlink(os.path.abspath(input_fasta), output_fasta)\n print("No perfect duplicates in file, %i unique entries" % unique)\n \n-#print("Starting...")\n+\n+# print("Starting...")\n check_duplicate_ids(fasta_a)\n if not self_comparison:\n check_duplicate_ids(fasta_b)\n@@ -286,18 +319,18 @@\n fasta_a = tmp_a\n fasta_b = tmp_b\n \n-#TODO - Report log in case of error?\n+# TODO - Report log in case of error?\n run(\'%s -dbtype %s -in "%s" -out "%s" -logfile "%s"\' % (makeblastdb_exe, dbtype, fasta_a, db_a, log))\n if not self_comparison:\n run(\'%s -dbtype %s -in "%s" -out "%s" -logfile "%s"\' % (makeblastdb_exe, dbtype, fasta_b, db_b, log))\n-#print("BLAST databases prepared.")\n+# print("BLAST databases prepared.")\n run(\'%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i\'\n % (blast_cmd, fasta_a, db_b, a_vs_b, cols, threads))\n-#print("BLAST species A vs species B done.")\n+# print("BLAST species A vs species B done.")\n if not self_comparison:\n run(\'%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i\'\n % (blast_cmd, fasta_b, db_a, b_vs_a, cols, threads))\n- #print("BLAST species B vs species A done.")\n+ # print("BLAST species B vs species A done.")\n \n \n best_b_vs_a = dict(best_hits(b_vs_a, self_comparison))\n@@ -306,19 +339,20 @@\n count = 0\n outfile = open(out_file, \'w\')\n outfile.write("#A_id\\tB_id\\tA_length\\tB_length\\tA_qcovhsp\\tB_qcovhsp\\tlength\\tpident\\tbitscore\\n")\n-for a, (b, a_score_float, a_score_str, a_identity_str, a_coverage_str, a_qlen, a_length) in best_hits(a_vs_b, self_comparison):\n+for a, (b, a_score_float, a_score_str,\n+ a_identity_str, a_coverage_str, a_qlen, a_length) in best_hits(a_vs_b, self_comparison):\n if b not in best_b_vs_a:\n- #Match b has no best hit\n+ # Match b has no best hit\n continue\n a2, b_score_float, b_score_str, b_identity_str, b_coverage_str, b_qlen, b_length = best_b_vs_a[b]\n if a != a2:\n- #Not an RBH\n+ # Not an RBH\n continue\n- #Start with IDs, lengths, coverage\n+ # Start with IDs, lengths, coverage\n values = [a, b, a_qlen, b_qlen, a_coverage_str, b_coverage_str]\n- #Alignment length was an integer so don\'t care about original string\n+ # Alignment length was an integer so don\'t care about original string\n values.append(min(a_length, b_length))\n- #Output the original string versions of the scores\n+ # Output the original string versions of the scores\n if float(a_identity_str) < float(b_identity_str):\n values.append(a_identity_str)\n else:\n@@ -330,9 +364,9 @@\n outfile.write("%s\\t%s\\t%i\\t%i\\t%s\\t%s\\t%i\\t%s\\t%s\\n" % tuple(values))\n count += 1\n outfile.close()\n-print "Done, %i RBH found" % count\n+print("Done, %i RBH found" % count)\n if tie_warning:\n sys.stderr.write("Warning: Sequences with tied best hits found, you may have duplicates/clusters\\n")\n \n-#Remove temp files...\n+# Remove temp files...\n shutil.rmtree(base_path)\n' |
| b |
| diff -r 9ba8ebb636f4 -r d8d9a9069586 tools/blast_rbh/blast_rbh.xml --- a/tools/blast_rbh/blast_rbh.xml Mon Sep 07 04:40:51 2015 -0400 +++ b/tools/blast_rbh/blast_rbh.xml Wed Apr 19 07:44:47 2017 -0400 |
| b |
| @@ -1,12 +1,8 @@ -<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.8"> +<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11"> <description>from two FASTA files</description> <requirements> - <requirement type="package" version="1.64">biopython</requirement> - <requirement type="python-module">Bio</requirement> - <requirement type="binary">makeblastdb</requirement> - <requirement type="binary">blastp</requirement> - <requirement type="binary">blastn</requirement> - <requirement type="package" version="2.2.31">blast+</requirement> + <requirement type="package" version="1.67">biopython</requirement> + <requirement type="package" version="2.5.0">blast</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -33,10 +29,10 @@ <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> <param name="fasta_a" type="data" format="fasta" label="Genes/proteins from species A" - description="FASTA file, one sequence per gene/protein." /> + help="FASTA file, one sequence per gene/protein." /> <param name="fasta_b" type="data" format="fasta" label="Genes/proteins from species B" - description="FASTA file, one sequence per gene/protein." /> + help="FASTA file, one sequence per gene/protein." /> <conditional name="seq"> <param name="dbtype" type="select" label="Molecule type of FASTA inputs"> <option value="prot">protein</option> |
| b |
| diff -r 9ba8ebb636f4 -r d8d9a9069586 tools/blast_rbh/tool_dependencies.xml --- a/tools/blast_rbh/tool_dependencies.xml Mon Sep 07 04:40:51 2015 -0400 +++ b/tools/blast_rbh/tool_dependencies.xml Wed Apr 19 07:44:47 2017 -0400 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.64"> - <repository changeset_revision="5477a05cc158" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="blast+" version="2.2.31"> - <repository changeset_revision="e36f75574aec" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="blast" version="2.5.0"> + <repository changeset_revision="5dd2b68c7d04" name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |