# HG changeset patch # User peterjc # Date 1392892788 18000 # Node ID 22b7cdcf49603e8626ee5a7d15e961df8d947b5f # Parent 2f7fac29bb3c62143204845cd0e344522aa6bbda Uploaded v0.1.0 preview 2, includes missing new test files diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/blastn_rhodopsin_vs_three_human.columns.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.columns.tabular Thu Feb 20 05:39:48 2014 -0500 @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 4301 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 4301 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 4301 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 4301 1213 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 983 1213 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1047 1213 diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/blastn_rhodopsin_vs_three_human.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Thu Feb 20 05:39:48 2014 -0500 @@ -0,0 +1,549 @@ + + + + blastn + BLASTN 2.2.29+ + Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. + + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + 1e-40 + 1 + -2 + 0 + 0 + L;m; + + + + + 1 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 2 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 3 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 1474.75 + 798 + 0 + 1 + 1047 + 88 + 1134 + 1 + 1 + 964 + 964 + 0 + 1047 + ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCTCATCGTGCTTGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCACCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACCTGGGTCATGGCACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATGCGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGGCAGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCATGGTCATTGCTTTCCTGATCTGTTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGGTCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCTTCGCAAAGTCCTCCTCCATCTACAACCCTGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACCGGCCTAA + ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA + ||||| || || || ||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| | ||||||||||||| |||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| ||||||||||| |||||||| |||| || ||||||||||||||||| || ||| ||||||| || || || |||||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||| || ||||| |||||||| |||||||| ||||||||||| || |||||||||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||||||||| |||| |||||||| || ||| | || |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||||||||||||||| || ||||| || | |||| |||||||||||||| ||||||||||| ||||||||| + + + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + + + 4 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 15 + 7453579 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 5 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 15 + 7453579 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 6 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 15 + 7453579 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 7 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 16 + 20482300 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 8 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 16 + 20482300 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 9 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 460.936 + 249 + 3.59583e-132 + 1 + 333 + 118 + 450 + 1 + 1 + 305 + 305 + 0 + 333 + GTGCCCTTCTCCAACAAGACAGGCGTGGTGCGCAGTCCCTTCGAGCATCCACAGTACTACCTGGCCGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTCGGCTTCCCCATCAACTTCCTCACGCTCTATGTCACGGTTCAGCACAAGAAGCTGCGTACGCCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCCGACCTCTTCATGGTCTTCGGAGGCTTCACCACCACCCTCTACACCTCCCTGCATGGATACTTTGTCTTCGGGCCTACGGGATGCAATCTGGAGGGCTTTTTTGCCACCCTGGGAGGT + GTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGT + |||||||||||||| ||| || ||||| ||||| ||||||||| | ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||| | || |||||||||| ||||||||||||||| |||||||||||||| ||||||||||| || ||||||||| |||||||||| |||||||||||||| ||| + + + 2 + 331.671 + 179 + 2.94161e-93 + 3127 + 3368 + 782 + 1023 + 1 + 1 + 222 + 222 + 2 + 243 + AGGCAGCTGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCCGAGAAGGAGGTCACCCGTATGGTCATCATCATGGTCATTGCTTTCCTAATCTGTTGGCTGCCGTATGCCGGCGTGGCATTCTACATCTTCACCCACCAGGGCTCTAACTTTGGCCCCATCTTCATGACCCTCCCGGCATTCTTTGCCAAG-TCGTCCTCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAG + AGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCG-CCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAG + |||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||| |||| || ||| |||||||||||||||||||||||||||||||||| ||||| || ||||||||||||||| |||| || |||||||||||| || || ||||||||||||||||||||||||||||||||||||||||| + + + 3 + 265.191 + 143 + 3.02604e-73 + 1410 + 1582 + 448 + 620 + 1 + 1 + 163 + 163 + 0 + 173 + GGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTATGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCCTTGCCCTCACCTGGGTCATGGCACTGGCCTGCGCCGCGCCCCCGCTAGTCGGCTGGTCCAGGTA + GGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||| ||||| |||||||||||||||| |||||||||||||| ||||| || | ||||||||||||||| + + + 4 + 248.571 + 134 + 3.04752e-68 + 2854 + 3023 + 615 + 784 + 1 + 1 + 158 + 158 + 0 + 170 + CAGGTACATCCCAGAGGGCATGCAGTGCTCATGTGGAATCGACTACTACACCCTCAAGCCGGAGGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCTATGATTGTCATATTCTTTTGCTATGGACAGCTGGTCTTCACCGTCAAGGAGG + CAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGG + |||||||||||| |||||| |||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||| |||| || || |||||||| ||||| ||||||||||||||||||| + + + + + + + 0 + 0 + 16 + 20482300 + 0.46 + 1.28 + 0.85 + + + + + 10 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 15 + 4628008 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 11 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 15 + 4628008 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 12 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 1323.32 + 716 + 0 + 1 + 959 + 118 + 1076 + 1 + 1 + 878 + 878 + 0 + 959 + GTGCCCTTCTCCAACAAGACGGGTGTGGTGCGCAGCCCCTTCGAGTACCCGCAGTACTACCTGGCTGAGCCCTGGCAGTTCTCCATGCTGGCTGCCTACATGTTTCTGCTGATCGTGCTCGGATTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCTGTGGCCAACCTCTTCATGGTCTTTGGAGGCTTCACCACCACCCTGTATACCTCTATGCATGGATACTTCGTCTTCGGGGCCACGGGATGCAATCTGGAGGGCTTCTTTGCCACGCTGGGCGGTGAAATCGCCCTGTGGTCCCTGGTGGTCCTGGCCATCGAGCGGTATGTGGTGGTCTGCAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCACGCCATCATGGGCCTCGCCTTCACGTGGGTCATGGCACTGGCCTGCGCTGCACCCCCACTAGCCGGCTGGTCCAGGTACATCCCAGAGGGCATGCAGTGCTCGTGTGGGATTGACTACTACACGCTCAAACCGGAGGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTGTCATTTTCTTCTGCTACGGACAGCTGGTGTTCACAGTGAAGGAGGCGGCTGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCCGAGAAGGAAGTCACGCGCATGGTCATCATCATGGTCGTTGCGTTCCTAATCTGTTGGCTGCCCTACGCCAGCGTGGCATTCTACATCTTTACCCACCAGGGCTCTAACTTTGGCCCTGTCTTCATGACCATCCCGGCATTCTTCGCCAAGTCATCCTCCATCTACAACCCGGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCCTCTGCTGTGGCAAGAACCCACTGGGTGA + GTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGA + |||||||||||||| |||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||| | || |||||||||| |||||| || |||||| ||||||||||||||||||||||| |||| ||||||||| ||||||||||||||||||| |||||||||||||| |||||||||||| ||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||| ||||||||||| |||||||||||| | |||||||| ||||||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||| |||||||||||||||| || ||||||||||||||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||| |||| || |||||||| || ||||| || ||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| |||||||| ||||| ||||||||||||||||||||| | || ||||| ||||| ||| ||||||||||||||||||||||||||||||| |||||||||||||| ||||| || || |||||||||||||||| || ||||| |||||| || ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||||| + + + + + + + 0 + 0 + 15 + 4628008 + 0.46 + 1.28 + 0.85 + + + + + 13 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 14 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 15 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 1208.83 + 654 + 0 + 1 + 1047 + 88 + 1134 + 1 + 1 + 917 + 917 + 2 + 1048 + ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCTTCGAGGCGCCGCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCTGATCATGCTTGGCTTCCCCATCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACCCCCCTCAACTACATCCTGCTCAACCTGGCCGTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCACCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCCGACGGGCTGCAACCTCGAGGGCTTCTTTGCCACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCGAGCGGTACGTAGTGGTGTGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACCTGGGTCATGGCTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTGCGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTACACTTCATCATCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTGCAGCCCAGCAGCAGGAGTCGGCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCATGGTCATCGCTTTCCTCATATGCTGGCTGCCCTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGATCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCTTTGCCAAGA-CGTCTGCCGTCTATAACCCCGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACTCTCTGCTGTGGCAAGAACCCCCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCCTGCCTAA + ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCC-GCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA + ||||| || || || ||||| |||||||||||||| |||||||| |||||| || |||||||||||||||||| || |||||||||||||||||||||||||||||| ||||||||||||||||||||| ||||||||| |||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||| | || || ||||||||||||||||||||||| |||||||| || ||||||||||| | || |||||||||| |||||| || ||||||||||| || |||||||| ||||| || || || ||||| | |||||||||||||||||| | |||||||||||||| ||||||||||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||| |||||||| || || ||||| |||| ||||||||| || |||||||| ||||| ||||||||||||| || ||||| |||||||||| | | |||| |||||| ||||| || ||||||||||||||||| || ||||||| ||||||| ||||| |||| || |||||||| |||||||| |||||||||||||||||||| || ||||||||||||||||| |||||||| |||||||| |||||||||||||| || ||||||||||||||||||||||||||||| || |||||| |||||||||| | ||||| ||||||||||||||||| ||||| ||| |||| || |||||||||||||||||||| || ||||||||||||| || | ||| |||| ||||| |||||||| ||||||||||||||||||||||||||||||||| ||||||| ||||||| ||||||||||| || |||||||| |||||||| | |||||||||||||| ||||| ||||| |||||||| |||||| + + + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + + + 16 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 15 + 6353949 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 17 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 15 + 6353949 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 18 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 15 + 6353949 + 0.46 + 1.28 + 0.85 + + + No hits found + + + + diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_taxid.fasta.log Thu Feb 20 05:39:48 2014 -0500 @@ -0,0 +1,10 @@ + + +Building a new DB, current time: 02/10/2014 18:40:09 +New DB name: four_human_proteins_taxid.fasta +New DB title: Just 4 human proteins +Sequence type: Protein +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B +Adding sequences from FASTA; added 4 sequences in 0.00230002 seconds. diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.phd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_taxid.fasta.phd Thu Feb 20 05:39:48 2014 -0500 @@ -0,0 +1,4 @@ +11117184492 +29249033410 +36665887501 +5392473183 diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.phi Binary file test-data/four_human_proteins_taxid.fasta.phi has changed diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.phr Binary file test-data/four_human_proteins_taxid.fasta.phr has changed diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.pin Binary file test-data/four_human_proteins_taxid.fasta.pin has changed diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.pog Binary file test-data/four_human_proteins_taxid.fasta.pog has changed diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.psd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_taxid.fasta.psd Thu Feb 20 05:39:48 2014 -0500 @@ -0,0 +1,4 @@ +gnl|bl_ord_id|00 +gnl|bl_ord_id|11 +gnl|bl_ord_id|22 +gnl|bl_ord_id|33 diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.psi Binary file test-data/four_human_proteins_taxid.fasta.psi has changed diff -r 2f7fac29bb3c -r 22b7cdcf4960 test-data/four_human_proteins_taxid.fasta.psq Binary file test-data/four_human_proteins_taxid.fasta.psq has changed diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/README.rst Thu Feb 20 05:39:48 2014 -0500 @@ -25,17 +25,7 @@ (``blastxml``) and protein and nucleotide BLAST databases (``blastdbp`` and ``blastdbn``). -You must tell Galaxy about any system level BLAST databases using configuration -files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein -databases like NR), and blastdb_d.loc (protein domain databases like CDD or -SMART) which are located in the tool-data/ folder. Sample files are included -which explain the tab-based format to use. - -You can download the NCBI provided databases as tar-balls from here: - -* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) -* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) - +See the configuration notes below. Manual Installation =================== @@ -78,6 +68,31 @@ ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools +Configuration +============= + +You must tell Galaxy about any system level BLAST databases using configuration +files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein +databases like NR), and blastdb_d.loc (protein domain databases like CDD or +SMART) which are located in the tool-data/ folder. Sample files are included +which explain the tab-based format to use. + +You can download the NCBI provided databases as tar-balls from here: + +* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) +* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) + +The BLAST+ binaries support multi-threaded operation, which is handled via the +$GALAXY_SLOTS environment variable. This should be set automatically by Galaxy +via your job runner settings, which allows you to (for example) allocate four +cores to each BLAST job. + +In addition, the BLAST+ wrappers also support high level parallelism by task +splitting if ``use_tasked_jobs = True`` is enabled in your ``universe_wsgi.ini`` +configuration file. Essentially, the FASTA input query files are broken up into +batches of 1000 sequences, a separate BLAST child job is run for each chunk, +and then the BLAST output files are merged (in order). This is transparent +for the end user. History ======= @@ -105,7 +120,7 @@ (all too often our users where having to re-run searches just to get one of the missing columns like query or subject length) v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, - BLAST+ handling of some mult-file arguments is problematic). + BLAST+ handling of some multi-file arguments is problematic). v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc for the domain databases they use (e.g. CDD, PFAM or SMART). - Correct case of exception regular expression (for error handling @@ -139,6 +154,7 @@ - Tablar output now includes option to pick specific columns - BLAST XML to tabular tool supports multiple input files. - More detailed descriptions for BLASTN and BLASTP task option + - Supports setting a taxonomy ID in makeblastdb wrapper. ======= ====================================================================== diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/blastxml_to_tabular.py --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Feb 20 05:39:48 2014 -0500 @@ -66,7 +66,7 @@ from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.23" + print "v0.1.00" sys.exit(0) if sys.version_info[:2] >= ( 2, 5 ): diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Feb 20 05:39:48 2014 -0500 @@ -28,33 +28,33 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Thu Feb 20 05:39:48 2014 -0500 @@ -83,13 +83,14 @@ **What it does** -This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST algorithm. +This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST_ algorithm. If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 **References** diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Feb 20 05:39:48 2014 -0500 @@ -31,33 +31,33 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Feb 20 05:39:48 2014 -0500 @@ -29,7 +29,10 @@ ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful -title "BLAST Database" #end if --dbtype $dbtype +-dbtype $dbtype +## -------------------------------------------------------------------- +## Masking +## -------------------------------------------------------------------- #set $mask_string = '' #set $sep = '-mask_data ' #for $i in $mask_data @@ -44,11 +47,15 @@ ## #set $sep = ',' ## #end for ## $gi_mask_string -## #if $tax.select == 'id': -## -taxid $tax.id -## #else if $tax.select == 'map': -## -taxid_map $tax.map -## #end if +## -------------------------------------------------------------------- +## Taxonomy +## -------------------------------------------------------------------- +#if $tax.taxselect == 'id': +-taxid $tax.taxid +## TODO - Can we use a tabular file for the taxonomy mapping? +## #else if $tax.taxselect == 'map': +## -taxid_map $tax.taxmap +#end if ## -------------------------------------------------------------------- ## Capture the stdout log information to the primary file (plain text): >> "$outfile" @@ -83,23 +90,25 @@ --> - - + + - --> @@ -112,6 +121,8 @@ @@ -130,6 +141,25 @@ + + + + + + + + + + + + + + + + + + + **What it does** diff -r 2f7fac29bb3c -r 22b7cdcf4960 tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Wed Jan 15 05:38:14 2014 -0500 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Thu Feb 20 05:39:48 2014 -0500 @@ -1,6 +1,6 @@ - +