details: http://www.bx.psu.edu/hg/galaxy/rev/7698e2ecca3e changeset: 2999:7698e2ecca3e user: Kelly Vincent kpvincent@bx.psu.edu date: Tue Nov 10 13:06:20 2009 -0500 description: Fixed megablast_wrapper test to use phiX database and modified parameter passing to use named parameters
diffstat:
test-data/megablast_wrapper_test1.fa | 200 +++------------------------------ test-data/megablast_wrapper_test1.out | 123 +++----------------- tools/metag_tools/megablast_wrapper.py | 35 ++++- tools/metag_tools/megablast_wrapper.xml | 14 ++- 4 files changed, 78 insertions(+), 294 deletions(-)
diffs (446 lines):
diff -r e2420f742a0a -r 7698e2ecca3e test-data/megablast_wrapper_test1.fa --- a/test-data/megablast_wrapper_test1.fa Tue Nov 10 12:35:00 2009 -0500 +++ b/test-data/megablast_wrapper_test1.fa Tue Nov 10 13:06:20 2009 -0500 @@ -1,200 +1,40 @@
0_0.666667
-CGGACAGCGCCGCCACCAACAAAGCCACCA +GAGTTTTATCGCTTCCATGACGCAGAAGTT
1_0.600000
-AAAACACCGGATGCTCCGGCGCTGGCAGAT +AACACTTTCGGATATTTCTGATGAGTCGAA
2_0.400000
-TTTGCTTTTAGTACACCGGATTCAGAACCA +AGCAGGAATTACTACTGCTTGTTTACGAAT
3_0.566667
-CCGTCCCCATGAATACACCTTTCTGGACGG +TAAATCGAAGTGGACTGCTGGCGGAAAATG
4_0.766667
-CACGCTACGTGCGCCCCCGCCCAGAAGGCG +TCCTTGCGCAGCTCGAGAAGCTCTTACTTT
5_0.533333
-AAACAAAACCCGCCGAAGCGGGTTAAGTGC +GCGACCTTTCGCCATCAACTAACGATTCTG
6_0.533333
-TAAGCCGTTACTGGCAGCAAGTGCAGGCAA +TTGGATGAGGAGAAGTGGCTTAATATGCTT
7_0.400000
-TGAATTTACCGTTATCTATCTTGCCTGCCT +GGCACGTTCGTCAAGGACTGGTTTAGATAT
8_0.500000
-TTAGCGGGAATAAAACAGGCTGTCAGCCAG +CATGGTAGAGATTCTCTTGTTGACATTTTA
9_0.400000
-GCGTTTTGCTAAACTTCTGCCGGAATATAA +AAAGAGCGTGGATTACTATCTGAGTCCGAT
10_0.500000
-AAAGAGGCGAGCAGAGTAAAACGCAGGCAA +ATAGGTAAGAAATCATGAGTCAAGTTACTG
11_0.533333
-CAAAAGCAGAGTCTGTTGACCCATACGCGC +AACAATCCGTACGTTTCCAGACCGCTTTGG
12_0.700000
-GCGGACGATCTTCACGGTCGCCACGCGGAC +TTCAGGCTTCTGCCGTTTTGGATTTAACCG
13_0.533333
-TTCTTGTTGGATGGCATACTCCGGCAGCCA +AAGATGATTTCGATTTTCTGACGAGTAACA
14_0.666667
-ACCCCGATATCGTCGCAGGCGTTGCCGCAC +CTGACCGCTCTCGTGCTCGTCGCTGCGTTG
15_0.666667
-GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC +AGGCTTGCGTTTATGGTACGCTGGACTTTG
16_0.566667
-ATGTCCTGATCGAGCGGCGTTTTACCGACC +TTCCTGCTCCTGTTGAGTTTATTGCTGCCG
17_0.533333
-GGTGTTGAGTGTCCAGGTAATACGCTCTCG +TCATTGCTTATTATGTTCATCCCGTCAACA
18_0.566667
-GTGGTCTCAAGCCCAAAGGAAGAGTGAGGC +TCATCATGGAAGGCGCTGAATTTACGGAAA
19_0.566667
-GTTGTAAGCGTCAGAACCGATGCGGTCGGT ->20_0.566667 -CGACATCCTGTAGGCTGGCTTCAATGCGAC ->21_0.733333 -GGGAAGGCTGACGGGCGTCCACACCACGGC ->22_0.566667 -CGGTATTCCTCAGTTCTCGCTGCATGCCTG ->23_0.600000 -TTGCCGTTACGCACCACGCCTTCAGTAGCG ->24_0.733333 -CGCGGGCGCACCACGTCGCTGCTGCTGTTC ->25_0.266667 -TTTTGGGAAAACTAAATACGCATCAAAAAT ->26_0.566667 -CAACGAGGCGCTACCGAGTTGTTCAATGCG ->27_0.600000 -TTACCGAGGCCAGAACCGATACCACGACCC ->28_0.666667 -CGCTCAATCTGCTCGCGCCTGGCTGGCGTT ->29_0.700000 -CTCGTCCGGCGGGCGGTTTTGCCGACAAGG ->30_0.233333 -GGAAATTGTACAATAGAAAAATTACTGTAT ->31_0.533333 -GTGCTGAACTGTTCCACGACCATGGAGATG ->32_0.600000 -TGAGGATGGTCCTCTGACTCTGCAGGCGCA ->33_0.300000 -TAGTAACCCTTTAATAAGATTGTCGATTAG ->34_0.533333 -TGATGTTAAATGCATGGCACCTGCCGGTGC ->35_0.466667 -ACTGCTTTGCCGAGATATTCGAGGTTAACC ->36_0.433333 -TGTTGGCAACATGGCGAGCGTAATCAATTA ->37_0.366667 -ACTTCGTCAGTAAGGATGAGATTAGCAAAT ->38_0.533333 -GCAGCAGGATCGGATCGAACTCTGGTTTCT ->39_0.400000 -TAATGCGGCATTCTCCTGATTTATTGTCAC ->40_0.400000 -AGCGTAATGATAATCGCTATCACTGCGATT ->41_0.566667 -AGCTGACGGTCAGCAGGGATACTTCCTGCA ->42_0.566667 -GCAGTGACTACATCCGCGAGGTGAATGTGG ->43_0.466667 -GCTTTTTCCAGCATCAACGCCACTGAACAA ->44_0.433333 -AAAGTGGTAGATAACGTGGTGCAGACTATG ->45_0.500000 -TTCCTGATACCGGATGACCTTATCGCGGAT ->46_0.466667 -ACCTGTACCCCAGGACCATGGTACATTTAT ->47_0.533333 -ACAATGCAACCAGACCAGCCCGGATCGATA ->48_0.500000 -GGGTAACCAGCTGATGATGGCCATTAACCT ->49_0.433333 -CGTTATACGGAACAACATTTAACTCCAGCG ->50_0.466667 -TTGCTGTTGCCATCGCTTTTCAGGACATAC ->51_0.533333 -CGACGGTATCGGTACGCAGATTGTGATGGA ->52_0.366667 -ATGAGCATCAACATCGAAATCTCAAACCAA ->53_0.533333 -CCAGGCACTCCGCCATATTTTTGCCATGAC ->54_0.400000 -GTATTCTTCATTGATTTGTAAGCGGGTACC ->55_0.466667 -AAGCGCTGTTCAACATAAATTGGCTGACGG ->56_0.433333 -AACCGTCAGCTCTTTACGCAATATTTTGCC ->57_0.566667 -CGCGAAATCCTCGACGTCCAGGCACGTATT ->58_0.300000 -GTTATCCATTAAAATAGATCGGATCGATAT ->59_0.300000 -AAAATCTGCATATCATGATAAGAGTGGTTA ->60_0.533333 -AATCTGGCGAATGCTGATAGCGTGACCGGT ->61_0.366667 -TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT ->62_0.366667 -AATCCTAAACCTAGGAATGCCAGAATATCT ->63_0.566667 -TCACGCTCGCAGTCAAGCTGGCTTATGCCA ->64_0.500000 -GAGATGACGGTTGCAGAGTCATGCGTTTGA ->65_0.533333 -TCTGGATCACGCGCAAACACTGGCTATCGT ->66_0.466667 -TCTGCTTTAGCAAACAGAGTGTGGTCACGA ->67_0.400000 -GCCTTTTGTCTGATCATCCACAATAATGAC ->68_0.566667 -GAAGGATAGTTGGTCAGCAACACCAGCGGC ->69_0.733333 -GGCGCGCTGTCGGCCACGGCGAAATCGACC ->70_0.466667 -TGGTGTTCAGCATCTCAACGGTAATTCGCT ->71_0.533333 -CAGGATGCAAACTGCCGGGAGATCCAGTTA ->72_0.533333 -AACTGGAAGGGCTTGGGATGACACAACAGC ->73_0.500000 -TTTAAGCGCCAACCAGGCTTCTTTGGTTGC ->74_0.433333 -ACCCTTCTTTCGCCATATCAAACTGATGTC ->75_0.533333 -ATAACCCTCTGCAACCGCCGCTTCAGCAAA ->76_0.600000 -TGAAGCCGTACAACGGGCGCTGGAATTCGC ->77_0.700000 -GAGCTGCAACGCGGTCAGCCAGCTGGCGGT ->78_0.566667 -CGGAGTATCCGTTCCCCAACGACAAGCATC ->79_0.500000 -AATACCGGGAAGAGACAACGGGGTCTCTTT ->80_0.500000 -TAATGACAGGGTTGCGAAGCCCTGATTCTC ->81_0.433333 -ATTAATGTTGCCGGCACAACATAATAGGGC ->82_0.500000 -ACTGGGTTGCTCTGAACAAGAAAGGCGCTA ->83_0.533333 -CGCCAGGGACGTATCGCGTCGATATCTATT ->84_0.533333 -TGCTCGTTCCCGTCGTGATGAAGCTCGAAA ->85_0.500000 -AGGAAAGCAAACAACACGACCACCATCAGC ->86_0.566667 -GGCAACGCAGGCGCATGATTCTGCTTGGAA ->87_0.433333 -CGCTGGATGAAAANCGTGAATATCACACCA ->88_0.533333 -CGTACCGGGCTGAAAGTAGAAGAGCGTTTC ->89_0.466667 -ATTAAAAAACAGGCGGTGCGTTTTCCCTGG ->90_0.466667 -ATCACCGTTTCGCTAACCGGTACGTTTAAC ->91_0.566667 -TTCGCCCGGCAAGCTTACCCAACGCTTATC ->92_0.533333 -TTTTCCCCGCCGTTAGTAGCGACTGCAGTT ->93_0.400000 -TTATTTGCCCGATGAGTCAGTTTATTGCAG ->94_0.466667 -CCACGGTGATATCTGGTGCCATACTGATAA ->95_0.466667 -TCCCCCGTAAGGCCTTTCTTTTTCTTTCGT ->96_0.533333 -TTGCCGGGAAGAGAGATATCAATGGCAGGC ->97_0.566667 -TGCGCCGCCGGATTGTTGCTCAACATGCTT ->98_0.366667 -AACGCGCTAACCGCCAATAATAACAAAATT ->99_0.366667 -TAAGAGTTTATTCATGATGTCATCCTGCGA +ACATTATTAATGGCGTCGAGCGTCCGGTTA \ No newline at end of file diff -r e2420f742a0a -r 7698e2ecca3e test-data/megablast_wrapper_test1.out --- a/test-data/megablast_wrapper_test1.out Tue Nov 10 12:35:00 2009 -0500 +++ b/test-data/megablast_wrapper_test1.out Tue Nov 10 13:06:20 2009 -0500 @@ -1,103 +1,20 @@ -0_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 5436010 5436039 8e-11 60.0 -1_0.600000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 696993 697022 8e-11 60.0 -2_0.400000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4100018 4100047 8e-11 60.0 -3_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2305873 2305844 8e-11 60.0 -4_0.766667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3457901 3457930 8e-11 60.0 -5_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1264160 1264131 8e-11 60.0 -5_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1636514 1636485 8e-11 60.0 -5_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2318694 2318723 8e-11 60.0 -5_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2777043 2777072 8e-11 60.0 -6_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1185124 1185153 8e-11 60.0 -7_0.400000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2458203 2458232 8e-11 60.0 -9_0.400000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 5286666 5286695 8e-11 60.0 -10_0.500000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2787672 2787701 8e-11 60.0 -12_0.700000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4116145 4116174 8e-11 60.0 -13_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 5442351 5442380 8e-11 60.0 -14_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4626492 4626521 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 346897 346926 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1466565 1466536 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1750132 1750161 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1908046 1908075 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2279107 2279136 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2813407 2813436 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3939162 3939191 8e-11 60.0 -15_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4656510 4656539 8e-11 60.0 -16_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2595157 2595186 8e-11 60.0 -17_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 717743 717772 8e-11 60.0 -19_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1237938 1237967 8e-11 60.0 -20_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4792054 4792083 8e-11 60.0 -21_0.733333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 269757 269786 8e-11 60.0 -21_0.733333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 274007 274036 8e-11 60.0 -22_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2706426 2706455 8e-11 60.0 -23_0.600000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1512107 1512136 8e-11 60.0 -24_0.733333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2032108 2032137 8e-11 60.0 -25_0.266667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1343811 1343840 8e-11 60.0 -26_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3112551 3112580 8e-11 60.0 -28_0.666667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4405442 4405471 8e-11 60.0 -29_0.700000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3600547 3600576 8e-11 60.0 -32_0.600000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1435670 1435699 8e-11 60.0 -33_0.300000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3788178 3788207 8e-11 60.0 -34_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 484499 484528 8e-11 60.0 -35_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2250064 2250093 8e-11 60.0 -36_0.433333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3698178 3698207 8e-11 60.0 -38_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4242501 4242530 8e-11 60.0 -39_0.400000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3683151 3683180 8e-11 60.0 -41_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 789086 789115 8e-11 60.0 -42_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1714771 1714800 8e-11 60.0 -43_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4272582 4272611 8e-11 60.0 -44_0.433333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 5481023 5481052 8e-11 60.0 -45_0.500000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1271858 1271829 8e-11 60.0 -45_0.500000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1357981 1357952 8e-11 60.0 -45_0.500000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2310674 2310703 8e-11 60.0 -45_0.500000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2769319 2769348 8e-11 60.0 -45_0.500000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2991293 2991322 8e-11 60.0 -46_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1080570 1080599 8e-11 60.0 -46_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1476177 1476206 8e-11 60.0 -47_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2887871 2887900 8e-11 60.0 -49_0.433333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4152853 4152882 8e-11 60.0 -50_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3568677 3568706 8e-11 60.0 -51_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3739788 3739817 8e-11 60.0 -52_0.366667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3789407 3789436 8e-11 60.0 -54_0.400000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3161991 3162020 8e-11 60.0 -55_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4384753 4384782 8e-11 60.0 -56_0.433333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2915787 2915816 8e-11 60.0 -57_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 294604 294633 8e-11 60.0 -58_0.300000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1553483 1553512 8e-11 60.0 -59_0.300000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1351506 1351535 8e-11 60.0 -59_0.300000 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 2997487 2997458 8e-11 60.0 -61_0.366667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1987157 1987186 8e-11 60.0 -62_0.366667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1667830 1667859 8e-11 60.0 -63_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 231447 231418 8e-11 60.0 -63_0.566667 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/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3307050 3307079 8e-11 60.0 -94_0.466667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 1813009 1813038 8e-11 60.0 -96_0.533333 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 573782 573811 8e-11 60.0 -97_0.566667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 3570563 3570592 8e-11 60.0 -98_0.366667 /depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445 100.00 30 0 0 1 30 4545136 4545165 8e-11 60.0 +0_0.666667 PHIX174 100.00 30 0 0 1 30 1 30 1e-13 60.0 +1_0.600000 PHIX174 100.00 30 0 0 1 30 31 60 1e-13 60.0 +2_0.400000 PHIX174 100.00 30 0 0 1 30 76 105 1e-13 60.0 +3_0.566667 PHIX174 100.00 30 0 0 1 30 106 135 1e-13 60.0 +4_0.766667 PHIX174 100.00 30 0 0 1 30 151 180 1e-13 60.0 +5_0.533333 PHIX174 100.00 30 0 0 1 30 181 210 1e-13 60.0 +6_0.533333 PHIX174 100.00 30 0 0 1 30 226 255 1e-13 60.0 +7_0.400000 PHIX174 100.00 30 0 0 1 30 256 285 1e-13 60.0 +8_0.500000 PHIX174 100.00 30 0 0 1 30 301 330 1e-13 60.0 +9_0.400000 PHIX174 100.00 30 0 0 1 30 331 360 1e-13 60.0 +10_0.500000 PHIX174 100.00 30 0 0 1 30 376 405 1e-13 60.0 +11_0.533333 PHIX174 100.00 30 0 0 1 30 406 435 1e-13 60.0 +12_0.700000 PHIX174 100.00 30 0 0 1 30 451 480 1e-13 60.0 +13_0.533333 PHIX174 100.00 30 0 0 1 30 481 510 1e-13 60.0 +14_0.666667 PHIX174 100.00 30 0 0 1 30 526 555 1e-13 60.0 +15_0.666667 PHIX174 100.00 30 0 0 1 30 556 585 1e-13 60.0 +16_0.566667 PHIX174 100.00 30 0 0 1 30 601 630 1e-13 60.0 +17_0.533333 PHIX174 100.00 30 0 0 1 30 631 660 1e-13 60.0 +18_0.566667 PHIX174 100.00 30 0 0 1 30 676 705 1e-13 60.0 +19_0.566667 PHIX174 100.00 30 0 0 1 30 706 735 1e-13 60.0 diff -r e2420f742a0a -r 7698e2ecca3e tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Tue Nov 10 12:35:00 2009 -0500 +++ b/tools/metag_tools/megablast_wrapper.py Tue Nov 10 13:06:20 2009 -0500 @@ -1,9 +1,24 @@ #! /usr/bin/python """ run megablast for metagenomics data + +usage: %prog [options] + -d, --db_build=d: The database to use + -i, --input=i: Input FASTQ candidate file + -w, --word_size=w: Size of best perfect match + -c, --identity_cutoff=c: Report hits at or above this identity + -e, --eval_cutoff=e: Expectation value cutoff + -f, --filter_query=f: Filter out low complexity regions + -x, --index_dir=x: Data index directory + -o, --output=o: Output file + +usage: %prog db_build input_file word_size identity_cutoff eval_cutoff filter_query index_dir output_file """
import sys, os, tempfile +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse
assert sys.version_info[:2] >= ( 2, 4 )
@@ -12,16 +27,18 @@ sys.exit()
def __main__(): + #Parse Command Line + options, args = doc_optparse.parse( __doc__ )
- db_build = sys.argv[1] - query_filename = sys.argv[2].strip() - output_filename = sys.argv[3].strip() - mega_word_size = sys.argv[4] # -W - mega_iden_cutoff = sys.argv[5] # -p - mega_evalue_cutoff = sys.argv[6] # -e + db_build = options.db_build + query_filename = options.input.strip() + output_filename = options.output.strip() + mega_word_size = options.word_size # -W + mega_iden_cutoff = options.identity_cutoff # -p + mega_evalue_cutoff = options.eval_cutoff # -e mega_temp_output = tempfile.NamedTemporaryFile().name - mega_filter = sys.argv[7] # -F - GALAXY_DATA_INDEX_DIR = sys.argv[8] + mega_filter = options.filter_query # -F + GALAXY_DATA_INDEX_DIR = options.index_dir DB_LOC = "%s/blastdb.loc" % GALAXY_DATA_INDEX_DIR
# megablast parameters @@ -81,7 +98,7 @@ output.write( "%s\n" % new_line ) output.close()
- os.unlink( mega_temp_output ) #remove the tempfile that we just reformated the contents of + os.unlink( mega_temp_output ) #remove the tempfile that we just reformatted the contents of
if invalid_lines: print "Unable to parse %d lines. Keep the default format." % invalid_lines diff -r e2420f742a0a -r 7698e2ecca3e tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml Tue Nov 10 12:35:00 2009 -0500 +++ b/tools/metag_tools/megablast_wrapper.xml Tue Nov 10 13:06:20 2009 -0500 @@ -1,6 +1,16 @@ <tool id="megablast_wrapper" name="Megablast" version="1.0.0"> <description> compare short reads against nt and wgs databases</description> - <command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $evalue_cutoff $filter_query ${GALAXY_DATA_INDEX_DIR}</command> + <command interpreter="python"> + megablast_wrapper.py + --db_build=$source_select + --input=$input_query + --word_size=$word_size + --identity_cutoff=$iden_cutoff + --eval_cutoff=$evalue_cutoff + --filter_query=$filter_query + --index_dir=${GALAXY_DATA_INDEX_DIR} + --output=$output1 + </command> <inputs> <param name="input_query" type="data" format="fasta" label="Compare these sequences"/> <param name="source_select" type="select" display="radio" label="against target database"> @@ -29,7 +39,7 @@ <tests> <test> <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> - <param name="source_select" value="test" /> + <param name="source_select" value="phiX" /> <param name="word_size" value="28" /> <param name="iden_cutoff" value="99.0" /> <param name="evalue_cutoff" value="10.0" />