| Previous changeset 9:9dabbfd73c8a (2013-04-25) Next changeset 11:4c4a0da938ff (2013-12-05) |
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Commit message:
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback. |
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modified:
test-data/blastp_four_human_vs_rhodopsin_converted.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastx_rhodopsin_vs_four_human_converted.tabular test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular test-data/blastx_sample.xml tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml tools/ncbi_blast_plus/repository_dependencies.xml tools/ncbi_blast_plus/tool_dependencies.xml |
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added:
test-data/blastn_rhodopsin_vs_three_human.tabular test-data/tblastx_rhodopsin_vs_three_human.tabular test-data/three_human_mRNA.fasta tools/ncbi_blast_plus/README.rst |
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removed:
tools/ncbi_blast_plus/ncbi_blast_plus.txt |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/blastn_rhodopsin_vs_three_human.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.10 1050 77 6 1 1047 88 1134 0.0 1474 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 9e-133 460 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 7e-94 331 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 8e-74 265 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.98 171 10 2 2854 3023 615 784 8e-69 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.58 962 75 6 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.55 1052 121 10 1 1047 88 1134 0.0 1208 |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/blastp_four_human_vs_rhodopsin_converted.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_converted.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted.tabular Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -3,4 +3,4 @@ sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 3e-176 599 +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -3,4 +3,4 @@ sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 3e-176 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/blastx_rhodopsin_vs_four_human_converted.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,10 +1,10 @@ gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 1e-168 575 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-62 224 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-34 129 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 2e-31 120 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-30 118 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 6e-12 56.2 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 2e-180 613 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 6e-164 559 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 |
| b |
| b'@@ -1,10 +1,10 @@\n gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t662\tsp|P08100|OPSD_HUMAN\t1707\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t1e-168\t575\tsp|P08100|OPSD_HUMAN\t1481\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t2e-62\t224\tsp|P08100|OPSD_HUMAN\t570\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t5e-34\t129\tsp|P08100|OPSD_HUMAN\t324\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.43\t56\t2\t0\t2855\t3022\t177\t232\t2e-31\t120\tsp|P08100|OPSD_HUMAN\t302\t54\t56\t0\t100.00\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-30\t118\tsp|P08100|OPSD_HUMAN\t295\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.00\t25\t2\t0\t4222\t4296\t312\t336\t6e-12\t56.2\tsp|P08100|OPSD_HUMAN\t134\t23\t24\t0\t96.00\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTT\tQFRNCMLTTICCGKNPLGDDEASAT\t4301\t348\n-gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t2e-180\t613\tsp|P08100|OPSD_HUMAN\t1582\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n+gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t575\tsp|P08100|OPSD_HUMAN\t1481\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLA'..b'FFAKSAAIYNPVIYIMMNKQ\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.43\t56\t2\t0\t2855\t3022\t177\t232\t3e-33\t120\tsp|P08100|OPSD_HUMAN\t302\t54\t56\t0\t100.00\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t2e-32\t118\tsp|P08100|OPSD_HUMAN\t295\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.00\t25\t2\t0\t4222\t4296\t312\t336\t2e-12\t56.2\tsp|P08100|OPSD_HUMAN\t134\t23\t24\t0\t96.00\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTT\tQFRNCMLTTICCGKNPLGDDEASAT\t4301\t348\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t613\tsp|P08100|OPSD_HUMAN\t1582\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t641\tsp|P08100|OPSD_HUMAN\t1654\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.93\t332\t60\t0\t23\t1018\t1\t332\t6e-164\t559\tsp|P08100|OPSD_HUMAN\t1440\t272\t307\t0\t92.47\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1344\t348\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.93\t332\t60\t0\t23\t1018\t1\t332\t0.0\t559\tsp|P08100|OPSD_HUMAN\t1440\t272\t307\t0\t92.47\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1344\t348\n' |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/tblastx_rhodopsin_vs_three_human.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastx_rhodopsin_vs_three_human.tabular Mon Sep 23 06:14:13 2013 -0400 |
| b |
| b'@@ -0,0 +1,117 @@\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t97.39\t230\t6\t0\t1\t690\t88\t777\t0.0\t 559\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t94.12\t102\t6\t0\t742\t1047\t829\t1134\t0.0\t 236\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t91.22\t148\t13\t0\t1046\t603\t1133\t690\t0.0\t 308\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t94.32\t88\t5\t0\t566\t303\t653\t390\t0.0\t 207\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t96.34\t82\t3\t0\t248\t3\t335\t90\t0.0\t 182\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t83.33\t204\t34\t0\t18\t629\t105\t716\t4e-158\t 404\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t75.28\t89\t22\t0\t780\t1046\t867\t1133\t4e-158\t 161\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t81.28\t203\t38\t0\t609\t1\t696\t88\t5e-153\t 360\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t80.60\t67\t13\t0\t916\t716\t1003\t803\t5e-153\t 135\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t70.27\t37\t11\t0\t1047\t937\t1134\t1024\t5e-153\t64.2\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t100.00\t7\t0\t0\t646\t626\t733\t713\t5e-153\t24.0\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t89.23\t65\t7\t0\t460\t266\t547\t353\t4e-105\t 167\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t89.58\t48\t5\t0\t184\t41\t271\t128\t4e-105\t 104\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t77.78\t45\t10\t0\t882\t748\t969\t835\t4e-105\t93.9\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t67.86\t28\t9\t0\t1045\t962\t1132\t1049\t4e-105\t51.9\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t59.09\t22\t9\t0\t586\t521\t673\t608\t4e-105\t33.1\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t81.40\t86\t16\t0\t296\t553\t383\t640\t2e-87\t 185\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t84.38\t32\t5\t0\t11\t106\t98\t193\t2e-87\t74.8\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t71.43\t35\t10\t0\t941\t1045\t1028\t1132\t2e-87\t61.6\n+gi|57163782|ref|NM_001009242.1|\tENA|BC112106|BC112106.1\t94.44\t18\t1\t0\t794\t847\t881\t934\t2e-87\t50.1\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t83.61\t238\t39\t0\t18\t731\t64\t777\t0.0\t 507\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t82.35\t85\t15\t0\t783\t1037\t829\t1083\t0.0\t 188\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t70.96\t303\t88\t0\t925\t17\t971\t63\t2e-130\t 435\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t72.22\t18\t5\t0\t1027\t974\t1073\t1020\t2e-130\t35.0\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t55.32\t188\t84\t0\t605\t42\t651\t88\t7e-89\t 245\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t61.11\t72\t28\t0\t1037\t822\t1083\t868\t7e-89\t91.3\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t49.02\t204\t104\t0\t29\t640\t75\t686\t4e-78\t 197\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t66.04\t53\t18\t0\t860\t1018\t906\t1064\t4e-78\t85.8\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t44.44\t27\t15\t0\t689\t769\t735\t815\t4e-78\t32.2\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t47.47\t198\t104\t0\t633\t40\t679\t86\t4e-65\t 177\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t68.09\t47\t15\t0\t1017\t877\t1063\t923\t4e-65\t80.3\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t57.89\t114\t48\t0\t265\t606\t311\t652\t3e-46\t 137\n+gi|2734705|gb|U59921.1|BBU59921\tENA|BC112106|BC112106.1\t46.30\t54\t29\t0\t19\t180\t65\t226\t3e-46\t52.4\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t96.40\t111\t4\t0\t1\t333\t118\t450\t0.0\t 264\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t92.31\t65\t5\t0\t3174\t3368\t829\t1023\t0.0\t 151\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t96.43\t56\t2\t0\t2855\t3022\t616\t783\t0.0\t 141\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t93.22\t59\t4\t0\t1404\t1580\t442\t618\t0.0\t 138\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t92.00\t25\t2\t0\t4222\t4296\t1021\t1095\t0.0\t64.3\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t88.89\t9\t1\t0\t3128\t3154\t783\t809\t0.0\t22.6\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t78.38\t111\t24\t0\t333\t1\t450\t118\t7e-171\t 212\n+gi|283855845|gb|GQ290303.1|\tENA|BC112106|BC112106.1\t88.75\t80\t9\t0\t3367\t3128\t1022\t783\t7e-171\t 1'..b'06|BC112106.1\t77.43\t319\t72\t0\t3\t959\t120\t1076\t4e-174\t 593\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t79.07\t129\t27\t0\t558\t172\t675\t289\t2e-133\t 248\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t76.83\t82\t19\t0\t963\t718\t1080\t835\t2e-133\t 159\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t84.09\t44\t7\t0\t133\t2\t250\t119\t2e-133\t97.3\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t73.08\t78\t21\t0\t433\t200\t550\t317\t6e-102\t 145\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t70.15\t67\t20\t0\t799\t599\t916\t716\t6e-102\t 106\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t80.49\t41\t8\t0\t123\t1\t240\t118\t6e-102\t84.5\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t77.78\t27\t6\t0\t553\t473\t670\t590\t6e-102\t51.9\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t71.43\t14\t4\t0\t889\t848\t1006\t965\t6e-102\t32.7\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t81.82\t11\t2\t0\t958\t926\t1075\t1043\t6e-102\t28.6\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t84.85\t33\t5\t0\t239\t337\t356\t454\t4e-48\t72.5\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t86.67\t30\t4\t0\t2\t91\t119\t208\t4e-48\t71.2\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t81.40\t43\t8\t0\t404\t532\t521\t649\t4e-48\t47.3\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t88.89\t18\t2\t0\t764\t817\t881\t934\t4e-48\t44.6\n+gi|283855822|gb|GQ290312.1|\tENA|BC112106|BC112106.1\t87.50\t8\t1\t0\t935\t958\t1052\t1075\t4e-48\t21.7\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t93.91\t230\t14\t0\t1\t690\t88\t777\t0.0\t 538\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t91.18\t102\t9\t0\t742\t1047\t829\t1134\t0.0\t 233\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t88.83\t188\t21\t0\t566\t3\t653\t90\t0.0\t 394\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t84.06\t138\t22\t0\t1046\t633\t1133\t720\t0.0\t 260\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t67.11\t228\t75\t0\t684\t1\t771\t88\t7e-132\t 333\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t67.27\t110\t36\t0\t1045\t716\t1132\t803\t7e-132\t 141\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t70.20\t151\t45\t0\t3\t455\t90\t542\t1e-128\t 236\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t64.04\t89\t32\t0\t780\t1046\t867\t1133\t1e-128\t 136\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t66.22\t74\t25\t0\t510\t731\t597\t818\t1e-128\t 111\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t66.04\t106\t36\t0\t242\t559\t329\t646\t2e-58\t 161\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t85.71\t21\t3\t0\t92\t154\t179\t241\t2e-58\t53.8\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t73.68\t19\t5\t0\t791\t847\t878\t934\t2e-58\t39.1\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t61.29\t62\t24\t0\t424\t239\t511\t326\t4e-55\t81.3\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t74.36\t39\t10\t0\t133\t17\t220\t104\t4e-55\t69.8\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t65.71\t35\t12\t0\t882\t778\t969\t865\t4e-55\t56.3\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t58.14\t43\t18\t0\t649\t521\t736\t608\t4e-55\t50.6\n+gi|18148870|dbj|AB062417.1|\tENA|BC112106|BC112106.1\t66.67\t12\t4\t0\t972\t937\t1059\t1024\t4e-55\t23.9\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t82.13\t235\t42\t0\t11\t715\t76\t780\t0.0\t 498\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t78.31\t83\t18\t0\t770\t1018\t835\t1083\t0.0\t 177\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t72.29\t332\t92\t0\t1017\t22\t1082\t87\t1e-150\t 516\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t48.30\t147\t76\t0\t712\t272\t777\t337\t2e-98\t 169\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t54.17\t72\t33\t0\t1030\t815\t1095\t880\t2e-98\t 103\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t47.83\t69\t36\t0\t220\t14\t285\t79\t2e-98\t83.5\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t72.00\t25\t7\t0\t782\t708\t847\t773\t2e-98\t45.1\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t56.00\t75\t33\t0\t532\t756\t597\t821\t5e-65\t87.7\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t39.42\t104\t63\t0\t19\t330\t84\t395\t5e-65\t86.8\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t56.90\t58\t25\t0\t829\t1002\t894\t1067\t5e-65\t81.3\n+gi|12583664|dbj|AB043817.1|\tENA|BC112106|BC112106.1\t50.00\t30\t15\t0\t388\t477\t453\t542\t5e-65\t33.6\n' |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 test-data/three_human_mRNA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta Mon Sep 23 06:14:13 2013 -0400 |
| b |
| b'@@ -0,0 +1,183 @@\n+>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\n+GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG\n+CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC\n+GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC\n+CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA\n+TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC\n+TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT\n+TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA\n+CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA\n+TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA\n+CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC\n+TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA\n+TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT\n+TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG\n+GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA\n+TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA\n+ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG\n+TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA\n+CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC\n+AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT\n+CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA\n+ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC\n+CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA\n+TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG\n+CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC\n+TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC\n+CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA\n+GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT\n+ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA\n+GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT\n+CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT\n+GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA\n+TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA\n+CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA\n+AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG\n+GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG\n+AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT\n+TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT\n+TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT\n+TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG\n+CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA\n+CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT\n+TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC\n+TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT\n+GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT\n+AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT\n+TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT\n+GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT\n+TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA\n+GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA\n+TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA\n+TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT\n+AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT\n+TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT\n+ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT\n+GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA\n+GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT\n+GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT\n+TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT\n+TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT\n+AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG\n+AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC\n+TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT\n+CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGT'..b'AAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT\n+CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG\n+ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT\n+TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC\n+CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG\n+CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG\n+CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC\n+TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC\n+AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT\n+GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG\n+AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG\n+GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT\n+GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC\n+TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT\n+GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT\n+ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT\n+TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC\n+GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC\n+GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG\n+GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG\n+GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC\n+AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC\n+CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA\n+GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG\n+TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA\n+ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC\n+AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC\n+ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA\n+CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT\n+CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA\n+TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG\n+CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT\n+GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC\n+TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC\n+TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG\n+ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT\n+CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT\n+ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC\n+TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA\n+GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT\n+TTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT\n+CTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAA\n+AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA\n+>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\n+CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC\n+CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG\n+CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG\n+GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC\n+TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT\n+CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC\n+ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT\n+TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG\n+GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC\n+CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA\n+CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC\n+TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC\n+TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG\n+GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC\n+CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG\n+GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA\n+GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG\n+CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT\n+GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG\n+CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA\n+GCCATCCCACCAG\n' |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/README.rst Mon Sep 23 06:14:13 2013 -0400 |
| b |
| b'@@ -0,0 +1,168 @@\n+Galaxy wrappers for NCBI BLAST+ suite\n+=====================================\n+\n+These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute\n+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.\n+See the licence text below.\n+\n+Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+),\n+and does not work with the NCBI \'legacy\' BLAST suite (e.g. blastall).\n+\n+Note that these wrappers (and the associated datatypes) were originally\n+distributed as part of the main Galaxy repository, but as of August 2012\n+moved to the Galaxy Tool Shed as \'ncbi_blast_plus\' (and \'blast_datatypes\').\n+My thanks to Dannon Baker from the Galaxy development team for his assistance\n+with this.\n+\n+These wrappers are available from the Galaxy Tool Shed at:\n+http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus\n+\n+\n+Automated Installation\n+======================\n+\n+Galaxy should be able to automatically install the dependencies, i.e. the\n+\'blast_datatypes\' repository which defines the BLAST XML file format\n+(\'blastxml\') and protein and nucleotide BLAST databases (\'blastdbp\' and\n+\'blastdbn\').\n+\n+You must tell Galaxy about any system level BLAST databases using configuration\n+files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein\n+databases like NR), and blastdb_d.loc (protein domain databases like CDD or\n+SMART) which are located in the tool-data/ folder. Sample files are included\n+which explain the tab-based format to use.\n+\n+You can download the NCBI provided databases as tar-balls from here:\n+\n+* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR)\n+* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD)\n+\n+\n+Manual Installation\n+===================\n+\n+For those not using Galaxy\'s automated installation from the Tool Shed, put\n+the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML\n+files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample\n+in order to run the unit tests). For example, use::\n+\n+ <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">\n+ <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" />\n+ <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />\n+ </section>\n+\n+You will also need to install \'blast_datatypes\' from the Tool Shed. This\n+defines the BLAST XML file format (\'blastxml\') and protein and nucleotide\n+BLAST databases composite file formats (\'blastdbp\' and \'blastdbn\').\n+\n+As described above for an automated installation, you must also tell Galaxy\n+about any system level BLAST databases using the tool-data/blastdb*.loc files.\n+\n+You must install the NCBI BLAST+ standalone tools somewhere on the system\n+path. Currently the unit tests are written using "BLAST 2.2.26+".\n+\n+Run the functional tests (adjusting the section identifier to match your\n+tool_conf.xml.sample file)::\n+\n+ ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools\n+\n+\n+History\n+=======\n+\n+======= ======================================================================\n+Version Changes\n+------- ----------------------------------------------------------------------\n+v0.0.11 - Final revision as part of the Galaxy main repository, and the\n+ first release via the Tool Shed\n+v0.0.12 - Implements genetic code option for translation searches.\n+ - Changes <parallelism> to 1000 sequences at a time (t'..b'clude warning that BLAST+ with subject FASTA gives pairwise\n+ e-values\n+v0.0.13 - Use the new error handling options in Galaxy (the previously\n+ bundled hide_stderr.py script is no longer needed).\n+v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases\n+ in the history (using work from Edward Kirton), requires v0.0.14\n+ of the \'blast_datatypes\' repository from the Tool Shed.\n+v0.0.15 - Stronger warning in help text against searching against subject\n+ FASTA files (better looking e-values than you might be expecting).\n+v0.0.16 - Added repository_dependencies.xml for automates installation of the\n+ \'blast_datatypes\' repository from the Tool Shed.\n+v0.0.17 - The BLAST+ search tools now default to extended tabular output\n+ (all too often our users where having to re-run searches just to\n+ get one of the missing columns like query or subject length)\n+v0.0.18 - Defensive quoting of filenames in case of spaces (where possible,\n+ BLAST+ handling of some mult-file arguments is problematic).\n+v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc\n+ for the domain databases they use (e.g. CDD, PFAM or SMART).\n+ - Correct case of exception regular expression (for error handling\n+ fall-back in case the return code is not set properly).\n+ - Clearer naming of output files.\n+v0.0.20 - Added unit tests for BLASTN and TBLASTX.\n+ - Added percentage identity option to BLASTN.\n+ - Fallback on ElementTree if cElementTree missing in XML to tabular.\n+ - Link to Tool Shed added to help text and this documentation.\n+ - Tweak dependency on blast_datatypes to also work on Test Tool Shed.\n+ - Dependency on new package_blast_plus_2_2_26 in Tool Shed.\n+ - Adopted standard MIT License.\n+ - Development moved to GitHub, https://github.com/peterjc/galaxy_blast\n+ - Updated citation information (Cock et al. 2013).\n+======= ======================================================================\n+\n+\n+Bug Reports\n+===========\n+\n+You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask\n+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev\n+\n+\n+Developers\n+==========\n+\n+This script and related tools were originally developed on the \'tools\' branch\n+of the following Mercurial repository:\n+https://bitbucket.org/peterjc/galaxy-central/\n+\n+As of July 2013, development is continuing on a dedicated GitHub repository:\n+https://github.com/peterjc/galaxy_blast\n+\n+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use\n+the following command from the GitHub repository root folder::\n+\n+ $ ./ncbi_blast_plus/make_ncbi_blast_plus.sh\n+\n+This simplifies ensuring a consistent set of files is bundled each time,\n+including all the relevant test files.\n+\n+\n+Licence (MIT)\n+=============\n+\n+Permission is hereby granted, free of charge, to any person obtaining a copy\n+of this software and associated documentation files (the "Software"), to deal\n+in the Software without restriction, including without limitation the rights\n+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n+copies of the Software, and to permit persons to whom the Software is\n+furnished to do so, subject to the following conditions:\n+\n+The above copyright notice and this permission notice shall be included in\n+all copies or substantial portions of the Software.\n+\n+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n+THE SOFTWARE.\n' |
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| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/blastxml_to_tabular.py --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Sep 23 06:14:13 2013 -0400 |
| [ |
| @@ -1,5 +1,5 @@ #!/usr/bin/env python -"""Convert a BLAST XML file to 12 column tabular output +"""Convert a BLAST XML file to tabular output. Takes three command line options, input BLAST XML filename, output tabular BLAST filename, output format (std for standard 12 columns, or ext for the @@ -62,8 +62,15 @@ import sys import re +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.12" + sys.exit(0) + if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as ElementTree + try: + from xml.etree import cElementTree as ElementTree + except ImportError: + from xml.etree import ElementTree as ElementTree else: from galaxy import eggs import pkg_resources; pkg_resources.require( "elementtree" ) |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,5 +1,6 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.10"> +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.11"> <description>Convert BLAST XML output to tabular</description> + <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> <command interpreter="python"> blastxml_to_tabular.py $blastxml_file $tabular_file $out_format </command> @@ -128,5 +129,17 @@ low complexity (columns 21 and 22), and thus also calculated figures like the percentage identity (column 3). +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_blast_plus.txt --- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Apr 25 09:38:37 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,144 +0,0 @@ -Galaxy wrappers for NCBI BLAST+ suite -===================================== - -These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), -and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). - -Note that these wrappers (and the associated datatypes) were originally -distributed as part of the main Galaxy repository, but as of August 2012 -moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). -My thanks to Dannon Baker from the Galaxy development team for his assistance -with this. - - -Automated Installation -====================== - -Galaxy should be able to automatically install the dependencies, i.e. the -'blast_datatypes' repository which defines the BLAST XML file format -('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) - - -Manual Installation -=================== - -For those not using Galaxy's automated installation from the Tool Shed, put -the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML -files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample -in order to run the unit tests). For example, use: - - <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> - <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> - <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> - </section> - -You will also need to install 'blast_datatypes' from the Tool Shed. This -defines the BLAST XML file format ('blastxml') and protein and nucleotide -BLAST databases composite file formats ('blastdbp' and 'blastdbn'). - -As described above for an automated installation, you must also tell Galaxy -about any system level BLAST databases using the tool-data/blastdb*.loc files. - -You must install the NCBI BLAST+ standalone tools somewhere on the system -path. Currently the unit tests are written using "BLAST 2.2.26+". - -Run the functional tests (adjusting the section identifier to match your -tool_conf.xml.sample file): - -./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools - - -History -======= - -v0.0.11 - Final revision as part of the Galaxy main repository, and the - first release via the Tool Shed -v0.0.12 - Implements genetic code option for translation searches. - - Changes <parallelism> to 1000 sequences at a time (to cope with - very large sets of queries where BLAST+ can become memory hungry) - - Include warning that BLAST+ with subject FASTA gives pairwise - e-values -v0.0.13 - Use the new error handling options in Galaxy (the previously - bundled hide_stderr.py script is no longer needed). -v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases - in the history (using work from Edward Kirton), requires v0.0.14 - of the 'blast_datatypes' repository from the Tool Shed. -v0.0.15 - Stronger warning in help text against searching against subject - FASTA files (better looking e-values than you might be expecting). -v0.0.16 - Added repository_dependencies.xml for automates installation of the - 'blast_datatypes' repository from the Tool Shed. -v0.0.17 - The BLAST+ search tools now default to extended tabular output - (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). -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 - fall-back in case the return code is not set properly). - - Clearer naming of output files. - - -Developers -========== - -This script and related tools are being developed on the 'tools' branch of the -following Mercurial repository: -https://bitbucket.org/peterjc/galaxy-central/ - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use -the following command from the Galaxy root folder: - -$ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh - -This simplifies ensuring a consistent set of files is bundled each time, -including all the relevant test files. - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. - -NOTE: This is the licence for the Galaxy Wrapper only. NCBI BLAST+ and -associated data files are available and licenced separately. |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> <description>Show BLAST database information from blastdbcmd</description> <requirements> <requirement type="binary">blastdbcmd</requirement> @@ -57,9 +57,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.5"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6"> <description>Extract sequence(s) from BLAST database</description> <requirements> <requirement type="binary">blastdbcmd</requirement> @@ -129,9 +129,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.19"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.20"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -37,6 +37,9 @@ #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): +-perc_identity $adv_opts.identity_cutoff +#end if #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if @@ -126,6 +129,7 @@ <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> <validator type="in_range" min="0" /> </param> + <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> <!-- I'd like word_size to be optional, with minimum 4 for blastn --> <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> <validator type="in_range" min="0" /> @@ -148,6 +152,18 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-40" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> + </test> + </tests> <help> .. class:: warningmark @@ -233,7 +249,20 @@ **References** -Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.19"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.20"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -298,9 +298,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -286,7 +286,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| b'@@ -1,5 +1,5 @@\n-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.4">\n- <description>Make BLAST database</description>\n+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5">\n+ <description>Make BLAST database</description>\n <requirements>\n <requirement type="binary">makeblastdb</requirement>\n <requirement type="package" version="2.2.26+">blast+</requirement>\n@@ -14,7 +14,8 @@\n ## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy:\n -in "\n #for $i in $in\n-${i.file} #end for\n+${i.file}\n+#end for\n "\n #if $title:\n -title "$title"\n@@ -38,71 +39,73 @@\n ## #else if $tax.select == \'map\':\n ## -taxid_map $tax.map\n ## #end if\n-</command>\n-<stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- <!-- In case the return code has not been set propery check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n-</stdio>\n-<inputs>\n- <param name="dbtype" type="select" display="radio" label="Molecule type of input">\n- <option value="prot">protein</option>\n- <option value="nucl">nucleotide</option>\n- </param>\n- <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)\n- <repeat name="in" title="Blast or Fasta Database" min="1">\n- <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="Blast or Fasta database" />\n- </repeat>\n- -->\n- <repeat name="in" title="FASTA file" min="1">\n- <param name="file" type="data" format="fasta" />\n- </repeat>\n- <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />\n- <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe \'|\' symbols" />\n- <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />\n+ </command>\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ <inputs>\n+ <param name="dbtype" type="select" display="radio" label="Molecule type of input">\n+ <option value="prot">protein</option>\n+ <option value="nucl">nucleotide</option>\n+ </param>\n+ <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)\n+ <repeat name="in" title="BLAST or FASTA Database" min="1">\n+ <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="BLAST or FASTA database" />\n+ </repeat>\n+ -->\n+ <repeat name="in" title="FASTA file" min="1">\n+ <param name="file" type="data" format="fasta" />\n+ </repeat>\n+ <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />\n+ <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe \'|\' symbols" />\n+ <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />\n \n- <!-- SEQUENCE MASKING OPTI'..b'itle="Provide one or more files containing masking data">\n+ <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" />\n+ </repeat>\n+ <repeat name="gi_mask" title="Create GI indexed masking data">\n+ <param name="file" type="data" format="asnb" label="Masking data output file" />\n+ </repeat>\n+ -->\n \n- <!-- TAXONOMY OPTIONS -->\n- <!-- TODO\n- <conditional name="tax">\n- <param name="select" type="select" label="Taxonomy options">\n- <option value="">Do not assign sequences to Taxonomy IDs</option>\n- <option value="id">Assign all sequences to one Taxonomy ID</option>\n- <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option>\n- </param>\n- <when value="">\n- </when>\n- <when value="id">\n- <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" />\n- </when>\n- <when value="map">\n- <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />\n- </when>\n- </conditional>\n- -->\n-</inputs>\n-<outputs>\n- <!-- If we only accepted one FASTA file, we could use its human name here... -->\n- <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}">\n- <change_format>\n- <when input="dbtype" value="nucl" format="blastdbn"/>\n- <when input="dbtype" value="prot" format="blastdbp"/>\n- </change_format>\n- </data>\n-</outputs>\n-<help>\n+ <!-- TAXONOMY OPTIONS -->\n+ <!-- TODO\n+ <conditional name="tax">\n+ <param name="select" type="select" label="Taxonomy options">\n+ <option value="">Do not assign sequences to Taxonomy IDs</option>\n+ <option value="id">Assign all sequences to one Taxonomy ID</option>\n+ <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option>\n+ </param>\n+ <when value="">\n+ </when>\n+ <when value="id">\n+ <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" />\n+ </when>\n+ <when value="map">\n+ <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />\n+ </when>\n+ </conditional>\n+ -->\n+ </inputs>\n+ <outputs>\n+ <!-- If we only accepted one FASTA file, we could use its human name here... -->\n+ <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}">\n+ <change_format>\n+ <when input="dbtype" value="nucl" format="blastdbn" />\n+ <when input="dbtype" value="prot" format="blastdbp" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ </tests>\n+ <help>\n **What it does**\n \n Make BLAST database from one or more FASTA files and/or BLAST databases.\n@@ -118,5 +121,23 @@\n **Documentation**\n \n http://www.ncbi.nlm.nih.gov/books/NBK1763/\n-</help>\n+\n+**References**\n+\n+If you use this Galaxy tool in work leading to a scientific publication please\n+cite the following papers:\n+\n+Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n+Galaxy tools and workflows for sequence analysis with applications\n+in molecular plant pathology. PeerJ 1:e167\n+http://dx.doi.org/10.7717/peerj.167\n+\n+Christiam Camacho et al. (2009).\n+BLAST+: architecture and applications.\n+BMC Bioinformatics. 15;10:421.\n+http://dx.doi.org/10.1186/1471-2105-10-421\n+\n+This wrapper is available to install into other Galaxy Instances via the Galaxy\n+Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus\n+ </help>\n </tool>\n' |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.3"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.4"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> @@ -230,7 +230,20 @@ **References** -Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.3"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.4"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> @@ -19,13 +19,13 @@ #end if -evalue $evalue_cutoff -out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected +## Set the extended list here so if/when we add things, saved workflows are not affected #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: -outfmt $out_format #end if -##Seems rpstblastn does not currently support multiple threads :( +## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. ##-num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query @@ -231,7 +231,20 @@ **References** -Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.19"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.20"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -332,7 +332,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.19"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.20"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -190,6 +190,18 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-40" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="tblastx_rhodopsin_vs_three_human.tabular" ftype="tabular" /> + </test> + </tests> <help> .. class:: warningmark @@ -274,7 +286,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/repository_dependencies.xml --- a/tools/ncbi_blast_plus/repository_dependencies.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,5 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> -<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases --> -<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> + <repository changeset_revision="b3a3ba0c1d47" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories> |
| b |
| diff -r 9dabbfd73c8a -r 70e7dcbf6573 tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Mon Sep 23 06:14:13 2013 -0400 |
| b |
| @@ -1,21 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.26+"> - <install version="1.0"> - <actions> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> - <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -These links provide information for building the NCBI Blast+ package in most environments. - -System requirements -http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download - </readme> + <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> - |