Mercurial > repos > devteam > ncbi_blast_plus
changeset 8:1f546099212f draft
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
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--- a/test-data/blastp_four_human_vs_rhodopsin.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -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
--- a/test-data/blastp_four_human_vs_rhodopsin.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.2.25+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID> @@ -375,7 +375,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>701.049065538619</Hsp_bit-score> + <Hsp_bit-score>701.049</Hsp_bit-score> <Hsp_score>1808</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -422,7 +422,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>619.001555868222</Hsp_bit-score> + <Hsp_bit-score>619.002</Hsp_bit-score> <Hsp_score>1595</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -469,7 +469,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>653.284318124867</Hsp_bit-score> + <Hsp_bit-score>653.284</Hsp_bit-score> <Hsp_score>1684</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>11</Hsp_query-from> @@ -516,7 +516,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>631.327942297578</Hsp_bit-score> + <Hsp_bit-score>631.328</Hsp_bit-score> <Hsp_score>1627</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>11</Hsp_query-from> @@ -563,7 +563,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>673.314696072569</Hsp_bit-score> + <Hsp_bit-score>673.315</Hsp_bit-score> <Hsp_score>1736</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -610,9 +610,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>599.356377496438</Hsp_bit-score> + <Hsp_bit-score>599.356</Hsp_bit-score> <Hsp_score>1544</Hsp_score> - <Hsp_evalue>3.49521227372659e-176</Hsp_evalue> + <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>341</Hsp_query-to> <Hsp_hit-from>1</Hsp_hit-from> @@ -643,4 +643,4 @@ </Iteration_stat> </Iteration> </BlastOutput_iterations> -</BlastOutput> +</BlastOutput> \ No newline at end of file
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -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
--- a/test-data/blastp_rhodopsin_vs_four_human.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastp_rhodopsin_vs_four_human.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -1,6 +1,6 @@ gi|57163783|ref|NP_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 348 1 348 0.0 679 -gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 6e-178 605 +gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 0.0 605 gi|283855846|gb|ADB45242.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630 gi|283855823|gb|ADB45229.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630 gi|223523|prf||0811197A sp|P08100|OPSD_HUMAN 93.10 348 23 1 1 347 1 348 0.0 651 -gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 2e-172 587 +gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 0.0 587
--- a/test-data/blastx_rhodopsin_vs_four_human.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -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
--- a/test-data/blastx_rhodopsin_vs_four_human.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> - <BlastOutput_version>BLASTX 2.2.25+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.2.26+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -90,7 +90,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>662.143908370966</Hsp_bit-score> + <Hsp_bit-score>662.144</Hsp_bit-score> <Hsp_score>1707</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -194,9 +194,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>575.088804213644</Hsp_bit-score> + <Hsp_bit-score>575.089</Hsp_bit-score> <Hsp_score>1481</Hsp_score> - <Hsp_evalue>1.31349806431671e-168</Hsp_evalue> + <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>42</Hsp_query-from> <Hsp_query-to>1037</Hsp_query-to> <Hsp_hit-from>1</Hsp_hit-from> @@ -298,9 +298,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>224.171990552935</Hsp_bit-score> + <Hsp_bit-score>224.172</Hsp_bit-score> <Hsp_score>570</Hsp_score> - <Hsp_evalue>1.57574304751949e-62</Hsp_evalue> + <Hsp_evalue>1.84906e-68</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>333</Hsp_query-to> <Hsp_hit-from>11</Hsp_hit-from> @@ -317,9 +317,9 @@ </Hsp> <Hsp> <Hsp_num>2</Hsp_num> - <Hsp_bit-score>129.412894877266</Hsp_bit-score> + <Hsp_bit-score>129.413</Hsp_bit-score> <Hsp_score>324</Hsp_score> - <Hsp_evalue>5.28220874623366e-34</Hsp_evalue> + <Hsp_evalue>4.62305e-36</Hsp_evalue> <Hsp_query-from>3174</Hsp_query-from> <Hsp_query-to>3368</Hsp_query-to> <Hsp_hit-from>248</Hsp_hit-from> @@ -336,9 +336,9 @@ </Hsp> <Hsp> <Hsp_num>3</Hsp_num> - <Hsp_bit-score>120.938504207085</Hsp_bit-score> + <Hsp_bit-score>120.939</Hsp_bit-score> <Hsp_score>302</Hsp_score> - <Hsp_evalue>1.87871691987854e-31</Hsp_evalue> + <Hsp_evalue>2.85192e-33</Hsp_evalue> <Hsp_query-from>2855</Hsp_query-from> <Hsp_query-to>3022</Hsp_query-to> <Hsp_hit-from>177</Hsp_hit-from> @@ -355,9 +355,9 @@ </Hsp> <Hsp> <Hsp_num>4</Hsp_num> - <Hsp_bit-score>118.242107175663</Hsp_bit-score> + <Hsp_bit-score>118.242</Hsp_bit-score> <Hsp_score>295</Hsp_score> - <Hsp_evalue>1.21774886471054e-30</Hsp_evalue> + <Hsp_evalue>2.16231e-32</Hsp_evalue> <Hsp_query-from>1404</Hsp_query-from> <Hsp_query-to>1580</Hsp_query-to> <Hsp_hit-from>119</Hsp_hit-from> @@ -374,9 +374,9 @@ </Hsp> <Hsp> <Hsp_num>5</Hsp_num> - <Hsp_bit-score>56.2249754529693</Hsp_bit-score> + <Hsp_bit-score>56.225</Hsp_bit-score> <Hsp_score>134</Hsp_score> - <Hsp_evalue>5.68296036241677e-12</Hsp_evalue> + <Hsp_evalue>2.05678e-12</Hsp_evalue> <Hsp_query-from>4222</Hsp_query-from> <Hsp_query-to>4296</Hsp_query-to> <Hsp_hit-from>312</Hsp_hit-from> @@ -478,9 +478,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>613.993961381297</Hsp_bit-score> + <Hsp_bit-score>613.994</Hsp_bit-score> <Hsp_score>1582</Hsp_score> - <Hsp_evalue>1.57028732393616e-180</Hsp_evalue> + <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>978</Hsp_query-to> <Hsp_hit-from>11</Hsp_hit-from> @@ -582,7 +582,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>641.728330847346</Hsp_bit-score> + <Hsp_bit-score>641.728</Hsp_bit-score> <Hsp_score>1654</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -686,9 +686,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>559.295621601033</Hsp_bit-score> + <Hsp_bit-score>559.296</Hsp_bit-score> <Hsp_score>1440</Hsp_score> - <Hsp_evalue>6.32632556748138e-164</Hsp_evalue> + <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>23</Hsp_query-from> <Hsp_query-to>1018</Hsp_query-to> <Hsp_hit-from>1</Hsp_hit-from> @@ -719,4 +719,4 @@ </Iteration_stat> </Iteration> </BlastOutput_iterations> -</BlastOutput> +</BlastOutput> \ No newline at end of file
--- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -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 sp|P08100|OPSD_HUMAN 1707 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 1e-168 575 sp|P08100|OPSD_HUMAN 1481 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-62 224 sp|P08100|OPSD_HUMAN 570 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-34 129 sp|P08100|OPSD_HUMAN 324 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 2e-31 120 sp|P08100|OPSD_HUMAN 302 54 56 0 100.00 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-30 118 sp|P08100|OPSD_HUMAN 295 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 6e-12 56.2 sp|P08100|OPSD_HUMAN 134 23 24 0 96.00 1 0 QFRNCMLTTLCCGKNPLGDDEASTT QFRNCMLTTICCGKNPLGDDEASAT 4301 348 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 2e-180 613 sp|P08100|OPSD_HUMAN 1582 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 sp|P08100|OPSD_HUMAN 1481 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 sp|P08100|OPSD_HUMAN 570 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 sp|P08100|OPSD_HUMAN 324 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 sp|P08100|OPSD_HUMAN 302 54 56 0 100.00 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 sp|P08100|OPSD_HUMAN 295 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 sp|P08100|OPSD_HUMAN 134 23 24 0 96.00 1 0 QFRNCMLTTLCCGKNPLGDDEASTT QFRNCMLTTICCGKNPLGDDEASAT 4301 348 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 sp|P08100|OPSD_HUMAN 1582 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 sp|P08100|OPSD_HUMAN 1654 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 6e-164 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348
--- a/test-data/tblastn_four_human_vs_rhodopsin.html Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Tue Feb 19 12:49:43 2013 -0500 @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.2.25+</b> +<b>TBLASTN 2.2.26+</b> <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 @@ -563,7 +563,7 @@ <script src="blastResult.js"></script> Score = 151 bits (342), Expect(2) = 1e-72, Method: Compositional matrix adjust. - Identities = 69/74 (94%), Positives = 73/74 (99%), Gaps = 0/74 (0%) + Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%) Frame = +3 Query 239 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA 298 @@ -584,8 +584,8 @@ Sbjct 2855 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 3031 - Score = 229 bits (523), Expect = 1e-64, Method: Compositional matrix adjust. - Identities = 107/111 (97%), Positives = 109/111 (99%), Gaps = 0/111 (0%) + Score = 229 bits (523), Expect = 9e-67, Method: Compositional matrix adjust. + Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%) Frame = +1 Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70 @@ -598,7 +598,7 @@ Score = 122 bits (276), Expect = 1e-32, Method: Compositional matrix adjust. - Identities = 55/59 (94%), Positives = 56/59 (95%), Gaps = 0/59 (0%) + Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%) Frame = +3 Query 119 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 177 @@ -606,8 +606,8 @@ Sbjct 1404 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 1580 - Score = 57.7 bits (125), Expect = 6e-13, Method: Compositional matrix adjust. - Identities = 23/26 (89%), Positives = 24/26 (93%), Gaps = 0/26 (0%) + Score = 57.7 bits (125), Expect = 2e-12, Method: Compositional matrix adjust. + Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%) Frame = +1 Query 312 QFRNCMLTTICCGKNPLGDDEASATV 337 @@ -637,7 +637,7 @@ <script src="blastResult.js"></script> Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust. - Identities = 310/326 (96%), Positives = 322/326 (99%), Gaps = 0/326 (0%) + Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%) Frame = +1 Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70 @@ -687,7 +687,7 @@ <script src="blastResult.js"></script> Score = 711 bits (1640), Expect = 0.0, Method: Compositional matrix adjust. - Identities = 325/348 (94%), Positives = 337/348 (97%), Gaps = 0/348 (0%) + Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%) Frame = +1 Query 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60 @@ -737,7 +737,7 @@ <script src="blastResult.js"></script> Score = 626 bits (1444), Expect = 0.0, Method: Compositional matrix adjust. - Identities = 281/342 (83%), Positives = 311/342 (91%), Gaps = 1/342 (0%) + Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%) Frame = +2 Query 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -2,9 +2,9 @@ sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.2.26+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -375,7 +375,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>732.392902459534</Hsp_bit-score> + <Hsp_bit-score>732.393</Hsp_bit-score> <Hsp_score>1689</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -422,7 +422,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>646.119739014374</Hsp_bit-score> + <Hsp_bit-score>646.12</Hsp_bit-score> <Hsp_score>1489</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -469,9 +469,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>151.343146656381</Hsp_bit-score> + <Hsp_bit-score>151.343</Hsp_bit-score> <Hsp_score>342</Hsp_score> - <Hsp_evalue>1.39566684546685e-72</Hsp_evalue> + <Hsp_evalue>1.39567e-72</Hsp_evalue> <Hsp_query-from>239</Hsp_query-from> <Hsp_query-to>312</Hsp_query-to> <Hsp_hit-from>3147</Hsp_hit-from> @@ -488,9 +488,9 @@ </Hsp> <Hsp> <Hsp_num>2</Hsp_num> - <Hsp_bit-score>126.323929257285</Hsp_bit-score> + <Hsp_bit-score>126.324</Hsp_bit-score> <Hsp_score>284</Hsp_score> - <Hsp_evalue>1.39566684546685e-72</Hsp_evalue> + <Hsp_evalue>1.39567e-72</Hsp_evalue> <Hsp_query-from>177</Hsp_query-from> <Hsp_query-to>235</Hsp_query-to> <Hsp_hit-from>2855</Hsp_hit-from> @@ -507,9 +507,9 @@ </Hsp> <Hsp> <Hsp_num>3</Hsp_num> - <Hsp_bit-score>229.420359574251</Hsp_bit-score> + <Hsp_bit-score>229.42</Hsp_bit-score> <Hsp_score>523</Hsp_score> - <Hsp_evalue>9.84654801241353e-65</Hsp_evalue> + <Hsp_evalue>9.34154e-67</Hsp_evalue> <Hsp_query-from>11</Hsp_query-from> <Hsp_query-to>121</Hsp_query-to> <Hsp_hit-from>1</Hsp_hit-from> @@ -526,9 +526,9 @@ </Hsp> <Hsp> <Hsp_num>4</Hsp_num> - <Hsp_bit-score>122.873002719478</Hsp_bit-score> + <Hsp_bit-score>122.873</Hsp_bit-score> <Hsp_score>276</Hsp_score> - <Hsp_evalue>1.40732096096596e-32</Hsp_evalue> + <Hsp_evalue>1.03783e-32</Hsp_evalue> <Hsp_query-from>119</Hsp_query-from> <Hsp_query-to>177</Hsp_query-to> <Hsp_hit-from>1404</Hsp_hit-from> @@ -545,9 +545,9 @@ </Hsp> <Hsp> <Hsp_num>5</Hsp_num> - <Hsp_bit-score>57.7367643183824</Hsp_bit-score> + <Hsp_bit-score>57.7368</Hsp_bit-score> <Hsp_score>125</Hsp_score> - <Hsp_evalue>5.60065526485586e-13</Hsp_evalue> + <Hsp_evalue>1.50808e-12</Hsp_evalue> <Hsp_query-from>312</Hsp_query-from> <Hsp_query-to>337</Hsp_query-to> <Hsp_hit-from>4222</Hsp_hit-from> @@ -592,7 +592,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>658.197981896696</Hsp_bit-score> + <Hsp_bit-score>658.198</Hsp_bit-score> <Hsp_score>1517</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>11</Hsp_query-from> @@ -639,7 +639,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>711.255977415469</Hsp_bit-score> + <Hsp_bit-score>711.256</Hsp_bit-score> <Hsp_score>1640</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -686,7 +686,7 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>626.708277239213</Hsp_bit-score> + <Hsp_bit-score>626.708</Hsp_bit-score> <Hsp_score>1444</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> @@ -719,4 +719,4 @@ </Iteration_stat> </Iteration> </BlastOutput_iterations> -</BlastOutput> +</BlastOutput> \ No newline at end of file
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Fri Feb 08 05:51:26 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Tue Feb 19 12:49:43 2013 -0500 @@ -2,9 +2,9 @@ sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 gi|283855845|gb|GQ290303.1| 284 54 57 0 96.61 0 2 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 348 4301 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 gi|283855845|gb|GQ290303.1| 276 55 56 0 94.92 0 3 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 348 4301 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301 sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047 sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344
--- a/test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular Fri Feb 08 05:51:26 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732 -sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 -sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 -sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 -sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,13 +1,18 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8"> +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.10"> <description>Convert BLAST XML output to tabular</description> <command interpreter="python"> blastxml_to_tabular.py $blastxml_file $tabular_file $out_format </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <inputs> <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> <param name="out_format" type="select" label="Output format"> - <option value="std" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="std">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> </param> </inputs> <outputs> @@ -74,7 +79,7 @@ may need both the XML and the tabular output - but running BLAST twice is slow and wasteful. -This tool takes the BLAST XML output and by default converts it into the +This tool takes the BLAST XML output and can convert it into the standard 12 column tabular equivalent: ====== ========= ============================================ @@ -99,7 +104,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 22 column tabular -BLAST output. +BLAST output. This tool now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description @@ -121,7 +126,7 @@ Beware that the XML file (and thus the conversion) and the tabular output direct from BLAST+ may differ in the presence of XXXX masking on regions low complexity (columns 21 and 22), and thus also calculated figures like -the percentage idenity (column 3). +the percentage identity (column 3). </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Tue Feb 19 12:49:43 2013 -0500 @@ -34,7 +34,20 @@ For those not using Galaxy's automated installation from the Tool Shed, put the XML and Python files under tools/ncbi_blast_plus and add the XML files -to your tool_conf.xml as normal. +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/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 @@ -45,6 +58,14 @@ databases like NR), located in the tool-data folder. Sample fils are included which explain the tab based format to use. +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 (adusting the section identifier to match your +tool_conf.xml.sample file): + +./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools + History ======= @@ -65,6 +86,9 @@ 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) Developers
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.15"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.17"> <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> @@ -91,8 +91,8 @@ </param> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> <option value="5">BLAST XML</option> <option value="0">Pairwise text</option> <option value="0 -html">Pairwise HTML</option> @@ -200,7 +200,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. +BLAST output. Galaxy now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.15"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.17"> <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> @@ -86,8 +86,8 @@ </param> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> <option value="5">BLAST XML</option> <option value="0">Pairwise text</option> <option value="0 -html">Pairwise HTML</option> @@ -265,7 +265,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. +BLAST output. Galaxy now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.15"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.17"> <description>Search protein 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> @@ -103,8 +103,8 @@ </param> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> <option value="5">BLAST XML</option> <option value="0">Pairwise text</option> <option value="0 -html">Pairwise HTML</option> @@ -253,7 +253,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. +BLAST output. Galaxy now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.15"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.17"> <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> @@ -82,8 +82,8 @@ </conditional> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> <option value="5">BLAST XML</option> <option value="0">Pairwise text</option> <option value="0 -html">Pairwise HTML</option> @@ -216,7 +216,7 @@ <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> - <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference --> + <!-- Same as above, but parse deflines - on BLAST 2.2.25+ - 2.2.27+ makes no difference --> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> @@ -299,7 +299,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. +BLAST output. Galaxy now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.15"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.17"> <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> @@ -103,8 +103,8 @@ </param> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> <option value="5">BLAST XML</option> <option value="0">Pairwise text</option> <option value="0 -html">Pairwise HTML</option> @@ -241,7 +241,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. +BLAST output. Galaxy now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description