# HG changeset patch # User peterjc # Date 1389782294 18000 # Node ID 2f7fac29bb3c62143204845cd0e344522aa6bbda # Parent 72170c3f515ae4a358c2dc1137ab0f12b3617135 Uploaded v0.1.00 preview 1, updated to wrap BLAST+ 2.2.29 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastn_rhodopsin_vs_three_human.tabular --- a/test-data/blastn_rhodopsin_vs_three_human.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,7 +1,7 @@ -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 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 92.94 170 12 0 2854 3023 615 784 8e-69 248 -gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 -gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 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 4e-132 460 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 3e-93 331 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 3e-73 265 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 170 12 0 2854 3023 615 784 3e-68 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastp_four_human_vs_rhodopsin.tabular --- a/test-data/blastp_four_human_vs_rhodopsin.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,6 +1,6 @@ -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 -sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 -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 0.0 599 +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 +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 0.0 599 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Wed Jan 15 05:38:14 2014 -0500 @@ -2,7 +2,7 @@ blastp - BLASTP 2.2.28+ + BLASTP 2.2.29+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, 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. sp|Q9BS26|ERP44_HUMAN diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastp_four_human_vs_rhodopsin_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,6 +1,6 @@ -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 N/A -sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 N/A -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 N/A -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 N/A -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 N/A -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 N/A +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 N/A +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 N/A +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 N/A +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 N/A +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 N/A +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 N/A diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastp_rhodopsin_vs_four_human.tabular --- a/test-data/blastp_rhodopsin_vs_four_human.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastp_rhodopsin_vs_four_human.tabular Wed Jan 15 05:38:14 2014 -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 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 0.0 587 +gi|57163783|ref|NP_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 348 1 348 0.0 701 +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 0.0 587 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastx_rhodopsin_vs_four_human.tabular --- a/test-data/blastx_rhodopsin_vs_four_human.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Wed Jan 15 05:38:14 2014 -0500 @@ -2,7 +2,7 @@ blastx - BLASTX 2.2.28+ + BLASTX 2.2.29+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, 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. Query_1 @@ -307,9 +307,9 @@ 1 - 220.32 - 560 - 4.29169e-67 + 220.705 + 561 + 3.21377e-67 1 333 11 @@ -345,9 +345,9 @@ 3 - 121.324 - 303 - 1.96633e-33 + 121.709 + 304 + 1.62516e-33 2855 3031 177 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastx_rhodopsin_vs_four_human_converted.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,6 +1,6 @@ gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,8 +1,8 @@ gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 sp|P08100|OPSD_HUMAN 560 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 303 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 diff -r 72170c3f515a -r 2f7fac29bb3c test-data/blastx_rhodopsin_vs_four_human_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Wed Jan 15 05:38:14 2014 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 sp|P08100|OPSD_HUMAN 560 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 303 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 N/A gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 N/A -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A diff -r 72170c3f515a -r 2f7fac29bb3c test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Tue Dec 03 10:02:17 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Wed Jan 15 05:38:14 2014 -0500 @@ -3,7 +3,7 @@ 
 
-TBLASTN 2.2.28+
+TBLASTN 2.2.29+
 
 
 Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
@@ -461,8 +461,8 @@
 
 Length=1047
 
-
- Score =  732 bits (1689),  Expect = 0.0, Method: Compositional matrix adjust.
+
+ Score =   732 bits (1689),  Expect = 0.0, Method: Compositional matrix adjust.
  Identities = 336/348 (97%), Positives = 343/348 (99%), Gaps = 0/348 (0%)
  Frame = +1
 
@@ -511,8 +511,8 @@
 
 Length=1574
 
-
- Score =  646 bits (1489),  Expect = 0.0, Method: Compositional matrix adjust.
+
+ Score =   646 bits (1489),  Expect = 0.0, Method: Compositional matrix adjust.
  Identities = 290/342 (85%), Positives = 320/342 (94%), Gaps = 1/342 (0%)
  Frame = +3
 
@@ -561,8 +561,8 @@
 
 Length=4301
 
-
- Score =  151 bits (342),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
+
+ Score =   151 bits (342),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
  Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
  Frame = +3
 
@@ -575,7 +575,7 @@
 Sbjct  3327  SIYNPVIYIMMNKQ  3368
 
 
- Score =  126 bits (284),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
+ Score =   126 bits (284),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
  Identities = 54/59 (92%), Positives = 57/59 (97%), Gaps = 0/59 (0%)
  Frame = +2
 
@@ -584,7 +584,7 @@
 Sbjct  2855  RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS  3031
 
 
- Score =  229 bits (523),  Expect = 9e-67, Method: Compositional matrix adjust.
+ 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
 
@@ -597,7 +597,7 @@
 Sbjct  181  PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG  333
 
 
- Score =  122 bits (276),  Expect = 1e-32, Method: Compositional matrix adjust.
+ Score =   122 bits (276),  Expect = 1e-32, Method: Compositional matrix adjust.
  Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
  Frame = +3
 
@@ -635,8 +635,8 @@
 
 Length=983
 
-
- Score =  658 bits (1517),  Expect = 0.0, Method: Compositional matrix adjust.
+
+ Score =   658 bits (1517),  Expect = 0.0, Method: Compositional matrix adjust.
  Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
  Frame = +1
 
@@ -685,8 +685,8 @@
 
 Length=1047
 
-
- Score =  711 bits (1640),  Expect = 0.0, Method: Compositional matrix adjust.
+
+ Score =   711 bits (1640),  Expect = 0.0, Method: Compositional matrix adjust.
  Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
  Frame = +1
 
@@ -735,8 +735,8 @@
 
 Length=1344
 
-
- Score =  626 bits (1444),  Expect = 0.0, Method: Compositional matrix adjust.
+
+ Score =   626 bits (1444),  Expect = 0.0, Method: Compositional matrix adjust.
  Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
  Frame = +2
 
diff -r 72170c3f515a -r 2f7fac29bb3c test-data/tblastn_four_human_vs_rhodopsin.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular	Tue Dec 03 10:02:17 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular	Wed Jan 15 05:38:14 2014 -0500
@@ -1,10 +1,10 @@
-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	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|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	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	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
+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
diff -r 72170c3f515a -r 2f7fac29bb3c test-data/tblastn_four_human_vs_rhodopsin.xml
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -2,7 +2,7 @@
 
 
   tblastn
-  TBLASTN 2.2.28+
+  TBLASTN 2.2.29+
   Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, 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.
   
   Query_1
diff -r 72170c3f515a -r 2f7fac29bb3c test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular	Tue Dec 03 10:02:17 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular	Wed Jan 15 05:38:14 2014 -0500
@@ -1,10 +1,10 @@
-sp|P08100|OPSD_HUMAN	gi|57163782|ref|NM_001009242.1|	96.55	348	12	0	1	348	1	1044	0.0	 732	gi|57163782|ref|NM_001009242.1|	1689	336	343	0	98.56	0	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	1047	N/A
-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	N/A
-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	N/A
-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	N/A
-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	N/A
-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	N/A
+sp|P08100|OPSD_HUMAN	gi|57163782|ref|NM_001009242.1|	96.55	348	12	0	1	348	1	1044	0.0	  732	gi|57163782|ref|NM_001009242.1|	1689	336	343	0	98.56	0	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	1047	N/A
+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	N/A
+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	N/A
+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	N/A
+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	N/A
+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	N/A
 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	N/A
-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	N/A
-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	N/A
-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	N/A
+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	N/A
+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	N/A
+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	N/A
diff -r 72170c3f515a -r 2f7fac29bb3c test-data/tblastx_rhodopsin_vs_three_human.tabular
--- a/test-data/tblastx_rhodopsin_vs_three_human.tabular	Tue Dec 03 10:02:17 2013 -0500
+++ b/test-data/tblastx_rhodopsin_vs_three_human.tabular	Wed Jan 15 05:38:14 2014 -0500
@@ -1,57 +1,57 @@
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	97.39	230	6	0	1	690	88	777	0.0	 559
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	94.12	102	6	0	742	1047	829	1134	0.0	 236
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	91.22	148	13	0	1046	603	1133	690	0.0	 308
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	94.32	88	5	0	566	303	653	390	0.0	 207
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	96.34	82	3	0	248	3	335	90	0.0	 182
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	83.33	204	34	0	18	629	105	716	4e-158	 404
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	75.28	89	22	0	780	1046	867	1133	4e-158	 161
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	81.28	203	38	0	609	1	696	88	5e-153	 360
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	80.60	67	13	0	916	716	1003	803	5e-153	 135
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	97.39	230	6	0	1	690	88	777	0.0	  559
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	94.12	102	6	0	742	1047	829	1134	0.0	  236
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	91.22	148	13	0	1046	603	1133	690	0.0	  308
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	94.32	88	5	0	566	303	653	390	0.0	  207
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	96.34	82	3	0	248	3	335	90	0.0	  182
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	83.33	204	34	0	18	629	105	716	4e-158	  404
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	75.28	89	22	0	780	1046	867	1133	4e-158	  161
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	81.28	203	38	0	609	1	696	88	5e-153	  360
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	80.60	67	13	0	916	716	1003	803	5e-153	  135
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	70.27	37	11	0	1047	937	1134	1024	5e-153	64.2
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	100.00	7	0	0	646	626	733	713	5e-153	24.0
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	89.23	65	7	0	460	266	547	353	4e-105	 167
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	89.58	48	5	0	184	41	271	128	4e-105	 104
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	89.23	65	7	0	460	266	547	353	4e-105	  167
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	89.58	48	5	0	184	41	271	128	4e-105	  104
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	77.78	45	10	0	882	748	969	835	4e-105	93.9
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	67.86	28	9	0	1045	962	1132	1049	4e-105	51.9
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	59.09	22	9	0	586	521	673	608	4e-105	33.1
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	81.40	86	16	0	296	553	383	640	2e-87	 185
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	81.40	86	16	0	296	553	383	640	2e-87	  185
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	84.38	32	5	0	11	106	98	193	2e-87	74.8
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	71.43	35	10	0	941	1045	1028	1132	2e-87	61.6
 gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	94.44	18	1	0	794	847	881	934	2e-87	50.1
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	83.61	238	39	0	18	731	64	777	0.0	 507
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	82.35	85	15	0	783	1037	829	1083	0.0	 188
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	70.96	303	88	0	925	17	971	63	2e-130	 435
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	83.61	238	39	0	18	731	64	777	0.0	  507
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	82.35	85	15	0	783	1037	829	1083	0.0	  188
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	70.96	303	88	0	925	17	971	63	2e-130	  435
 gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	72.22	18	5	0	1027	974	1073	1020	2e-130	35.0
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	55.32	188	84	0	605	42	651	88	7e-89	 245
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	55.32	188	84	0	605	42	651	88	7e-89	  245
 gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	61.11	72	28	0	1037	822	1083	868	7e-89	91.3
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	49.02	204	104	0	29	640	75	686	4e-78	 197
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	49.02	204	104	0	29	640	75	686	4e-78	  197
 gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	66.04	53	18	0	860	1018	906	1064	4e-78	85.8
 gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	44.44	27	15	0	689	769	735	815	4e-78	32.2
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	47.47	198	104	0	633	40	679	86	4e-65	 177
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	47.47	198	104	0	633	40	679	86	4e-65	  177
 gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	68.09	47	15	0	1017	877	1063	923	4e-65	80.3
-gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	57.89	114	48	0	265	606	311	652	3e-46	 137
+gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	57.89	114	48	0	265	606	311	652	3e-46	  137
 gi|2734705|gb|U59921.1|BBU59921	ENA|BC112106|BC112106.1	46.30	54	29	0	19	180	65	226	3e-46	52.4
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	96.40	111	4	0	1	333	118	450	0.0	 264
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	92.31	65	5	0	3174	3368	829	1023	0.0	 151
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	96.43	56	2	0	2855	3022	616	783	0.0	 141
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	93.22	59	4	0	1404	1580	442	618	0.0	 138
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	96.40	111	4	0	1	333	118	450	0.0	  264
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	92.31	65	5	0	3174	3368	829	1023	0.0	  151
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	96.43	56	2	0	2855	3022	616	783	0.0	  141
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	93.22	59	4	0	1404	1580	442	618	0.0	  138
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	92.00	25	2	0	4222	4296	1021	1095	0.0	64.3
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	88.89	9	1	0	3128	3154	783	809	0.0	22.6
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	78.38	111	24	0	333	1	450	118	7e-171	 212
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	88.75	80	9	0	3367	3128	1022	783	7e-171	 161
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	93.33	60	4	0	1582	1403	620	441	7e-171	 136
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	91.07	56	5	0	3021	2854	782	615	7e-171	 119
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	78.38	111	24	0	333	1	450	118	7e-171	  212
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	88.75	80	9	0	3367	3128	1022	783	7e-171	  161
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	93.33	60	4	0	1582	1403	620	441	7e-171	  136
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	91.07	56	5	0	3021	2854	782	615	7e-171	  119
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	84.62	26	4	0	4301	4224	1100	1023	7e-171	52.8
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	95.83	72	3	0	218	3	335	120	8e-142	 152
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	77.78	63	14	0	3368	3180	1023	835	8e-142	 125
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	85.11	47	7	0	1544	1404	582	442	8e-142	 108
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	80.36	56	11	0	3022	2855	783	616	8e-142	 101
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	95.83	72	3	0	218	3	335	120	8e-142	  152
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	77.78	63	14	0	3368	3180	1023	835	8e-142	  125
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	85.11	47	7	0	1544	1404	582	442	8e-142	  108
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	80.36	56	11	0	3022	2855	783	616	8e-142	  101
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	75.86	29	7	0	325	239	442	356	8e-142	58.3
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	86.36	22	3	0	4287	4222	1086	1021	8e-142	48.7
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	90.91	11	1	0	3159	3127	814	782	8e-142	31.3
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	81.03	58	11	0	2854	3027	615	788	2e-122	 128
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	83.33	60	10	0	1403	1582	441	620	2e-122	 125
-gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	80.60	67	13	0	3	203	120	320	2e-122	 119
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	81.03	58	11	0	2854	3027	615	788	2e-122	  128
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	83.33	60	10	0	1403	1582	441	620	2e-122	  125
+gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	80.60	67	13	0	3	203	120	320	2e-122	  119
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	91.30	23	2	0	4220	4288	1019	1087	2e-122	53.8
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	78.26	23	5	0	266	334	383	451	2e-122	48.3
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	80.00	20	4	0	3308	3367	963	1022	2e-122	46.0
@@ -68,16 +68,16 @@
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	77.27	22	5	0	267	332	384	449	6e-43	45.1
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	86.36	22	3	0	4224	4289	1023	1088	6e-43	44.1
 gi|283855845|gb|GQ290303.1|	ENA|BC112106|BC112106.1	83.33	12	2	0	2856	2891	617	652	6e-43	25.4
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	95.91	220	9	0	1	660	118	777	0.0	 526
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	92.13	89	7	0	712	978	829	1095	0.0	 212
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	91.01	178	16	0	536	3	653	120	1e-178	 353
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	88.32	137	16	0	983	573	1100	690	1e-178	 277
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	77.43	319	72	0	3	959	120	1076	4e-174	 593
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	79.07	129	27	0	558	172	675	289	2e-133	 248
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	76.83	82	19	0	963	718	1080	835	2e-133	 159
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	95.91	220	9	0	1	660	118	777	0.0	  526
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	92.13	89	7	0	712	978	829	1095	0.0	  212
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	91.01	178	16	0	536	3	653	120	1e-178	  353
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	88.32	137	16	0	983	573	1100	690	1e-178	  277
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	77.43	319	72	0	3	959	120	1076	4e-174	  593
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	79.07	129	27	0	558	172	675	289	2e-133	  248
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	76.83	82	19	0	963	718	1080	835	2e-133	  159
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	84.09	44	7	0	133	2	250	119	2e-133	97.3
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	73.08	78	21	0	433	200	550	317	6e-102	 145
-gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	70.15	67	20	0	799	599	916	716	6e-102	 106
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	73.08	78	21	0	433	200	550	317	6e-102	  145
+gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	70.15	67	20	0	799	599	916	716	6e-102	  106
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	80.49	41	8	0	123	1	240	118	6e-102	84.5
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	77.78	27	6	0	553	473	670	590	6e-102	51.9
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	71.43	14	4	0	889	848	1006	965	6e-102	32.7
@@ -87,16 +87,16 @@
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	81.40	43	8	0	404	532	521	649	4e-48	47.3
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	88.89	18	2	0	764	817	881	934	4e-48	44.6
 gi|283855822|gb|GQ290312.1|	ENA|BC112106|BC112106.1	87.50	8	1	0	935	958	1052	1075	4e-48	21.7
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	93.91	230	14	0	1	690	88	777	0.0	 538
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	91.18	102	9	0	742	1047	829	1134	0.0	 233
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	88.83	188	21	0	566	3	653	90	0.0	 394
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	84.06	138	22	0	1046	633	1133	720	0.0	 260
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	67.11	228	75	0	684	1	771	88	7e-132	 333
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	67.27	110	36	0	1045	716	1132	803	7e-132	 141
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	70.20	151	45	0	3	455	90	542	1e-128	 236
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	64.04	89	32	0	780	1046	867	1133	1e-128	 136
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	66.22	74	25	0	510	731	597	818	1e-128	 111
-gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	66.04	106	36	0	242	559	329	646	2e-58	 161
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	93.91	230	14	0	1	690	88	777	0.0	  538
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	91.18	102	9	0	742	1047	829	1134	0.0	  233
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	88.83	188	21	0	566	3	653	90	0.0	  394
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	84.06	138	22	0	1046	633	1133	720	0.0	  260
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	67.11	228	75	0	684	1	771	88	7e-132	  333
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	67.27	110	36	0	1045	716	1132	803	7e-132	  141
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	70.20	151	45	0	3	455	90	542	1e-128	  236
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	64.04	89	32	0	780	1046	867	1133	1e-128	  136
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	66.22	74	25	0	510	731	597	818	1e-128	  111
+gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	66.04	106	36	0	242	559	329	646	2e-58	  161
 gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	85.71	21	3	0	92	154	179	241	2e-58	53.8
 gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	73.68	19	5	0	791	847	878	934	2e-58	39.1
 gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	61.29	62	24	0	424	239	511	326	4e-55	81.3
@@ -104,11 +104,11 @@
 gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	65.71	35	12	0	882	778	969	865	4e-55	56.3
 gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	58.14	43	18	0	649	521	736	608	4e-55	50.6
 gi|18148870|dbj|AB062417.1|	ENA|BC112106|BC112106.1	66.67	12	4	0	972	937	1059	1024	4e-55	23.9
-gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	82.13	235	42	0	11	715	76	780	0.0	 498
-gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	78.31	83	18	0	770	1018	835	1083	0.0	 177
-gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	72.29	332	92	0	1017	22	1082	87	1e-150	 516
-gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	48.30	147	76	0	712	272	777	337	2e-98	 169
-gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	54.17	72	33	0	1030	815	1095	880	2e-98	 103
+gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	82.13	235	42	0	11	715	76	780	0.0	  498
+gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	78.31	83	18	0	770	1018	835	1083	0.0	  177
+gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	72.29	332	92	0	1017	22	1082	87	1e-150	  516
+gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	48.30	147	76	0	712	272	777	337	2e-98	  169
+gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	54.17	72	33	0	1030	815	1095	880	2e-98	  103
 gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	47.83	69	36	0	220	14	285	79	2e-98	83.5
 gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	72.00	25	7	0	782	708	847	773	2e-98	45.1
 gi|12583664|dbj|AB043817.1|	ENA|BC112106|BC112106.1	56.00	75	33	0	532	756	597	821	5e-65	87.7
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/README.rst	Wed Jan 15 05:38:14 2014 -0500
@@ -1,9 +1,8 @@
 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.
+These wrappers are copyright 2010-2013 by Peter Cock (The James Hutton Institute,
+UK) and additional contributors. All rights reserved. See the licence text below.
 
 Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 of BLAST+),
 and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``).
@@ -136,6 +135,10 @@
         - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27
         - Now depends on package_blast_plus_2_2_28 in ToolShed
         - Extended tabular output includes 'salltitles' as column 25.
+v0.1.00 - Now depends on package_blast_plus_2_2_29 in ToolShed
+        - Tablar output now includes option to pick specific columns
+        - BLAST XML to tabular tool supports multiple input files.
+        - More detailed descriptions for BLASTN and BLASTP task option
 ======= ======================================================================
 
 
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py	Wed Jan 15 05:38:14 2014 -0500
@@ -62,9 +62,11 @@
 """
 import sys
 import re
+import os
+from optparse import OptionParser
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.22"
+    print "v0.0.23"
     sys.exit(0)
 
 if sys.version_info[:2] >= ( 2, 5 ):
@@ -81,34 +83,55 @@
     sys.stderr.write("%s\n" % msg)
     sys.exit(1)
 
-#Parse Command Line
-try:
-    in_file, out_file, out_fmt = sys.argv[1:]
-except:
-    stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
+if len(sys.argv) == 4 and sys.argv[3] in ["std", "x22", "ext"]:
+    #False positive if user really has a BLAST XML file called 'std' or 'ext'...
+    stop_err("ERROR: The script API has changed, sorry.")
+
+usage = """usage: %prog [options] blastxml[,...]
+
+Convert one (or more) BLAST XML files into a single tabular file.
 
+The columns option can be 'std' (standard 12 columns), 'ext'
+(extended 25 columns), or a list of BLAST+ column names like
+'qseqid,sseqid,pident' (space or comma separated).
+"""
+parser = OptionParser(usage=usage)
+parser.add_option('-o', '--output', dest='output', default=None, help='output filename (defaults to stdout)', metavar="FILE")
+parser.add_option("-c", "--columns", dest="columns", default='std', help="[std|ext|col1,col2,...] standard 12 columns, extended 25 columns, or list of column names")
+(options, args) = parser.parse_args()
+
+colnames = 'qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles'.split(',')
+
+if len(args) < 1:
+    stop_err("ERROR: No BLASTXML input files given; run with --help to see options.")
+
+out_fmt = options.columns
 if out_fmt == "std":
     extended = False
+    cols = None
 elif out_fmt == "x22":
     stop_err("Format argument x22 has been replaced with ext (extended 25 columns)")
 elif out_fmt == "ext":
     extended = True
+    cols = None
 else:
-    stop_err("Format argument should be std (12 column) or ext (extended 25 columns), not: %r" % out_fmt)
-
+    cols = out_fmt.replace(" ", ",").split(",") #Allow space or comma separated
+    #Remove any blank entries due to trailing comma,
+    #or annoying "None" dummy value from Galaxy if no columns
+    cols = [c for c in cols if c and c != "None"]
+    extra = set(cols).difference(colnames)
+    if extra:
+        stop_err("These are not recognised column names: %s" % ",".join(sorted(extra)))
+    del extra
+    assert set(colnames).issuperset(cols), cols
+    if not cols:
+        stop_err("No columns selected!")
+    extended = max(colnames.index(c) for c in cols) >= 12 #Do we need any higher columns?
+del out_fmt
 
-# get an iterable
-try: 
-    context = ElementTree.iterparse(in_file, events=("start", "end"))
-except:
-    stop_err("Invalid data format.")
-# turn it into an iterator
-context = iter(context)
-# get the root element
-try:
-    event, root = context.next()
-except:
-    stop_err( "Invalid data format." )
+for in_file in args:
+    if not os.path.isfile(in_file):
+        stop_err("Input BLAST XML file not found: %s" % in_file)
 
 
 re_default_query_id = re.compile("^Query_\d+$")
@@ -122,156 +145,187 @@
 assert not re_default_subject_id.match("TheSubject_1")
 
 
-outfile = open(out_file, 'w')
-blast_program = None
-for event, elem in context:
-    if event == "end" and elem.tag == "BlastOutput_program":
-        blast_program = elem.text
-    # for every  tag
-    if event == "end" and elem.tag == "Iteration":
-        #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
-        # sp|Q9BS26|ERP44_HUMAN
-        # Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
-        # 406
-        # 
-        #
-        #Or, from BLAST 2.2.24+ run online
-        # Query_1
-        # Sample
-        # 516
-        # ...
-        qseqid = elem.findtext("Iteration_query-ID")
-        if re_default_query_id.match(qseqid):
-            #Place holder ID, take the first word of the query definition
-            qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
-        qlen = int(elem.findtext("Iteration_query-len"))
-                                        
-        # for every  within 
-        for hit in elem.findall("Iteration_hits/Hit"):
-            #Expecting either this,
-            # gi|3024260|sp|P56514.1|OPSD_BUFBU
-            # RecName: Full=Rhodopsin
-            # P56514
-            #or,
-            # Subject_1
-            # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]
-            # Subject_1
+def convert(blastxml_filename, output_handle):
+    blast_program = None
+    # get an iterable
+    try: 
+        context = ElementTree.iterparse(in_file, events=("start", "end"))
+    except:
+        stop_err("Invalid data format.")
+    # turn it into an iterator
+    context = iter(context)
+    # get the root element
+    try:
+        event, root = context.next()
+    except:
+        stop_err( "Invalid data format." )
+    for event, elem in context:
+        if event == "end" and elem.tag == "BlastOutput_program":
+            blast_program = elem.text
+        # for every  tag
+        if event == "end" and elem.tag == "Iteration":
+            #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
+            # sp|Q9BS26|ERP44_HUMAN
+            # Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
+            # 406
+            # 
             #
-            #apparently depending on the parse_deflines switch
-            #
-            #Or, with BLAST 2.2.28+ can get this,
-            # gnl|BL_ORD_ID|2
-            # chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence
-            # 2
-            sseqid = hit.findtext("Hit_id").split(None,1)[0]
-            hit_def = sseqid + " " + hit.findtext("Hit_def")
-            if re_default_subject_id.match(sseqid) \
-            and sseqid == hit.findtext("Hit_accession"):
-                #Place holder ID, take the first word of the subject definition
-                hit_def = hit.findtext("Hit_def")
-                sseqid = hit_def.split(None,1)[0]
-            if sseqid.startswith("gnl|BL_ORD_ID|") \
-            and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"):
-                #Alternative place holder ID, again take the first word of hit_def
-                hit_def = hit.findtext("Hit_def")
-                sseqid = hit_def.split(None,1)[0]
-            # for every  within 
-            for hsp in hit.findall("Hit_hsps/Hsp"):
-                nident = hsp.findtext("Hsp_identity")
-                length = hsp.findtext("Hsp_align-len")
-                pident = "%0.2f" % (100*float(nident)/float(length))
+            #Or, from BLAST 2.2.24+ run online
+            # Query_1
+            # Sample
+            # 516
+            # ...
+            qseqid = elem.findtext("Iteration_query-ID")
+            if re_default_query_id.match(qseqid):
+                #Place holder ID, take the first word of the query definition
+                qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
+            qlen = int(elem.findtext("Iteration_query-len"))
 
-                q_seq = hsp.findtext("Hsp_qseq")
-                h_seq = hsp.findtext("Hsp_hseq")
-                m_seq = hsp.findtext("Hsp_midline")
-                assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
-                gapopen = str(len(q_seq.replace('-', ' ').split())-1  + \
-                              len(h_seq.replace('-', ' ').split())-1)
+            # for every  within 
+            for hit in elem.findall("Iteration_hits/Hit"):
+                #Expecting either this,
+                # gi|3024260|sp|P56514.1|OPSD_BUFBU
+                # RecName: Full=Rhodopsin
+                # P56514
+                #or,
+                # Subject_1
+                # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]
+                # Subject_1
+                #
+                #apparently depending on the parse_deflines switch
+                #
+                #Or, with a local database not using -parse_seqids can get this,
+                # gnl|BL_ORD_ID|2
+                # chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence
+                # 2
+                sseqid = hit.findtext("Hit_id").split(None,1)[0]
+                hit_def = sseqid + " " + hit.findtext("Hit_def")
+                if re_default_subject_id.match(sseqid) \
+                and sseqid == hit.findtext("Hit_accession"):
+                    #Place holder ID, take the first word of the subject definition
+                    hit_def = hit.findtext("Hit_def")
+                    sseqid = hit_def.split(None,1)[0]
+                if sseqid.startswith("gnl|BL_ORD_ID|") \
+                and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"):
+                    #Alternative place holder ID, again take the first word of hit_def
+                    hit_def = hit.findtext("Hit_def")
+                    sseqid = hit_def.split(None,1)[0]
+                # for every  within 
+                for hsp in hit.findall("Hit_hsps/Hsp"):
+                    nident = hsp.findtext("Hsp_identity")
+                    length = hsp.findtext("Hsp_align-len")
+                    pident = "%0.2f" % (100*float(nident)/float(length))
+
+                    q_seq = hsp.findtext("Hsp_qseq")
+                    h_seq = hsp.findtext("Hsp_hseq")
+                    m_seq = hsp.findtext("Hsp_midline")
+                    assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
+                    gapopen = str(len(q_seq.replace('-', ' ').split())-1  + \
+                                  len(h_seq.replace('-', ' ').split())-1)
+
+                    mismatch = m_seq.count(' ') + m_seq.count('+') \
+                             - q_seq.count('-') - h_seq.count('-')
+                    #TODO - Remove this alternative mismatch calculation and test
+                    #once satisifed there are no problems
+                    expected_mismatch = len(q_seq) \
+                                      - sum(1 for q,h in zip(q_seq, h_seq) \
+                                            if q == h or q == "-" or h == "-")
+                    xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
+                    if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
+                        stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
+                                 % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
+                                    int(mismatch), expected_mismatch))
 
-                mismatch = m_seq.count(' ') + m_seq.count('+') \
-                         - q_seq.count('-') - h_seq.count('-')
-                #TODO - Remove this alternative mismatch calculation and test
-                #once satisifed there are no problems
-                expected_mismatch = len(q_seq) \
-                                  - sum(1 for q,h in zip(q_seq, h_seq) \
-                                        if q == h or q == "-" or h == "-")
-                xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
-                if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
-                    stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
-                             % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
-                                int(mismatch), expected_mismatch))
+                    #TODO - Remove this alternative identity calculation and test
+                    #once satisifed there are no problems
+                    expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
+                    if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
+                        stop_err("%s vs %s identities, expected %i <= %i <= %i" \
+                                 % (qseqid, sseqid, expected_identity, int(nident),
+                                    expected_identity + q_seq.count("X")))
+
 
-                #TODO - Remove this alternative identity calculation and test
-                #once satisifed there are no problems
-                expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
-                if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
-                    stop_err("%s vs %s identities, expected %i <= %i <= %i" \
-                             % (qseqid, sseqid, expected_identity, int(nident),
-                                expected_identity + q_seq.count("X")))
+                    evalue = hsp.findtext("Hsp_evalue")
+                    if evalue == "0":
+                        evalue = "0.0"
+                    else:
+                        evalue = "%0.0e" % float(evalue)
                 
+                    bitscore = float(hsp.findtext("Hsp_bit-score"))
+                    if bitscore < 100:
+                        #Seems to show one decimal place for lower scores
+                        bitscore = "%0.1f" % bitscore
+                    else:
+                        #Note BLAST does not round to nearest int, it truncates
+                        bitscore = "%i" % bitscore
 
-                evalue = hsp.findtext("Hsp_evalue")
-                if evalue == "0":
-                    evalue = "0.0"
-                else:
-                    evalue = "%0.0e" % float(evalue)
-                
-                bitscore = float(hsp.findtext("Hsp_bit-score"))
-                if bitscore < 100:
-                    #Seems to show one decimal place for lower scores
-                    bitscore = "%0.1f" % bitscore
-                else:
-                    #Note BLAST does not round to nearest int, it truncates
-                    bitscore = "%i" % bitscore
+                    values = [qseqid,
+                              sseqid,
+                              pident,
+                              length, #hsp.findtext("Hsp_align-len")
+                              str(mismatch),
+                              gapopen,
+                              hsp.findtext("Hsp_query-from"), #qstart,
+                              hsp.findtext("Hsp_query-to"), #qend,
+                              hsp.findtext("Hsp_hit-from"), #sstart,
+                              hsp.findtext("Hsp_hit-to"), #send,
+                              evalue, #hsp.findtext("Hsp_evalue") in scientific notation
+                              bitscore, #hsp.findtext("Hsp_bit-score") rounded
+                              ]
 
-                values = [qseqid,
-                          sseqid,
-                          pident,
-                          length, #hsp.findtext("Hsp_align-len")
-                          str(mismatch),
-                          gapopen,
-                          hsp.findtext("Hsp_query-from"), #qstart,
-                          hsp.findtext("Hsp_query-to"), #qend,
-                          hsp.findtext("Hsp_hit-from"), #sstart,
-                          hsp.findtext("Hsp_hit-to"), #send,
-                          evalue, #hsp.findtext("Hsp_evalue") in scientific notation
-                          bitscore, #hsp.findtext("Hsp_bit-score") rounded
-                          ]
+                    if extended:
+                        try:
+                            sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >"))
+                            salltitles = "<>".join(name.split(None,1)[1] for name in hit_def.split(" >"))
+                        except IndexError as e:
+                            stop_err("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e))
+                        #print hit_def, "-->", sallseqid
+                        positive = hsp.findtext("Hsp_positive")
+                        ppos = "%0.2f" % (100*float(positive)/float(length))
+                        qframe = hsp.findtext("Hsp_query-frame")
+                        sframe = hsp.findtext("Hsp_hit-frame")
+                        if blast_program == "blastp":
+                            #Probably a bug in BLASTP that they use 0 or 1 depending on format
+                            if qframe == "0": qframe = "1"
+                            if sframe == "0": sframe = "1"
+                        slen = int(hit.findtext("Hit_len"))
+                        values.extend([sallseqid,
+                                       hsp.findtext("Hsp_score"), #score,
+                                       nident,
+                                       positive,
+                                       hsp.findtext("Hsp_gaps"), #gaps,
+                                       ppos,
+                                       qframe,
+                                       sframe,
+                                       #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
+                                       q_seq,
+                                       h_seq,
+                                       str(qlen),
+                                       str(slen),
+                                       salltitles,
+                                       ])
+                    if cols:
+                        #Only a subset of the columns are needed
+                        values = [values[colnames.index(c)] for c in cols]
+                    #print "\t".join(values) 
+                    outfile.write("\t".join(values) + "\n")
+            # prevents ElementTree from growing large datastructure
+            root.clear()
+            elem.clear()
 
-                if extended:
-                    try:
-                        sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >"))
-                        salltitles = "<>".join(name.split(None,1)[1] for name in hit_def.split(" >"))
-                    except IndexError as e:
-                        stop_err("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e))
-                    #print hit_def, "-->", sallseqid
-                    positive = hsp.findtext("Hsp_positive")
-                    ppos = "%0.2f" % (100*float(positive)/float(length))
-                    qframe = hsp.findtext("Hsp_query-frame")
-                    sframe = hsp.findtext("Hsp_hit-frame")
-                    if blast_program == "blastp":
-                        #Probably a bug in BLASTP that they use 0 or 1 depending on format
-                        if qframe == "0": qframe = "1"
-                        if sframe == "0": sframe = "1"
-                    slen = int(hit.findtext("Hit_len"))
-                    values.extend([sallseqid,
-                                   hsp.findtext("Hsp_score"), #score,
-                                   nident,
-                                   positive,
-                                   hsp.findtext("Hsp_gaps"), #gaps,
-                                   ppos,
-                                   qframe,
-                                   sframe,
-                                   #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
-                                   q_seq,
-                                   h_seq,
-                                   str(qlen),
-                                   str(slen),
-                                   salltitles,
-                                   ])
-                #print "\t".join(values) 
-                outfile.write("\t".join(values) + "\n")
-        # prevents ElementTree from growing large datastructure
-        root.clear()
-        elem.clear()
-outfile.close()
+
+if options.output:
+    outfile = open(options.output, "w")
+else:
+    outfile = sys.stdout
+
+for in_file in args:
+    blast_program = None
+    convert(in_file, outfile)
+
+if options.output:
+    outfile.close()
+else:
+    #Using stdout
+    pass
+
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,8 +1,15 @@
-
+
     Convert BLAST XML output to tabular
     blastxml_to_tabular.py --version
     
-      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
+blastxml_to_tabular.py -o "$tabular_file"
+#if $output.out_format == "cols":
+#set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ")
+-c "$cols"
+#else
+-c "$output.out_format"
+#end if
+#for i in $blastxml_file#${i} #end for#
     
     
         
@@ -10,14 +17,50 @@
         
     
     
-         
-        
-            
-            
-        
+        
+        
+          
+            
+            
+            
+          
+          
+          
+          
+            
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+            
+            
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+              
+            
+          
+        
     
     
-        
+        
     
     
     
@@ -80,6 +123,19 @@
             
             
         
+        
+        
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+        
     
     
     
@@ -120,7 +176,7 @@
 ====== ============= ===========================================
 Column NCBI name     Description
 ------ ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by ';'
+    13 sallseqid     All subject Seq-id(s), separated by a ';'
     14 score         Raw score
     15 nident        Number of identical matches
     16 positive      Number of positive-scoring matches
@@ -132,7 +188,7 @@
     22 sseq          Aligned part of subject sequence
     23 qlen          Query sequence length
     24 slen          Subject sequence length
-    25 salltitles    All subject title(s), separated by '<>'
+    25 salltitles    All subject title(s), separated by a '<>'
 ====== ============= ===========================================
 
 Beware that the XML file (and thus the conversion) and the tabular output
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Show BLAST database information from blastdbcmd
     
         blastdbcmd
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Extract sequence(s) from BLAST database
     
         blastdbcmd
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search nucleotide database with nucleotide query sequence(s)
     
     
@@ -36,14 +36,16 @@
         
 
         
-            
-            
-            
-            
+            
+            
+            
+            
             
+            
         
         
         
@@ -74,10 +76,32 @@
             
             
             
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
             
             
             
         
+        
+            
+            
+            
+            
+            
+            
+            
+            
+            
+            
+        
     
     
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein database with protein query sequence(s)
     
     
@@ -34,8 +34,8 @@
         
 
         
-            
-            
+            
+            
         
         
         
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein database with translated nucleotide query sequence(s)
     
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     
     masks low complexity regions
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -11,20 +11,64 @@
         
     
     
-        
-            
-            
-            
-            
-            
-            
-            
-            
-            
-            
-        
+        
+            
+                
+                
+                
+                
+                
+                
+                
+                
+                
+                
+                
+            
+            
+            
+            
+                
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                
+                
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                    
+                
+                
+            
+            
+            
+            
+            
+            
+            
+            
+        
     
     
         
@@ -240,7 +284,7 @@
     
         
             @BINARY@
-            blast+
+            blast+
         
         @BINARY@ -version
     
@@ -268,10 +312,15 @@
     
     -out "$output1"
 ##Set the extended list here so when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
+#if str($output.out_format)=="ext":
     -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles"
+#elif str($output.out_format)=="cols"
+##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated:
+##TODO - Can we catch the user picking no columns and raise an error here?
+#set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip()
+    -outfmt "6 $cols"
 #else:
-    -outfmt $out_format
+    -outfmt $output.out_format
 #end if
     
     $adv_opts.filter_query
@@ -339,7 +388,7 @@
 ====== ============= ===========================================
 Column NCBI name     Description
 ------ ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by ';'
+    13 sallseqid     All subject Seq-id(s), separated by a ';'
     14 score         Raw score
     15 nident        Number of identical matches
     16 positive      Number of positive-scoring matches
@@ -351,7 +400,7 @@
     22 sseq          Aligned part of subject sequence
     23 qlen          Query sequence length
     24 slen          Subject sequence length
-    25 salltitles    All subject title(s), separated by '<>'
+    25 salltitles    All subject title(s), separated by a '<>'
 ====== ============= ===========================================
 
 The third option is BLAST XML output, which is designed to be parsed by
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Make BLAST database
     
         makeblastdb
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein domain database (PSSMs) with protein query sequence(s)
     
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein domain database (PSSMs) with translated nucleotide query sequence(s)
     
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search translated nucleotide database with protein query sequence(s)
     
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,4 +1,4 @@
-
+
     Search translated nucleotide database with translated nucleotide query sequence(s)
     
     
diff -r 72170c3f515a -r 2f7fac29bb3c tools/ncbi_blast_plus/tool_dependencies.xml
--- a/tools/ncbi_blast_plus/tool_dependencies.xml	Tue Dec 03 10:02:17 2013 -0500
+++ b/tools/ncbi_blast_plus/tool_dependencies.xml	Wed Jan 15 05:38:14 2014 -0500
@@ -1,6 +1,6 @@
 
 
-    
-        
+    
+