# HG changeset patch # User peterjc # Date 1486143513 18000 # Node ID 60d0c6c1a71f982ef7de44b359dcfa1a4c630350 # Parent b46c041afbe4577272a787366bf481d60187c9bb planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty diff -r b46c041afbe4 -r 60d0c6c1a71f test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Fri May 15 05:56:41 2015 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Fri Feb 03 12:38:33 2017 -0500 @@ -2,10 +2,10 @@ blastp - BLASTP 2.2.30+ + BLASTP 2.5.0+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - sp|Q9BS26|ERP44_HUMAN + Q9BS26 Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 406 @@ -20,7 +20,7 @@ 1 - sp|Q9BS26|ERP44_HUMAN + Q9BS26 Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 406 @@ -29,8 +29,8 @@ 0 0 - 30 - 119568 + 42 + 657748 0.041 0.267 0.14 @@ -40,17 +40,17 @@ 2 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 + Q9NSY1 + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 0 0 - 30 - 119568 + 50 + 1954249 0.041 0.267 0.14 @@ -60,17 +60,17 @@ 3 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 + P06213 + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 0 0 - 30 - 119568 + 51 + 2333243 0.041 0.267 0.14 @@ -80,307 +80,7 @@ 4 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - sp|P08100|OPSD_HUMAN + P08100 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 348 @@ -412,74 +112,36 @@ - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 20 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - 1 - gi|3024260|sp|P56514.1|OPSD_BUFBU - RecName: Full=Rhodopsin - P56514 - 354 + 2 + gi|223523|prf||0811197A + rhodopsin [Bos taurus] + 0811197A + 347 1 - 619.002 - 1595 + 673.315 + 1736 0 1 - 341 + 348 1 - 342 + 347 0 0 - 290 - 322 + 324 + 336 1 - 342 - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE - MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE - MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 21 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - 1 + 3 gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] ADB45242 @@ -506,27 +168,8 @@ - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 22 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - 1 + 4 gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus] ADB45229 @@ -553,74 +196,36 @@ - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 23 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - 1 - gi|223523|prf||0811197A - rhodopsin [Bos taurus] - 0811197A - 347 + 5 + gi|3024260|sp|P56514.1|OPSD_BUFBU + RecName: Full=Rhodopsin + P56514 + 354 1 - 673.315 - 1736 + 619.002 + 1595 0 1 - 348 + 341 1 - 347 + 342 0 0 - 324 - 336 + 290 + 322 1 - 348 - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA - MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA - MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE + MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE + MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 24 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - 1 + 6 gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster] BAB21486 @@ -652,8 +257,8 @@ 0 0 - 29 - 101761 + 41 + 556591 0.041 0.267 0.14 diff -r b46c041afbe4 -r 60d0c6c1a71f test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Fri May 15 05:56:41 2015 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Fri Feb 03 12:38:33 2017 -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 rhodopsin [Felis catus] -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 RecName: Full=Rhodopsin -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 rhodopsin [Cynopterus brachyotis] -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 rhodopsin [Myotis pilosus] -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 rhodopsin [Bos taurus] -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 fresh water form rod opsin [Conger myriaster] +P08100 gi|57163783|ref|NP_001009242.1| 96.552 348 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 rhodopsin [Felis catus] +P08100 gi|223523|prf||0811197A 93.103 348 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 rhodopsin [Bos taurus] +P08100 gi|283855846|gb|ADB45242.1| 94.817 328 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 rhodopsin [Cynopterus brachyotis] +P08100 gi|283855823|gb|ADB45229.1| 94.817 328 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 rhodopsin [Myotis pilosus] +P08100 gi|3024260|sp|P56514.1|OPSD_BUFBU 84.795 342 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 RecName: Full=Rhodopsin +P08100 gi|12583665|dbj|BAB21486.1| 82.164 342 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 fresh water form rod opsin [Conger myriaster] diff -r b46c041afbe4 -r 60d0c6c1a71f test-data/blastp_four_human_vs_rhodopsin_top3.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Fri May 15 05:56:41 2015 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Fri Feb 03 12:38:33 2017 -0500 @@ -1,5 +1,5 @@ #Query BLAST hit 1 BLAST hit 2 BLAST hit 3 -sp|Q9BS26|ERP44_HUMAN -sp|Q9NSY1|BMP2K_HUMAN -sp|P06213|INSR_HUMAN -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] +Q9BS26 +Q9NSY1 +P06213 +P08100 gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] gi|223523|prf||0811197A rhodopsin [Bos taurus] gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] diff -r b46c041afbe4 -r 60d0c6c1a71f test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Fri May 15 05:56:41 2015 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Fri Feb 03 12:38:33 2017 -0500 @@ -1,2 +1,2 @@ #Query BLAST hit 1 BLAST hit 2 BLAST hit 3 -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] +P08100 gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] gi|223523|prf||0811197A rhodopsin [Bos taurus] gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] diff -r b46c041afbe4 -r 60d0c6c1a71f tools/blastxml_to_top_descr/README.rst --- a/tools/blastxml_to_top_descr/README.rst Fri May 15 05:56:41 2015 -0400 +++ b/tools/blastxml_to_top_descr/README.rst Fri Feb 03 12:38:33 2017 -0500 @@ -96,12 +96,12 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ ... or:: - $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ ... To just build and check the tar ball, use:: diff -r b46c041afbe4 -r 60d0c6c1a71f tools/blastxml_to_top_descr/blastxml_to_top_descr.py --- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Fri May 15 05:56:41 2015 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Fri Feb 03 12:38:33 2017 -0500 @@ -15,16 +15,14 @@ print "v0.1.1" sys.exit(0) -if sys.version_info[:2] >= ( 2, 5 ): +if sys.version_info[:2] >= (2, 5): import xml.etree.cElementTree as ElementTree else: from galaxy import eggs - import pkg_resources; pkg_resources.require( "elementtree" ) + import pkg_resources + pkg_resources.require("elementtree") from elementtree import ElementTree -def stop_err( msg ): - sys.stderr.write("%s\n" % msg) - sys.exit(1) usage = """Use as follows: @@ -55,7 +53,7 @@ (options, args) = parser.parse_args() if len(sys.argv) == 4 and len(args) == 3 and not options.out_file: - stop_err("""The API has changed, replace this: + sys.exit("""The API has changed, replace this: $ python blastxml_to_top_descr.py input.xml output.tab 3 @@ -67,9 +65,9 @@ """) if not args: - stop_err("Input filename missing, try -h") + sys.exit("Input filename missing, try -h") if len(args) > 1: - stop_err("Expects a single argument, one input filename") + sys.exit("Expects a single argument, one input filename") in_file = args[0] out_file = options.out_file topN = options.topN @@ -77,12 +75,12 @@ try: topN = int(topN) except ValueError: - stop_err("Number of hits argument should be an integer (at least 1)") + sys.exit("Number of hits argument should be an integer (at least 1)") if topN < 1: - stop_err("Number of hits argument should be an integer (at least 1)") + sys.exit("Number of hits argument should be an integer (at least 1)") if not os.path.isfile(in_file): - stop_err("Missing input file: %r" % in_file) + sys.exit("Missing input file: %r" % in_file) def get_column(value): @@ -92,11 +90,12 @@ value = value[1:] try: col = int(value) - except: - stop_err("Expected an integer column number, not %r" % value) + except ValueError: + sys.exit("Expected an integer column number, not %r" % value) if col < 1: - stop_err("Expect column numbers to be at least one, not %r" % value) - return col - 1 # Python counting! + sys.exit("Expect column numbers to be at least one, not %r" % value) + return col - 1 # Python counting! + def tabular_hits(in_file, qseqid, sseqid, salltitles): """Parse key data from tabular BLAST output. @@ -126,6 +125,7 @@ # Final query yield current_query, current_hits + def blastxml_hits(in_file): """Parse key data from BLAST XML output. @@ -133,19 +133,19 @@ """ try: context = ElementTree.iterparse(in_file, events=("start", "end")) - except: + except Exception: with open(in_file) as handle: header = handle.read(100) - stop_err("Invalid data format in XML file %r which starts: %r" % (in_file, header)) + sys.exit("Invalid data format in XML file %r which starts: %r" % (in_file, header)) # turn it into an iterator context = iter(context) # get the root element try: event, root = context.next() - except: + except Exception: with open(in_file) as handle: header = handle.read(100) - stop_err("Unable to get root element from XML file %r which starts: %r" % (in_file, header)) + sys.exit("Unable to get root element from XML file %r which starts: %r" % (in_file, header)) re_default_query_id = re.compile("^Query_\d+$") assert re_default_query_id.match("Query_101") @@ -164,7 +164,8 @@ 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 + # Endoplasmic reticulum resident protein 44 + # OS=Homo sapiens GN=ERP44 PE=1 SV=1 # 406 # # @@ -175,10 +176,10 @@ # ... qseqid = elem.findtext("Iteration_query-ID") if qseqid is None: - stop_err("Missing (could be really old BLAST XML data?)") + sys.exit("Missing (could be really old BLAST XML data?)") 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] + # Place holder ID, take the first word of the query definition + qseqid = elem.findtext("Iteration_query-def").split(None, 1)[0] if current_query is None: # First hit current_query = qseqid @@ -204,14 +205,13 @@ # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] # Subject_1 # - #apparently depending on the parse_deflines switch - sseqid = hit.findtext("Hit_id").split(None,1)[0] + # apparently depending on the parse_deflines switch + 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 + 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] + sseqid = hit_def.split(None, 1)[0] assert hit_def not in hit_descrs hit_descrs.append(hit_def) # prevents ElementTree from growing large datastructure @@ -229,12 +229,12 @@ salltitles = get_column(options.salltitles) hits = tabular_hits(in_file, qseqid, sseqid, salltitles) else: - stop_err("Unsupported format: %r" % options.format) + sys.exit("Unsupported format: %r" % options.format) def best_hits(descriptions, topN): if len(descriptions) < topN: - return descriptions + [""] * (topN - len(descriptions)) + return descriptions + [""] * (topN - len(descriptions)) else: return descriptions[:topN] @@ -243,7 +243,7 @@ outfile = sys.stdout else: outfile = open(out_file, 'w') -outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN))) +outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i + 1) for i in range(topN))) for query, descrs in hits: count += 1 outfile.write("%s\t%s\n" % (query, "\t".join(best_hits(descrs, topN)))) diff -r b46c041afbe4 -r 60d0c6c1a71f tools/blastxml_to_top_descr/repository_dependencies.xml --- a/tools/blastxml_to_top_descr/repository_dependencies.xml Fri May 15 05:56:41 2015 -0400 +++ b/tools/blastxml_to_top_descr/repository_dependencies.xml Fri Feb 03 12:38:33 2017 -0500 @@ -1,4 +1,4 @@ - +