# HG changeset patch # User peterjc # Date 1367255332 14400 # Node ID ec31e95c56e18afeac0b2eb4279ca36499af34ea # Parent b23e0a323bee7b63b45b8af72acfe20e330143d0 Uploaded v0.0.5 diff -r b23e0a323bee -r ec31e95c56e1 test-data/blastp_four_human_vs_rhodopsin.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Mon Apr 29 13:08:52 2013 -0400 @@ -0,0 +1,646 @@ + + + + blastp + BLASTP 2.2.26+ + 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 + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + BLOSUM62 + 1e-08 + 11 + 1 + F + + + + + 1 + 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 + + + 2 + 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 + + + 3 + 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 + + + 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 + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|57163783|ref|NP_001009242.1| + rhodopsin [Felis catus] + NP_001009242 + 348 + + + 1 + 701.049 + 1808 + 0 + 1 + 348 + 1 + 348 + 0 + 0 + 336 + 343 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA + + + + + + + 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 + + + 1 + 619.002 + 1595 + 0 + 1 + 341 + 1 + 342 + 0 + 0 + 290 + 322 + 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 + + + + + + + 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 + gi|283855846|gb|ADB45242.1| + rhodopsin [Cynopterus brachyotis] + ADB45242 + 328 + + + 1 + 653.284 + 1684 + 0 + 11 + 338 + 1 + 328 + 0 + 0 + 311 + 321 + 0 + 328 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS + VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S + + + + + + + 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 + gi|283855823|gb|ADB45229.1| + rhodopsin [Myotis pilosus] + ADB45229 + 328 + + + 1 + 631.328 + 1627 + 0 + 11 + 338 + 1 + 328 + 0 + 0 + 311 + 323 + 0 + 328 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS + VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S + + + + + + + 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 + + + 1 + 673.315 + 1736 + 0 + 1 + 348 + 1 + 347 + 0 + 0 + 324 + 336 + 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 + + + + + + + 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 + gi|12583665|dbj|BAB21486.1| + fresh water form rod opsin [Conger myriaster] + BAB21486 + 354 + + + 1 + 599.356 + 1544 + 0 + 1 + 341 + 1 + 342 + 0 + 0 + 281 + 314 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE + MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE + MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +D ASAT SKTE + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + \ No newline at end of file diff -r b23e0a323bee -r ec31e95c56e1 test-data/blastp_four_human_vs_rhodopsin_top3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Mon Apr 29 13:08:52 2013 -0400 @@ -0,0 +1,25 @@ +#Query BLAST hit 1 BLAST hit 2 BLAST hit 3 +sp|Q9BS26|ERP44_HUMAN +sp|Q9BS26|ERP44_HUMAN +sp|Q9BS26|ERP44_HUMAN +sp|Q9BS26|ERP44_HUMAN +sp|Q9BS26|ERP44_HUMAN +sp|Q9BS26|ERP44_HUMAN +sp|Q9NSY1|BMP2K_HUMAN +sp|Q9NSY1|BMP2K_HUMAN +sp|Q9NSY1|BMP2K_HUMAN +sp|Q9NSY1|BMP2K_HUMAN +sp|Q9NSY1|BMP2K_HUMAN +sp|Q9NSY1|BMP2K_HUMAN +sp|P06213|INSR_HUMAN +sp|P06213|INSR_HUMAN +sp|P06213|INSR_HUMAN +sp|P06213|INSR_HUMAN +sp|P06213|INSR_HUMAN +sp|P06213|INSR_HUMAN +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus] +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A rhodopsin [Bos taurus] +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster] diff -r b23e0a323bee -r ec31e95c56e1 tools/ncbi_blast_plus/blastxml_to_top_descr.py --- a/tools/ncbi_blast_plus/blastxml_to_top_descr.py Mon Apr 29 13:08:32 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.py Mon Apr 29 13:08:52 2013 -0400 @@ -7,6 +7,10 @@ import sys import re +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.5" + sys.exit(0) + if sys.version_info[:2] >= ( 2, 5 ): import xml.etree.cElementTree as ElementTree else: @@ -58,6 +62,7 @@ count = 0 +pos_count = 0 outfile = open(out_file, 'w') outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN))) for event, elem in context: @@ -103,6 +108,8 @@ assert hit_def not in hit_descrs hit_descrs.append(hit_def) #print "%r has %i hits" % (qseqid, len(hit_descrs)) + if hit_descrs: + pos_count += 1 hit_descrs = hit_descrs[:topN] while len(hit_descrs) < topN: hit_descrs.append("") @@ -112,4 +119,4 @@ root.clear() elem.clear() outfile.close() -print "%i BLAST results" % count +print "Of %i queries, %i had BLAST results" % (count, pos_count) diff -r b23e0a323bee -r ec31e95c56e1 tools/ncbi_blast_plus/blastxml_to_top_descr.txt --- a/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Mon Apr 29 13:08:32 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Mon Apr 29 13:08:52 2013 -0400 @@ -50,6 +50,9 @@ v0.0.1 - Initial version. v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency on the 'blast_datatypes' repository in the Tool Shed. +v0.0.3 - Include the test files required to run the unit tests +v0.0.4 - Quote filenames in case they contain spaces (internal change) +v0.0.5 - Include number of queries with BLAST matches in stdout (peek text) Developers @@ -58,10 +61,10 @@ This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools -For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml +$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular Check this worked: @@ -70,6 +73,8 @@ tools/ncbi_blast_plus/blastxml_to_top_descr.txt tools/ncbi_blast_plus/blastxml_to_top_descr.xml tools/ncbi_blast_plus/repository_dependencies.xml +test-data/blastp_four_human_vs_rhodopsin.xml +test-data/blastp_four_human_vs_rhodopsin_top3.tabular Licence (MIT/BSD style) diff -r b23e0a323bee -r ec31e95c56e1 tools/ncbi_blast_plus/blastxml_to_top_descr.xml --- a/tools/ncbi_blast_plus/blastxml_to_top_descr.xml Mon Apr 29 13:08:32 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.xml Mon Apr 29 13:08:52 2013 -0400 @@ -1,7 +1,8 @@ - + Make a table from BLAST XML + blastxml_to_top_descr.py --version - blastxml_to_top_descr.py $blastxml_file $tabular_file $topN + blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN}