| Previous changeset 14:b46c041afbe4 (2015-05-15) Next changeset 16:6ade4e7c63b3 (2017-02-09) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty |
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modified:
test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.py tools/blastxml_to_top_descr/repository_dependencies.xml |
| b |
| 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 |
| [ |
| b'@@ -2,10 +2,10 @@\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n <BlastOutput_program>blastp</BlastOutput_program>\n- <BlastOutput_version>BLASTP 2.2.30+</BlastOutput_version>\n+ <BlastOutput_version>BLASTP 2.5.0+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n <BlastOutput_db></BlastOutput_db>\n- <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>\n+ <BlastOutput_query-ID>Q9BS26</BlastOutput_query-ID>\n <BlastOutput_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>\n <BlastOutput_query-len>406</BlastOutput_query-len>\n <BlastOutput_param>\n@@ -20,7 +20,7 @@\n <BlastOutput_iterations>\n <Iteration>\n <Iteration_iter-num>1</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n+ <Iteration_query-ID>Q9BS26</Iteration_query-ID>\n <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n <Iteration_query-len>406</Iteration_query-len>\n <Iteration_hits>\n@@ -29,8 +29,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n+ <Statistics_hsp-len>42</Statistics_hsp-len>\n+ <Statistics_eff-space>657748</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -40,17 +40,17 @@\n </Iteration>\n <Iteration>\n <Iteration_iter-num>2</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n+ <Iteration_query-ID>Q9NSY1</Iteration_query-ID>\n+ <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>\n+ <Iteration_query-len>1161</Iteration_query-len>\n <Iteration_hits>\n </Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n+ <Statistics_hsp-len>50</Statistics_hsp-len>\n+ <Statistics_eff-space>1954249</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n@@ -60,17 +60,17 @@\n </Iteration>\n <Iteration>\n <Iteration_iter-num>3</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n+ <Iteration_query-ID>P06213</Iteration_query-ID>\n+ <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>\n+ <Iteration_query-len>1382</Iteration_query-len>\n <Iteration_hits>\n </Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n+ <Statistics_hsp-len>51</Statistics_hsp-len>\n+ <Statistics_eff-space>2333243</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <'..b' <Hsp_positive>336</Hsp_positive>\n+ <Hsp_identity>290</Hsp_identity>\n+ <Hsp_positive>322</Hsp_positive>\n <Hsp_gaps>1</Hsp_gaps>\n- <Hsp_align-len>348</Hsp_align-len>\n- <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>\n- <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>\n- <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>\n+ <Hsp_align-len>342</Hsp_align-len>\n+ <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>\n+ <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>\n+ <Hsp_midline>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</Hsp_midline>\n </Hsp>\n </Hit_hsps>\n </Hit>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>29</Statistics_hsp-len>\n- <Statistics_eff-space>101761</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>24</Iteration_iter-num>\n- <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>348</Iteration_query-len>\n-<Iteration_hits>\n <Hit>\n- <Hit_num>1</Hit_num>\n+ <Hit_num>6</Hit_num>\n <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>\n <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>\n <Hit_accession>BAB21486</Hit_accession>\n@@ -652,8 +257,8 @@\n <Statistics>\n <Statistics_db-num>0</Statistics_db-num>\n <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>29</Statistics_hsp-len>\n- <Statistics_eff-space>101761</Statistics_eff-space>\n+ <Statistics_hsp-len>41</Statistics_hsp-len>\n+ <Statistics_eff-space>556591</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n' |
| b |
| 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 |
| [ |
| b'@@ -1,6 +1,6 @@\n-sp|P08100|OPSD_HUMAN\tgi|57163783|ref|NP_001009242.1|\t96.55\t348\t12\t0\t1\t348\t1\t348\t0.0\t701\tgi|57163783|ref|NP_001009242.1|\t1808\t336\t343\t0\t98.56\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\t348\t348\trhodopsin [Felis catus]\n-sp|P08100|OPSD_HUMAN\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t84.80\t342\t51\t1\t1\t341\t1\t342\t0.0\t619\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t1595\t290\t322\t1\t94.15\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t354\tRecName: Full=Rhodopsin\n-sp|P08100|OPSD_HUMAN\tgi|283855846|gb|ADB45242.1|\t94.82\t328\t17\t0\t11\t338\t1\t328\t0.0\t653\tgi|283855846|gb|ADB45242.1|\t1684\t311\t321\t0\t97.87\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\trhodopsin [Cynopterus brachyotis]\n-sp|P08100|OPSD_HUMAN\tgi|283855823|gb|ADB45229.1|\t94.82\t328\t17\t0\t11\t338\t1\t328\t0.0\t631\tgi|283855823|gb|ADB45229.1|\t1627\t311\t323\t0\t98.48\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\trhodopsin [Myotis pilosus]\n-sp|P08100|OPSD_HUMAN\tgi|223523|prf||0811197A\t93.10\t348\t23\t1\t1\t348\t1\t347\t0.0\t673\tgi|223523|prf||0811197A\t1736\t324\t336\t1\t96.55\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFG'..b'YTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t347\trhodopsin [Bos taurus]\n+P08100\tgi|283855846|gb|ADB45242.1|\t94.817\t328\t17\t0\t11\t338\t1\t328\t0.0\t653\tgi|283855846|gb|ADB45242.1|\t1684\t311\t321\t0\t97.87\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\trhodopsin [Cynopterus brachyotis]\n+P08100\tgi|283855823|gb|ADB45229.1|\t94.817\t328\t17\t0\t11\t338\t1\t328\t0.0\t631\tgi|283855823|gb|ADB45229.1|\t1627\t311\t323\t0\t98.48\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\trhodopsin [Myotis pilosus]\n+P08100\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t84.795\t342\t51\t1\t1\t341\t1\t342\t0.0\t619\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t1595\t290\t322\t1\t94.15\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t354\tRecName: Full=Rhodopsin\n+P08100\tgi|12583665|dbj|BAB21486.1|\t82.164\t342\t60\t1\t1\t341\t1\t342\t0.0\t599\tgi|12583665|dbj|BAB21486.1|\t1544\t281\t314\t1\t91.81\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE\t348\t354\tfresh water form rod opsin [Conger myriaster]\n' |
| b |
| 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] |
| b |
| 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] |
| b |
| 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 |
| b |
| @@ -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:: |
| b |
| 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 # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + # <Iteration_query-def>Endoplasmic reticulum resident protein 44 + # OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> # <Iteration_query-len>406</Iteration_query-len> # <Iteration_hits></Iteration_hits> # @@ -175,10 +176,10 @@ # <Iteration_hits>... qseqid = elem.findtext("Iteration_query-ID") if qseqid is None: - stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)") + sys.exit("Missing <Iteration_query-ID> (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 @@ # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def> # <Hit_accession>Subject_1</Hit_accession> # - #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)))) |
| b |
| 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 |
| b |
| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Requires BLAST XML and database datatype definitions."> -<repository changeset_revision="da92fef90117" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="623a3fbe5340" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories> |