| Previous changeset 12:fe1ed74793c9 (2014-07-30) |
|
Commit message:
v0.1.2 with Python 3.9 declaration |
|
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/blastxml_to_top_descr.xml |
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removed:
tools/blastxml_to_top_descr/repository_dependencies.xml |
| b |
| diff -r fe1ed74793c9 -r 8dc4ba7eba5d test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Wed Jul 30 05:36:52 2014 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Sun Sep 17 13:01:56 2023 +0000 |
| [ |
| 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 2.2.29+</BlastOutput_version>\n+ <BlastOutput_version>BLASTP 2.10.1+</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 fe1ed74793c9 -r 8dc4ba7eba5d test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Wed Jul 30 05:36:52 2014 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Sun Sep 17 13:01:56 2023 +0000 |
| [ |
| 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 fe1ed74793c9 -r 8dc4ba7eba5d test-data/blastp_four_human_vs_rhodopsin_top3.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Wed Jul 30 05:36:52 2014 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Sun Sep 17 13:01:56 2023 +0000 |
| [ |
| @@ -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 fe1ed74793c9 -r 8dc4ba7eba5d test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Wed Jul 30 05:36:52 2014 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Sun Sep 17 13:01:56 2023 +0000 |
| [ |
| @@ -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 fe1ed74793c9 -r 8dc4ba7eba5d tools/blastxml_to_top_descr/README.rst --- a/tools/blastxml_to_top_descr/README.rst Wed Jul 30 05:36:52 2014 -0400 +++ b/tools/blastxml_to_top_descr/README.rst Sun Sep 17 13:01:56 2023 +0000 |
| b |
| @@ -1,7 +1,7 @@ Galaxy tool to extract top BLAST hit descriptions from BLAST XML ================================================================ -This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute +This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -12,38 +12,39 @@ It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr -This requires the 'blast_datatypes' repository from the Galaxy Tool Shed -to provide the 'blastxml' file format definition. +This requires the ``blast_datatypes`` repository from the Galaxy Tool Shed +to provide the ``blastxml`` file format definition. Automated Installation ====================== This should be straightforward, Galaxy should automatically install the -'blast_datatypes' dependency. +``blast_datatypes`` dependency. Manual Installation =================== -If you haven't done so before, first install the 'blast_datatypes' repository. +If you haven't done so before, first install the ``blast_datatypes`` repository. There are just two files to install (if doing this manually): -* blastxml_to_top_descr.py (the Python script) -* blastxml_to_top_descr.xml (the Galaxy tool definition) +- ``blastxml_to_top_descr.py`` (the Python script) +- ``blastxml_to_top_descr.xml`` (the Galaxy tool definition) -The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to -the NCBI BLAST+ tool wrappers. +The suggested location is in the Galaxy folder ``tools/ncbi_blast_plus/`` +next to the NCBI BLAST+ tool wrappers. -You will also need to modify the tools_conf.xml file to tell Galaxy to offer +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line:: <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" /> -To run the tool's tests, also add this line to tools_conf.xml.sample then:: +If you wish to run the unit tests, alsomove/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ sh run_functional_tests.sh -id blastxml_to_top_descr + $ sh run_tests.sh -id blastxml_to_top_descr History @@ -54,13 +55,13 @@ ------- ---------------------------------------------------------------------- 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. + 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) v0.0.6 - Check for errors via the script's return code (internal change) v0.0.7 - Link to Tool Shed added to help text and this documentation. - - Tweak dependency on blast_datatypes to also work on Test Tool Shed + - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed - Adopt standard MIT License. v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast v0.0.9 - Updated citation information (Cock et al. 2013). @@ -70,6 +71,11 @@ - Support BLAST XML with multiple ``<Iteration>`` blocks per query. - Support the default 25 column extended tabular BLAST output. v0.1.1 - Embed citation information in the tool XML (new Galaxy feature). +v0.1.2 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). + - Python 3 compatible syntax. ======= ====================================================================== @@ -89,22 +95,31 @@ As of July 2013, development is continuing on a dedicated GitHub repository: https://github.com/peterjc/galaxy_blast -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the GitHub repository root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +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_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ + ... + +or:: - $ tar -czf blastxml_to_top_descr.tar.gz tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.* tools/blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular + $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf blastxml_to_top_descr.tar.gz + $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ + ... + $ tar -tzf shed_upload.tar.gz + 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/blastxml_to_top_descr.xml tools/blastxml_to_top_descr/repository_dependencies.xml - test-data/blastp_four_human_vs_rhodopsin.xml - test-data/blastp_four_human_vs_rhodopsin_top3.tabular - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular - test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Licence (MIT) |
| b |
| diff -r fe1ed74793c9 -r 8dc4ba7eba5d tools/blastxml_to_top_descr/blastxml_to_top_descr.py --- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Wed Jul 30 05:36:52 2014 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Sun Sep 17 13:01:56 2023 +0000 |
| [ |
| b'@@ -6,25 +6,26 @@\n \n Assumes the hits are pre-sorted, so "best" 3 hits gives first 3 hits.\n """\n+from __future__ import print_function\n+\n import os\n+import re\n import sys\n-import re\n from optparse import OptionParser\n \n if "-v" in sys.argv or "--version" in sys.argv:\n- print "v0.1.0"\n+ print("v0.1.2")\n sys.exit(0)\n \n-if sys.version_info[:2] >= ( 2, 5 ):\n+if sys.version_info[:2] >= (2, 5):\n import xml.etree.cElementTree as ElementTree\n else:\n- from galaxy import eggs\n- import pkg_resources; pkg_resources.require( "elementtree" )\n+ from galaxy import eggs # noqa - ignore flake8 F401\n+ import pkg_resources\n+\n+ pkg_resources.require("elementtree")\n from elementtree import ElementTree\n \n-def stop_err( msg ):\n- sys.stderr.write("%s\\n" % msg)\n- sys.exit(1)\n \n usage = """Use as follows:\n \n@@ -39,23 +40,54 @@\n """\n \n parser = OptionParser(usage=usage)\n-parser.add_option("-t", "--topN", dest="topN", default=3,\n- help="Number of descriptions to collect (in order from file)")\n-parser.add_option("-o", "--output", dest="out_file", default=None,\n- help="Output filename for tabular file",\n- metavar="FILE")\n-parser.add_option("-f", "--format", dest="format", default="blastxml",\n- help="Input format (blastxml or tabular)")\n-parser.add_option("-q", "--qseqid", dest="qseqid", default="1",\n- help="Column for query \'qseqid\' (for tabular input; default 1)")\n-parser.add_option("-s", "--sseqid", dest="sseqid", default="2",\n- help="Column for subject \'sseqid\' (for tabular input; default 2)")\n-parser.add_option("-d", "--salltitles", dest="salltitles", default="25",\n- help="Column for descriptions \'salltitles\' (for tabular input; default 25)")\n+parser.add_option(\n+ "-t",\n+ "--topN",\n+ dest="topN",\n+ default=3,\n+ help="Number of descriptions to collect (in order from file)",\n+)\n+parser.add_option(\n+ "-o",\n+ "--output",\n+ dest="out_file",\n+ default=None,\n+ help="Output filename for tabular file",\n+ metavar="FILE",\n+)\n+parser.add_option(\n+ "-f",\n+ "--format",\n+ dest="format",\n+ default="blastxml",\n+ help="Input format (blastxml or tabular)",\n+)\n+parser.add_option(\n+ "-q",\n+ "--qseqid",\n+ dest="qseqid",\n+ default="1",\n+ help="Column for query \'qseqid\' (for tabular input; default 1)",\n+)\n+parser.add_option(\n+ "-s",\n+ "--sseqid",\n+ dest="sseqid",\n+ default="2",\n+ help="Column for subject \'sseqid\' (for tabular input; default 2)",\n+)\n+parser.add_option(\n+ "-d",\n+ "--salltitles",\n+ dest="salltitles",\n+ default="25",\n+ help="Column for descriptions \'salltitles\' (for tabular input; default 25)",\n+)\n (options, args) = parser.parse_args()\n \n if len(sys.argv) == 4 and len(args) == 3 and not options.out_file:\n- stop_err("""The API has changed, replace this:\n+ sys.exit(\n+ """The API has changed, replace this:\n \n $ python blastxml_to_top_descr.py input.xml output.tab 3\n \n@@ -64,12 +96,13 @@\n $ python blastxml_to_top_descr.py -o output.tab -t 3 input.xml\n \n Sorry.\n-""")\n+"""\n+ )\n \n if not args:\n- stop_err("Input filename missing, try -h")\n+ sys.exit("Input filename missing, try -h")\n if len(args) > 1:\n- stop_err("Expects a single argument, one input filename")\n+ sys.exit("Expects a single argument, one input filename")\n in_file = args[0]\n out_file = options.out_file\n topN = options.topN\n@@ -77,12 +110,12 @@\n try:\n topN = int(topN)\n except ValueError:\n- stop_err("Number of hits argument should be an integer (at least 1)")\n+ sys.exit("Number of hits argument should be an integer (at least 1)")\n if topN < 1:\n- stop_err("Number of hits argument should be an integer (at least 1)")\n+ sys.exit("Number of hits argument should be an integer (at least 1)")\n \n if not os.path.isfile(in_file):\n- stop_err("Missing input file: %r" % in_file)\n+ sys.exit("Missing input file: %r" % in_fil'..b' # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n+ # <Iteration_query-def>Endoplasmic reticulum resident protein 44\n+ # OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n # <Iteration_query-len>406</Iteration_query-len>\n # <Iteration_hits></Iteration_hits>\n #\n@@ -177,10 +216,12 @@\n # <Iteration_hits>...\n qseqid = elem.findtext("Iteration_query-ID")\n if qseqid is None:\n- stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)")\n+ sys.exit(\n+ "Missing <Iteration_query-ID> (could be really old BLAST XML data?)"\n+ )\n if re_default_query_id.match(qseqid):\n- #Place holder ID, take the first word of the query definition\n- qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]\n+ # Place holder ID, take the first word of the query definition\n+ qseqid = elem.findtext("Iteration_query-def").split(None, 1)[0]\n if current_query is None:\n # First hit\n current_query = qseqid\n@@ -203,17 +244,19 @@\n # <Hit_accession>P56514</Hit_accession>\n # or,\n # <Hit_id>Subject_1</Hit_id>\n- # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>\n+ # <Hit_def>gi|57163783|ref|NP_001009242.1|\n+ # rhodopsin [Felis catus]</Hit_def>\n # <Hit_accession>Subject_1</Hit_accession>\n #\n- #apparently depending on the parse_deflines switch\n- sseqid = hit.findtext("Hit_id").split(None,1)[0]\n+ # apparently depending on the parse_deflines switch\n+ sseqid = hit.findtext("Hit_id").split(None, 1)[0]\n hit_def = sseqid + " " + hit.findtext("Hit_def")\n- if re_default_subject_id.match(sseqid) \\\n- and sseqid == hit.findtext("Hit_accession"):\n- #Place holder ID, take the first word of the subject definition\n+ if re_default_subject_id.match(sseqid) and sseqid == hit.findtext(\n+ "Hit_accession"\n+ ):\n+ # Place holder ID, take the first word of the subject definition\n hit_def = hit.findtext("Hit_def")\n- sseqid = hit_def.split(None,1)[0]\n+ sseqid = hit_def.split(None, 1)[0]\n assert hit_def not in hit_descrs\n hit_descrs.append(hit_def)\n # prevents ElementTree from growing large datastructure\n@@ -223,6 +266,7 @@\n # Final query\n yield current_query, hit_descrs\n \n+\n if options.format == "blastxml":\n hits = blastxml_hits(in_file)\n elif options.format == "tabular":\n@@ -231,21 +275,23 @@\n salltitles = get_column(options.salltitles)\n hits = tabular_hits(in_file, qseqid, sseqid, salltitles)\n else:\n- stop_err("Unsupported format: %r" % options.format)\n+ sys.exit("Unsupported format: %r" % options.format)\n \n \n def best_hits(descriptions, topN):\n+ """Truncate given descriptions list to at most N entries."""\n if len(descriptions) < topN:\n- return descriptions + [""] * (topN - len(descriptions))\n+ return descriptions + [""] * (topN - len(descriptions))\n else:\n return descriptions[:topN]\n \n+\n count = 0\n if out_file is None:\n outfile = sys.stdout\n else:\n- outfile = open(out_file, \'w\')\n-outfile.write("#Query\\t%s\\n" % "\\t".join("BLAST hit %i" % (i+1) for i in range(topN)))\n+ outfile = open(out_file, "w")\n+outfile.write("#Query\\t%s\\n" % "\\t".join("BLAST hit %i" % (i + 1) for i in range(topN)))\n for query, descrs in hits:\n count += 1\n outfile.write("%s\\t%s\\n" % (query, "\\t".join(best_hits(descrs, topN))))\n' |
| b |
| diff -r fe1ed74793c9 -r 8dc4ba7eba5d tools/blastxml_to_top_descr/blastxml_to_top_descr.xml --- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Wed Jul 30 05:36:52 2014 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Sun Sep 17 13:01:56 2023 +0000 |
| b |
| @@ -1,27 +1,27 @@ -<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.1"> +<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.2" profile="16.10"> <description>Make a table from BLAST output</description> - <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> - <command interpreter="python"> -blastxml_to_top_descr.py --f "$input.in_format" + <requirements> + <requirement type="package" version="3.9">python</requirement> + </requirements> + <version_command> +python $__tool_directory__/blastxml_to_top_descr.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/blastxml_to_top_descr.py +-f '$input.in_format' #if $input.in_format == "tabular": --qseqid $input.qseqid --sseqid $input.sseqid --salltitles $input.salltitles #end if --o "${tabular_file}" +-o '${tabular_file}' -t ${topN} -"${in_file}" +'${in_file}' </command> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <inputs> <conditional name="input"> <param name="in_format" type="select" label="Input format"> - <option value="blastxml" select="True">BLAST XML</option> + <option value="blastxml" selected="true">BLAST XML</option> <option value="tabular">Tabular</option> </param> <when value="blastxml"> @@ -30,17 +30,17 @@ <when value="tabular"> <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/> <param name="qseqid" type="data_column" data_ref="in_file" - multiple="False" numerical="False" default_value="1" value="1" - label="Column containing query ID (qseqid)" - help="This is column 1 in standard BLAST tabular output" /> - <param name="sseqid" type="data_column" data_ref="in_file" - multiple="False" numerical="False" default_value="2" value="2" - label="Column containing match ID (sseqid)" - help="This is column 2 in standard BLAST tabular output"/> + multiple="false" numerical="false" default_value="1" value="1" + label="Column containing query ID (qseqid)" + help="This is column 1 in standard BLAST tabular output" /> + <param name="sseqid" type="data_column" data_ref="in_file" + multiple="false" numerical="false" default_value="2" value="2" + label="Column containing match ID (sseqid)" + help="This is column 2 in standard BLAST tabular output"/> <param name="salltitles" type="data_column" data_ref="in_file" - multiple="False" numerical="False" default_value="25" value="25" + multiple="false" numerical="false" default_value="25" value="25" label="Column containing containing descriptions (salltitles)" - help="This is column 25 in the default extended BLAST tabular output"/> + help="This is column 25 in the default extended BLAST tabular output"/> </when> </conditional> <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> @@ -48,8 +48,6 @@ <outputs> <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" /> </outputs> - <requirements> - </requirements> <tests> <test> <param name="in_format" value="blastxml" /> @@ -102,7 +100,7 @@ Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 +https://doi.org/10.7717/peerj.167 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr |
| b |
| diff -r fe1ed74793c9 -r 8dc4ba7eba5d tools/blastxml_to_top_descr/repository_dependencies.xml --- a/tools/blastxml_to_top_descr/repository_dependencies.xml Wed Jul 30 05:36:52 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Requires BLAST XML and database datatype definitions."> -<repository changeset_revision="de11e1a921c4" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> |