| Previous changeset 35:1b8a92016045 (2013-11-28) Next changeset 37:72170c3f515a (2013-12-03) |
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Commit message:
Uploaded v0.0.22e, adding 25 column to extended tabular output |
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modified:
test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_ext.tabular test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular test-data/blastx_rhodopsin_vs_four_human_ext.tabular test-data/tblastn_four_human_vs_rhodopsin_ext.tabular tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_macros.xml |
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| diff -r 1b8a92016045 -r 8f9023b30384 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Thu Nov 28 12:20:59 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Mon Dec 02 10:27:05 2013 -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\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\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\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\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\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEET'..b'LVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-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\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t347\trhodopsin [Bos taurus]\n+sp|P08100|OPSD_HUMAN\tgi|12583665|dbj|BAB21486.1|\t82.16\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 1b8a92016045 -r 8f9023b30384 test-data/blastp_four_human_vs_rhodopsin_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Thu Nov 28 12:20:59 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Mon Dec 02 10:27:05 2013 -0500 |
| b |
| 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\t 701\tgi|57163783|ref|NP_001009242.1|\t1808\t336\t343\t0\t98.56\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\t348\t348\n-sp|P08100|OPSD_HUMAN\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t84.80\t342\t51\t1\t1\t341\t1\t342\t0.0\t 619\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t1595\t290\t322\t1\t94.15\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t354\n-sp|P08100|OPSD_HUMAN\tgi|283855846|gb|ADB45242.1|\t94.82\t328\t17\t0\t11\t338\t1\t328\t0.0\t 653\tgi|283855846|gb|ADB45242.1|\t1684\t311\t321\t0\t97.87\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\n-sp|P08100|OPSD_HUMAN\tgi|283855823|gb|ADB45229.1|\t94.82\t328\t17\t0\t11\t338\t1\t328\t0.0\t 631\tgi|283855823|gb|ADB45229.1|\t1627\t311\t323\t0\t98.48\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\n-sp|P08100|OPSD_HUMAN\tgi|223523|prf||0811197A\t93.10\t348\t23\t1\t1\t348\t1\t347\t0.0\t 673\tgi|223523|prf||0811197A\t1736\t324\t336\t1\t96.55\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YT'..b'\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t354\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855846|gb|ADB45242.1|\t94.82\t328\t17\t0\t11\t338\t1\t328\t0.0\t 653\tgi|283855846|gb|ADB45242.1|\t1684\t311\t321\t0\t97.87\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855823|gb|ADB45229.1|\t94.82\t328\t17\t0\t11\t338\t1\t328\t0.0\t 631\tgi|283855823|gb|ADB45229.1|\t1627\t311\t323\t0\t98.48\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|223523|prf||0811197A\t93.10\t348\t23\t1\t1\t348\t1\t347\t0.0\t 673\tgi|223523|prf||0811197A\t1736\t324\t336\t1\t96.55\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t347\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|12583665|dbj|BAB21486.1|\t82.16\t342\t60\t1\t1\t341\t1\t342\t0.0\t 599\tgi|12583665|dbj|BAB21486.1|\t1544\t281\t314\t1\t91.81\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE\t348\t354\tN/A\n' |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular --- a/test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular Thu Nov 28 12:20:59 2013 -0500 +++ b/test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular Mon Dec 02 10:27:05 2013 -0500 |
| b |
| b'@@ -1,8 +1,8 @@\n-sp|Q9BS26|ERP44_HUMAN\tgi|193885198|pdb|2R2J|A\t97.11\t381\t11\t0\t26\t406\t2\t382\t0.0\t768\tgi|193885198|pdb|2R2J|A\t1982\t370\t372\t0\t97.64\t1\t1\tPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL\tPLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL\t406\t382\n-sp|Q9BS26|ERP44_HUMAN\tgi|88192228|pdb|2B5E|A\t25.17\t290\t193\t8\t25\t306\t10\t283\t4e-20\t95.1\tgi|88192228|pdb|2B5E|A;gi|206581884|pdb|3BOA|A\t235\t73\t133\t24\t45.86\t1\t1\tTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH\tAPEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH\t406\t504\n-sp|Q9NSY1|BMP2K_HUMAN\tgi|73536291|pdb|2BUJ|A\t29.39\t279\t182\t8\t40\t308\t21\t294\t1e-22\t105\tgi|73536291|pdb|2BUJ|A;gi|73536292|pdb|2BUJ|B\t262\t82\t130\t15\t46.59\t1\t1\tGVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI\tGHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI\t1161\t317\n-sp|Q9NSY1|BMP2K_HUMAN\tgi|270346335|pdb|2WQM|A\t27.21\t272\t166\t12\t53\t311\t36\t288\t6e-17\t86.3\tgi|270346335|pdb|2WQM|A;gi|270346336|pdb|2WQN|A\t212\t74\t129\t32\t47.43\t1\t1\tLEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV\tIEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV\t1161\t310\n-sp|P06213|INSR_HUMAN\tgi|116667097|pdb|2DTG|E\t95.91\t928\t7\t2\t28\t955\t1\t897\t0.0\t1846\tgi|116667097|pdb|2DTG|E\t4781\t890\t893\t31\t96.23\t1\t1\tHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSS'..b'83860|pdb|2I35|A;gi|157883861|pdb|2I36|A;gi|157883862|pdb|2I36|B;gi|157883863|pdb|2I36|C;gi|157883864|pdb|2I37|A;gi|157883865|pdb|2I37|B;gi|157883866|pdb|2I37|C;gi|159795066|pdb|2PED|A;gi|159795067|pdb|2PED|B;gi|192988480|pdb|3CAP|A;gi|192988481|pdb|3CAP|B;gi|195927457|pdb|3C9L|A;gi|197107530|pdb|1F88|A;gi|197107531|pdb|1F88|B;gi|206582030|pdb|3DQB|A\t1756\t325\t337\t0\t96.84\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t348\tChain A, Structure Of Bovine Rhodopsin (Dark Adapted)<>Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii)<>Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form<>Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form<>Chain A, Crystal Structure Of Bovine Rhodopsin<>Chain B, Crystal Structure Of Bovine Rhodopsin<>Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution<>Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution<>Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution<>Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution<>Chain A, Crystallographic Model Of Bathorhodopsin<>Chain B, Crystallographic Model Of Bathorhodopsin<>Chain A, Crystallographic Model Of Lumirhodopsin<>Chain B, Crystallographic Model Of Lumirhodopsin<>Chain A, Crystal Structure Of Rhombohedral Crystal Form Of Ground- State Rhodopsin<>Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain A, Crystal Structure Of A Photoactivated Rhodopsin<>Chain B, Crystal Structure Of A Photoactivated Rhodopsin<>Chain C, Crystal Structure Of A Photoactivated Rhodopsin<>Chain A, Crystallographic Model Of 9-Cis-Rhodopsin<>Chain B, Crystallographic Model Of 9-Cis-Rhodopsin<>Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State<>Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State<>Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal Crystal Form<>Chain A, Crystal Structure Of Bovine Rhodopsin<>Chain B, Crystal Structure Of Bovine Rhodopsin<>Chain A, Crystal Structure Of The Active G-Protein-Coupled Receptor Opsin In Complex With A C-Terminal Peptide Derived From The Galpha Subunit Of Transducin\n+sp|P08100|OPSD_HUMAN\tgi|195927458|pdb|3C9M|A\t93.10\t348\t24\t0\t1\t348\t1\t348\t0.0\t674\tgi|195927458|pdb|3C9M|A\t1738\t324\t335\t0\t96.26\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t348\tChain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal Crystal Form\n' |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Thu Nov 28 12:20:59 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Mon Dec 02 10:27:05 2013 -0500 |
| b |
| b'@@ -1,10 +1,10 @@\n-gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t639\tsp|P08100|OPSD_HUMAN\t1647\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t551\tsp|P08100|OPSD_HUMAN\t1419\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t4e-67\t220\tsp|P08100|OPSD_HUMAN\t560\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t121\tsp|P08100|OPSD_HUMAN\t303\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\n-gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n-gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPW'..b'AEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t121\tsp|P08100|OPSD_HUMAN\t303\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.68\t333\t61\t0\t23\t1021\t1\t333\t0.0\t532\tsp|P08100|OPSD_HUMAN\t1371\t272\t307\t0\t92.19\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA\t1344\t348\tRhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1\n' |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 test-data/blastx_rhodopsin_vs_four_human_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Thu Nov 28 12:20:59 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Mon Dec 02 10:27:05 2013 -0500 |
| b |
| b'@@ -1,10 +1,10 @@\n-gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t 639\tsp|P08100|OPSD_HUMAN\t1647\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t 551\tsp|P08100|OPSD_HUMAN\t1419\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t4e-67\t 220\tsp|P08100|OPSD_HUMAN\t560\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t 127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t 121\tsp|P08100|OPSD_HUMAN\t303\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\n-gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t 589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n-gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t 619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQ'..b'LKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\tN/A\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t4e-67\t 220\tsp|P08100|OPSD_HUMAN\t560\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\tN/A\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t 127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\tN/A\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t 121\tsp|P08100|OPSD_HUMAN\t303\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\tN/A\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\tN/A\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\tN/A\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t 589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\tN/A\n+gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t 619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\tN/A\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.68\t333\t61\t0\t23\t1021\t1\t333\t0.0\t 532\tsp|P08100|OPSD_HUMAN\t1371\t272\t307\t0\t92.19\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA\t1344\t348\tN/A\n' |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 test-data/tblastn_four_human_vs_rhodopsin_ext.tabular --- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Thu Nov 28 12:20:59 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Mon Dec 02 10:27:05 2013 -0500 |
| b |
| b'@@ -1,10 +1,10 @@\n-sp|P08100|OPSD_HUMAN\tgi|57163782|ref|NM_001009242.1|\t96.55\t348\t12\t0\t1\t348\t1\t1044\t0.0\t 732\tgi|57163782|ref|NM_001009242.1|\t1689\t336\t343\t0\t98.56\t0\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\t348\t1047\n-sp|P08100|OPSD_HUMAN\tgi|2734705|gb|U59921.1|BBU59921\t84.80\t342\t51\t1\t1\t341\t42\t1067\t0.0\t 646\tgi|2734705|gb|U59921.1|BBU59921\t1489\t290\t320\t1\t93.57\t0\t3\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t1574\n-sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t93.24\t74\t5\t0\t239\t312\t3147\t3368\t1e-72\t 151\tgi|283855845|gb|GQ290303.1|\t342\t69\t73\t0\t98.65\t0\t3\tESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\tESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\t348\t4301\n-sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t91.53\t59\t5\t0\t177\t235\t2855\t3031\t1e-72\t 126\tgi|283855845|gb|GQ290303.1|\t284\t54\t57\t0\t96.61\t0\t2\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\t348\t4301\n-sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t96.40\t111\t4\t0\t11\t121\t1\t333\t9e-67\t 229\tgi|283855845|gb|GQ290303.1|\t523\t107\t109\t0\t98.20\t0\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\t348\t4301\n-sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t93.22\t59\t4\t0\t119\t177\t1404\t1580\t1e-32\t 122\tgi|283855845|gb|GQ290303.1|\t276\t55\t56\t0\t94.92\t0\t3\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\t348\t4301\n-sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t88.46\t26\t3\t0\t312\t337\t4222\t4299\t2e-12\t57.7\tgi|283855845|gb|GQ290303.1|\t125\t23\t24\t0\t92.31\t0\t1\tQFRNCMLTTICCGKNPLGDDEASATV\tQFRNCMLTTLCCGKNPLGDDEASTTA\t348\t4301\n-sp|P08100|OPSD_HUMAN\tgi|283855822|gb|GQ290312.1|\t95.09\t326\t16\t0\t11\t336\t1\t978\t0.0\t 658\tgi|283855822|gb|GQ290312.1|\t1517\t310\t322\t0\t98.77\t0\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\t348\t983\n-sp|P08100|OPSD_HUMAN\tgi|18148870|dbj|AB062417.1|\t93.39\t348'..b'KSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t1574\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t93.24\t74\t5\t0\t239\t312\t3147\t3368\t1e-72\t 151\tgi|283855845|gb|GQ290303.1|\t342\t69\t73\t0\t98.65\t0\t3\tESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\tESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\t348\t4301\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t91.53\t59\t5\t0\t177\t235\t2855\t3031\t1e-72\t 126\tgi|283855845|gb|GQ290303.1|\t284\t54\t57\t0\t96.61\t0\t2\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\t348\t4301\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t96.40\t111\t4\t0\t11\t121\t1\t333\t9e-67\t 229\tgi|283855845|gb|GQ290303.1|\t523\t107\t109\t0\t98.20\t0\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\t348\t4301\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t93.22\t59\t4\t0\t119\t177\t1404\t1580\t1e-32\t 122\tgi|283855845|gb|GQ290303.1|\t276\t55\t56\t0\t94.92\t0\t3\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\t348\t4301\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855845|gb|GQ290303.1|\t88.46\t26\t3\t0\t312\t337\t4222\t4299\t2e-12\t57.7\tgi|283855845|gb|GQ290303.1|\t125\t23\t24\t0\t92.31\t0\t1\tQFRNCMLTTICCGKNPLGDDEASATV\tQFRNCMLTTLCCGKNPLGDDEASTTA\t348\t4301\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|283855822|gb|GQ290312.1|\t95.09\t326\t16\t0\t11\t336\t1\t978\t0.0\t 658\tgi|283855822|gb|GQ290312.1|\t1517\t310\t322\t0\t98.77\t0\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\t348\t983\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|18148870|dbj|AB062417.1|\t93.39\t348\t23\t0\t1\t348\t1\t1044\t0.0\t 711\tgi|18148870|dbj|AB062417.1|\t1640\t325\t337\t0\t96.84\t0\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t1047\tN/A\n+sp|P08100|OPSD_HUMAN\tgi|12583664|dbj|AB043817.1|\t82.16\t342\t60\t1\t1\t341\t23\t1048\t0.0\t 626\tgi|12583664|dbj|AB043817.1|\t1444\t281\t311\t1\t90.94\t0\t2\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE\t348\t1344\tN/A\n' |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Thu Nov 28 12:20:59 2013 -0500 +++ b/tools/ncbi_blast_plus/README.rst Mon Dec 02 10:27:05 2013 -0500 |
| b |
| @@ -6,11 +6,11 @@ See the licence text below. Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 of BLAST+), -and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). +and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). Note that these wrappers (and the associated datatypes) were originally distributed as part of the main Galaxy repository, but as of August 2012 -moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). +moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``). My thanks to Dannon Baker from the Galaxy development team for his assistance with this. @@ -22,9 +22,9 @@ ====================== Galaxy should be able to automatically install the dependencies, i.e. the -'blast_datatypes' repository which defines the BLAST XML file format -('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and -'blastdbn'). +``blast_datatypes`` repository which defines the BLAST XML file format +(``blastxml``) and protein and nucleotide BLAST databases (``blastdbp`` and +``blastdbn``). You must tell Galaxy about any system level BLAST databases using configuration files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein @@ -42,9 +42,9 @@ =================== For those not using Galaxy's automated installation from the Tool Shed, put -the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML -files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample -in order to run the unit tests). For example, use:: +the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the +XML files to your ``tool_conf.xml`` as normal (and do the same in +``tool_conf.xml.sample`` in order to run the unit tests). For example, use:: <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> @@ -61,20 +61,21 @@ <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> </section> -You will also need to install 'blast_datatypes' from the Tool Shed. This -defines the BLAST XML file format ('blastxml') and protein and nucleotide -BLAST databases composite file formats ('blastdbp' and 'blastdbn'): +You will also need to install ``blast_datatypes`` from the Tool Shed. This +defines the BLAST XML file format (``blastxml``) and protein and nucleotide +BLAST databases composite file formats (``blastdbp`` and ``blastdbn``): * http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As described above for an automated installation, you must also tell Galaxy -about any system level BLAST databases using the tool-data/blastdb*.loc files. +about any system level BLAST databases using the ``tool-data/blastdb*.loc`` +files. You must install the NCBI BLAST+ standalone tools somewhere on the system path. Currently the unit tests are written using "BLAST 2.2.28+". Run the functional tests (adjusting the section identifier to match your -tool_conf.xml.sample file):: +``tool_conf.xml.sample`` file):: ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools @@ -134,6 +135,7 @@ - Pre-check for duplicate identifiers in makeblastdb wrapper. - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27 - Now depends on package_blast_plus_2_2_28 in ToolShed + - Extended tabular output includes 'salltitles' as column 25. ======= ====================================================================== @@ -157,11 +159,16 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use the following command from the GitHub repository root folder:: - $ ./ncbi_blast_plus/make_ncbi_blast_plus.sh + $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh This simplifies ensuring a consistent set of files is bundled each time, including all the relevant test files. +When updating the version of BLAST+, many of the sample data files used for +the unit tests must be regenerated. This script automates that task:: + + $ tools/ncbi_blast_plus/update_test_files.sh + Licence (MIT) ============= |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 tools/ncbi_blast_plus/blastxml_to_tabular.py --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Nov 28 12:20:59 2013 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Dec 02 10:27:05 2013 -0500 |
| [ |
| @@ -31,7 +31,7 @@ ====== ============= =========================================== Column NCBI name Description ------ ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' + 13 sallseqid All subject Seq-id(s), separated by ';' 14 score Raw score 15 nident Number of identical matches 16 positive Number of positive-scoring matches @@ -43,6 +43,7 @@ 22 sseq Aligned part of subject sequence 23 qlen Query sequence length 24 slen Subject sequence length + 25 salltitles All subject titles, separated by '<>' ====== ============= =========================================== Most of these fields are given explicitly in the XML file, others some like @@ -89,11 +90,11 @@ if out_fmt == "std": extended = False elif out_fmt == "x22": - stop_err("Format argument x22 has been replaced with ext (extended 24 columns)") + stop_err("Format argument x22 has been replaced with ext (extended 25 columns)") elif out_fmt == "ext": extended = True else: - stop_err("Format argument should be std (12 column) or ext (extended 24 columns)") + stop_err("Format argument should be std (12 column) or ext (extended 25 columns), not: %r" % out_fmt) # get an iterable @@ -230,6 +231,7 @@ if extended: try: sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >")) + salltitles = "<>".join(name.split(None,1)[1] for name in hit_def.split(" >")) except IndexError as e: stop_err("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e)) #print hit_def, "-->", sallseqid @@ -255,6 +257,7 @@ h_seq, str(qlen), str(slen), + salltitles, ]) #print "\t".join(values) outfile.write("\t".join(values) + "\n") |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Nov 28 12:20:59 2013 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Dec 02 10:27:05 2013 -0500 |
| b |
| @@ -104,13 +104,13 @@ but this takes longer to calculate. Most (but not all) of these columns are included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 22 column tabular -BLAST output. This tool now uses this extended 24 column output by default. +workflow filtering steps that accept either the 12 or 25 column tabular +BLAST output. This tool now uses this extended 25 column output by default. ====== ============= =========================================== Column NCBI name Description ------ ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' + 13 sallseqid All subject Seq-id(s), separated by ';' 14 score Raw score 15 nident Number of identical matches 16 positive Number of positive-scoring matches @@ -122,6 +122,7 @@ 22 sseq Aligned part of subject sequence 23 qlen Query sequence length 24 slen Subject sequence length + 25 salltitles All subject titles, separated by '<>' ====== ============= =========================================== Beware that the XML file (and thus the conversion) and the tabular output |
| b |
| diff -r 1b8a92016045 -r 8f9023b30384 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Thu Nov 28 12:20:59 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon Dec 02 10:27:05 2013 -0500 |
| b |
| @@ -267,9 +267,9 @@ #end if </token> <token name="@BLAST_OUTPUT@">-out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected +##Set the extended list here so when we add things, saved workflows are not affected #if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles" #else: -outfmt $out_format #end if @@ -333,13 +333,13 @@ but this takes longer to calculate. Most (but not all) of these columns are included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. +workflow filtering steps that accept either the 12 or 25 column tabular +BLAST output. Galaxy now uses this extended 25 column output by default. ====== ============= =========================================== Column NCBI name Description ------ ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' + 13 sallseqid All subject Seq-id(s), separated by ';' 14 score Raw score 15 nident Number of identical matches 16 positive Number of positive-scoring matches @@ -351,6 +351,7 @@ 22 sseq Aligned part of subject sequence 23 qlen Query sequence length 24 slen Subject sequence length + 25 salltitles All subject titles, separated by '<>' ====== ============= =========================================== The third option is BLAST XML output, which is designed to be parsed by |