From: Sucheta T. <su...@vb...> - 2004-07-06 21:39:05
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I am trying to load a bunch of blast output files using the LoadBlastSimFast plugin. First I have parsed the blast output with a script 'ParseFileForSimilarity.pl' I obtained from Michael. As I see from the plugin comments, the blast output need to be parsed by a script 'generateBlastSimilarity.pl'. I am not sure if both the parsing scripts do the same job.. I am not sure for the LoadBlastSimFast plugin what value should I pass for --QueryTable and --SubjectTable and Which parameter takes the parsed blast output file. My blast output is currently formatted into the following fileds using ParseFileForSimilarity: Cutoff parameters: P value: 1e-05 Length: 10 Percent Identity: 20 >CL1Contig2 (35 subjects) Sum: AAA83776.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3 HSP1: AAA83776.1:54:63:83:99:6e-20:54:133:30:278:0:+3 Sum: XP_342001.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3 HSP1: XP_342001.1:54:63:83:99:6e-20:54:133:30:278:0:+3 Sum: AAB52915.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3 HSP1: AAB52915.1:54:63:83:99:6e-20:54:133:30:278:0:+3 Sum: NP_032016.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3 HSP1: NP_032016.1:54:63:83:99:6e-20:54:133:30:278:0:+3 Sum: NP_001988.1:99:6e-20:54:133:30:278:1:83:54:63:0:+3 HSP1: NP_001988.1:54:63:83:99:6e-20:54:133:30:278:0:+3 Sum: XP_345683.1:99:6e-20:72:151:30:278:1:83:54:63:0:+3 HSP1: XP_345683.1:54:63:83:99:6e-20:72:151:30:278:0:+3 Sum: BAB68608.1:99:6e-20:58:137:30:278:1:83:54:63:0:+3 HSP1: BAB68608.1:54:63:83:99:6e-20:58:137:30:278:0:+3 Sum: NP_777156.1:97:2e-19:54:133:30:278:1:83:53:63:0:+3 HSP1: NP_777156.1:53:63:83:97:2e-19:54:133:30:278:0:+3 Sum: NP_598374.1:97:2e-19:54:132:30:275:1:82:53:62:0:+3 HSP1: NP_598374.1:53:62:82:97:2e-19:54:132:30:275:0:+3 Sum: AAQ63318.1:96:3e-19:53:133:27:278:1:84:54:64:0:+3 HSP1: AAQ63318.1:54:64:84:96:3e-19:53:133:27:278:0:+3 Sum: BAB68610.1:96:4e-19:58:137:30:278:1:83:53:62:0:+3 HSP1: BAB68610.1:53:62:83:96:4e-19:58:137:30:278:0:+3 Sum: AAK95215.1:93:3e-18:54:133:30:278:1:83:54:60:0:+3 HSP1: AAK95215.1:54:60:83:93:3e-18:54:133:30:278:0:+3 Sum: AAN05597.1:90:2e-17:51:131:27:278:1:84:52:61:0:+3 HSP1: AAN05597.1:52:61:84:90:2e-17:51:131:27:278:0:+3 Sum: NP_505007.1:90:2e-17:51:130:30:278:1:83:51:62:0:+3 HSP1: NP_505007.1:51:62:83:90:2e-17:51:130:30:278:0:+3 Sum: AAL49305.2:90:3e-17:86:146:90:278:1:63:47:52:0:+3 HSP1: AAL49305.2:47:52:63:90:3e-17:86:146:90:278:0:+3 Sum: NP_650922.1:90:3e-17:71:131:90:278:1:63:47:52:0:+3 HSP1: NP_650922.1:47:52:63:90:3e-17:71:131:90:278:0:+3 Sum: AAK92197.1:89:6e-17:71:131:90:278:1:63:47:52:0:+3 HSP1: AAK92197.1:47:52:63:89:6e-17:71:131:90:278:0:+3 Sum: XP_343942.1:86:3e-16:68:144:30:278:1:83:50:58:0:+3 HSP1: XP_343942.1:50:58:83:86:3e-16:68:144:30:278:0:+3 Sum: Q05472:86:4e-16:1:59:96:278:1:61:46:50:0:+3 HSP1: Q05472:46:50:61:86:4e-16:1:59:96:278:0:+3 Sum: XP_311180.1:85:7e-16:61:139:42:281:1:81:48:60:0:+3 HSP1: XP_311180.1:48:60:81:85:7e-16:61:139:42:281:0:+3 Sum: CAC86461.1:84:2e-15:2:61:93:278:1:62:46:51:0:+3 HSP1: CAC86461.1:46:51:62:84:2e-15:2:61:93:278:0:+3 Sum: NP_473105.1:81:9e-15:2:58:93:278:1:62:45:47:0:+3 HSP1: NP_473105.1:45:47:62:81:9e-15:2:58:93:278:0:+3 Sum: NP_194668.1:80:2e-14:2:66:93:275:2:122:88:94:0:+3 HSP1: NP_194668.1:44:47:61:80:2e-14:2:60:93:275:0:+3 HSP2: NP_194668.1:44:47:61:80:2e-14:8:66:93:275:0:+3 Sum: CAD98413.1:80:3e-14:3:58:96:272:1:59:44:47:0:+3 HSP1: CAD98413.1:44:47:59:80:3e-14:3:58:96:272:0:+3 Sum: O22424:80:3e-14:1:259:195:971:1:259:169:209:1:-1 HSP1: O22424:169:209:259:80:3e-14:1:259:195:971:1:-1 Sum: P47961:80:3e-14:1:253:213:971:1:253:164:204:1:-1 Thanks Sucheta |