Re: [Gusdev-gusdev] LoadBlastSimFast plugin

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Sucheta-

At first glance, the output looks ok, so let's assume Michael's script 
works.

similarities are between two things, the query (your sequence) and the 
subject (the sequences you are blasting against).

the querytable is the table that holds the sequences you are blasting.

the subjecttable is the table that holds the sequences you are blasting 
against.

--file is the arg that you pass the file to.

hope that helps,
steve

Sucheta Tripathy wrote:

> 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
>
>
>
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