Easily parsable command line BLAST output

[Ben Busby]

Pardon the simple question, as I am new-ish to Perl, Bioperl, and
Computational Biology..
I am doing a whole bunch of large BLAST searches and am wondering what the
best command line BLAST commands are to put the output in a format best
parsable by Bio::SearchIO.

Thanks!

Ben



--
Economically, nothing is ever "extended by popular demand".
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[Jason Stajich-3]

Depends on what information you want to parse out.... do you need the  
actual alignment?  If no -> use -m 8 or -m 9 and you will have a  
tabular output that is easy to parse even without bioperl.

On Oct 2, 2009, at 9:29 AM, Ben Busby wrote:

> Pardon the simple question, as I am new-ish to Perl, Bioperl, and
> Computational Biology..
> I am doing a whole bunch of large BLAST searches and am wondering  
> what the
> best command line BLAST commands are to put the output in a format  
> best
> parsable by Bio::SearchIO.
>
> Thanks!
>
> Ben
>
>
>
> --
> Economically, nothing is ever "extended by popular demand".
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich@...
jason@...

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[Chris Fields-5]

Ben,

The following has that information:

http://www.bioperl.org/wiki/Module:Bio::SearchIO
http://www.bioperl.org/wiki/HOWTO:SearchIO#Design

In short:

-m      type       SearchIO -format
0       text       blast
7       XML        blastxml
8       tabular    blasttable
9       tabular    blasttable

You should read the HOWTO and specific documentation for the  
Bio::SearchIO module just in case, and let us know if there are any  
spots that need improvement.

There are varied reports some of the alignment-based output is  
parsable via AlignIO somehow, but I haven't attempted it.

chris

On Oct 2, 2009, at 11:29 AM, Ben Busby wrote:

> Pardon the simple question, as I am new-ish to Perl, Bioperl, and
> Computational Biology..
> I am doing a whole bunch of large BLAST searches and am wondering  
> what the
> best command line BLAST commands are to put the output in a format  
> best
> parsable by Bio::SearchIO.
>
> Thanks!
>
> Ben
>
>
>
> --
> Economically, nothing is ever "extended by popular demand".
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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