[Bioperl-l] Easily parsable command line BLAST output
cjfields at illinois.edu
Fri Oct 2 12:43:50 EDT 2009
The following has that information:
-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.
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
> parsable by Bio::SearchIO.
> Economically, nothing is ever "extended by popular demand".
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> Bioperl-l at lists.open-bio.org
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