[Bioperl-l] parsing output files from other tools

[Chris Fields]

These are the current report types parsed through SearchIO:

http://www.bioperl.org/wiki/Module:Bio::SearchIO

I don't see mpsrch among them.  If you want you could create a new plugin
module to parse those reports; the SearchIO HOWTO gives some pointers:

http://www.bioperl.org/wiki/HOWTO:SearchIO

You can always look at some of the current modules like blast, blastxml, or
fasta to get an idea of how it works.  Judging by the mpsrch output I'm
pretty sure you would have to build a custom plugin for it.  

A viable alternative: looking through the mail list it looks like mpsrch is
a multiprocessor implementation of ssearch, itself an implementation of the
Smith-Waterman algorithm for local alignments in the FASTA package of
programs:

http://www.bioperl.org/wiki/SSEARCH

You might be able to use SearchIO::fasta there...

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hubert Prielinger
> Sent: Saturday, May 13, 2006 10:46 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] parsing output files from other tools
> 
> hi,
> Is it possible to parse text outputfiles rather than blast output files,
> like the text outputfiles form the search tool mpSrch that is offered by
> EBI, because the WU Blast output files are possible to parse with bioperl.
> 
> thanks
> Hubert
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