[Bioperl-l] Fix for Bio::Tools::Blat

[Brian Osborne]

Neil,

I've added your patch, please check it to see that I've put it in the proper
place.

Pardon my ignorance but why do you use Tools::Blat rather than
SearchIO::psl?


Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Neil Saunders
Sent: Wednesday, November 10, 2004 1:16 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Fix for Bio::Tools::Blat

dear all,

I mentioned in a previous post that Bio::Tools::Blat has a problem with
"tblastx-like" blat output (i.e. using the -t=dnax -q=dnax options).
This generates PSL files with 2 strands in the 'strand' column - one
for query, one for target (e.g. ++).  If you use the next_result()
method of Bio::Tools::Blat.pm on such files, you get errors like:

Argument "++" isn't numeric in numeric ne (!=) at
/usr/local/share/perl/5.8.4/Bio/Location/Atomic.pm line 170, <GEN0>
line 228.


I have added the following lines to my Blat.pm:

if($strand =~/([+-])[+-]/) {
$strand = $1;
}

which seems to fix it up.  Perhaps we could make this an 'official'
fix?


Neil
--
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php
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