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

Neil Saunders neil.saunders at unsw.edu.au
Wed Nov 10 01:16:15 EST 2004

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' 

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


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