[Bioperl-l] Bio::Index::Blast bug

Till Bayer till.bayer at kaust.edu.sa
Wed Mar 10 03:20:15 EST 2010

Hi all!

I tried to use Bio::Index::Blast, but always got the first hit back, no 
matter what ID I used. The reason is that the Blast indexer seems to use 
'BLAST' as a record separator in all cases, except for RPS-BLAST.
I think however that for the current versions of blastall and blast+ 
'Query=' should be used.
Thus, changing line 222 in Blast.pm from

$indexpoint = tell($BLAST) - length $_ if ( $prefix eq 'RPS-' );


$indexpoint = tell($BLAST) - length $_;

makes it work for me.
However I have no idea what RPS-BLAST may be, or what different versions 
of blast output are used, so maybe someone who knows should have a look 
at that before changing things, and writing a cleaner version than the 
above hack.


Till Bayer
4700 King Abdullah University for Science and Technology
Building 2, Room 4231-W16
Thuwal 23955-6900
Saudi Arabia
Phone: +96628082373

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