[Bioperl-l] Strangeness in parsing blast file

[Torsten Seemann]

> sub do_blast {
>    my $bf = shift;
>    my $blastoutput = $bf . ".blastout";
>     print "Blasting against $db ...\n";
>    `blast/blast-2.2.10/bin/megablast -d /prodinfo/proddata_ntblastdb/nt 
> -e 1e-50 -p 99 -D 2 -i test -o test.blastout`;
 >     return $blastoutput;
 > }#end do_blast

Should "-o test.blastoutput" be "-o $blastoutput" ?

Otherwise you are returning the name of a non-existent file, which naturally 
Bio::SearchIO will not be able to find a blast result in.

Alternatively use Bio::Tools::Run::StandaloneBlast to invoke megablast rather 
than back-ticks - that way you avoid any intermediate file and get a 
Bio::SearchIO object back directly.

--Torsten