[Bioperl-l] Strangeness in parsing blast file

[Nabil Hafez]

I had modified the variables a bit to try and make them more readable 
than what is in my code, in my code -o $blastoutput is
what it is, like I said, the blast portion works absolutely fine - i.e. 
the do_blast sub routine is fully functional. 

here's a cut and paste from my actual code

my $MBLAST = "/prodinfo/prod3pty/blast/blast-2.2.10/bin/megablast";
my $blastdb = "/prodinfo/proddata_ntblastdb/nt";
my $e_val = "1e-50"; #Default e-value Getopt_long
my $percent_id = "99"; #Default percentage identity
my $per_to_sample ="10"; #Default for percentage of reads to sample

sub do_blast {
   my $bf = shift;
   my $blastoutput = $bf . ".blastout";

    print "Blasting against $db ...\n";
   `$MBLAST -d $blastdb -e $e_val -p $percent_id -D 2 -i $bf -o 
$blastoutput`;

    return $blastoutput;
}

I will try your suggestion to use the Bio::Tools::Run::StandaloneBlast, 
is megablast supported by this module?
Thanks
Nabil

Torsten Seemann wrote:

>
>> 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
>