[Bioperl-l] automated stand alone blast with repeat masker

[vdar at yorku.ca]

Following is the path to repeatmasker.pm on my system

/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/RepeatMasker.pm

but when I run my program, the error message comes

RepeatMasker program not found as  or not executable

Here is my piece of code which gives this error,
#!/usr/bin/perl

use strict;
use warnings;

use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Search::Hit::HitI;
use Bio::Search::Hit::BlastHit;
use Bio::Search::HSP::BlastHSP;
use Bio::Search::HSP::HSPI;
use Bio::SearchIO;
use Bio::Tools::Run::RepeatMasker;

BEGIN {

	$ENV{REPEATMASKERDIR} = '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';

 }


my @params = ("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
my $in  = Bio::SeqIO->new(-file => "boechera.fasta", -format => 'fasta');

I tried finding RepeatMasker directory by typing

which RepeatMasker

but the error message was

/usr/bin/which: no RepeatMasker in
(/opt/openmpi/1.1.4/bin:/opt/lsfhpc/ego/1.2/linux2.6-glibc2.3-x86_64/etc:/opt/lsfhpc/ego/1.2/linux2.6-glibc2.3-x86_64/bin:/opt/lsfhpc/7.0/linux2.6-glibc2.3-x86_64/etc:/opt/lsfhpc/7.0/linux2.6-glibc2.3-x86_64/bin:/usr/kerberos/bin:/usr/java/jdk1.5.0_07/bin:/share/iNquiry/biotools/bin:/share/iNquiry/bin/lx24-x86:/share/iNquiry/bin/lx24-amd64:/opt/Bio/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/modules/current/bin/:/opt/modules/bin/:/opt/Bio/glimmer/scripts:/opt/Bio/gromacs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/maven/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/vdar/bin)





Quoting Dave Messina <David.Messina at sbc.su.se>:

> I haven't done this myself, but from a quick search on the BioPerl website,
> it looks like you'll want to use the
>
Bio::Tools::Run::RepeatMasker<http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/RepeatMasker.html>module
> to create a repeat-masked fasta file.
>
> If you RepeatMask your query sequence(s), then you need to specify that
> sequence when you create your Bio::Seq object.
>
> If you instead RepeatMask your database, you'll need to create a blast
> database from the repeat-masked sequences and specify that db in your
> @params. I don't think there's a module for running formatdb, but you can do
> it through a system call.
>
>
>
> Dave
>