[Bioperl-l] FASTA parsing

simona bazzocchi simona_bazzocchi at yahoo.it
Tue Sep 19 18:54:53 EDT 2006


Hi, I have a problem.
I need to filter just the query sequences that match
with the first 4 bases vs library sequences.
I used FASTA to get the output (FASTA_RESULTS104.txt)
using my perl script below, but now I don't know how i
can filter that output.
I read the Bio::SearchIO manual but it's not so clear
to me.
Have you any idea?
Thank you very much
Simona 

#!/usr/bin/perl -w
use strict;
my $location="/home/kei/fasta/fasta34";
my $library="DNAUS.txt";
my $query="mature2.txt";
my $ktup=1;
my $options="-r +5/-4 -H -w 100 -m 9 -f -12 -g -4 -q";
my $command="$location $options $query $library
$ktup";
my $output = `$command`;
open FASTA,">>","FASTA_RESULTS104.txt";
print FASTA $output;
close (FASTA);


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