BOL: Extract a range from genome file with perl.

BioScripts
Abhimanyu Singh
Extract a range from genome file with perl.

Extract a range from genome file with perl.

#!/usr/bin/perl 

use strict;
use warnings;
use Bio::SeqIO;

my $in_file = $ARGV[0];
my $start_pos = $ARGV[1];
my $end_pos = $ARGV[2];

my $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fasta');
my $out = Bio::SeqIO->new( -file => ">$in_file.out", -format => 'fasta');


while (my $seq = $in->next_seq() ) {

    $seq->display_id( $seq->display_id() . "_$start_pos-$end_pos" );
    $out->write_seq( $seq->trunc($start_pos, $end_pos) );
}

BOL

Abhimanyu Singh

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Extract a range from genome file with perl.