Our Sponsors



Download BioinformaticsOnline(BOL) Apps in your chrome browser. BOLChromeApps

Freelancer

AdvertiseWithUs

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) ); }