BOL: Extract the fastq sequence with range in Perl

BioScripts
Neel
Extract the fastq sequence with range in Perl

Extract the fastq sequence with range in Perl

By Neel 2669 days ago

use Bio::DB::Fasta;
open(POSITIONS,"positions.txt");
while(<POSITIONS>){
    chomp;
    my ($seqName,$begin,$end) = split(/\s/);
    my $db = Bio::DB::Fasta->new('allGenomeContacted.fa');
	my $seq = $db->seq("$seqName", $begin => $end);
	print "$seq\n";
}
close(POSITIONS);