Extract the fastq sequence with range in Perl

Neel — Wed, 02 Aug 2017 04:29:06 -0500

use Bio::DB::Fasta;
open(POSITIONS,"positions.txt");
while(){
    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);

BOL: Extract the fastq sequence with range in Perl

Extract the fastq sequence with range in Perl