BOL: Extract the fastq sequence with range in Perl

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Neel
Extract the fastq sequence with range in Perl

Extract the fastq sequence with range in Perl

By Neel 2703 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);