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Extract the fastq sequence with range in Perl

  • Public
By Neelam Jha 55 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);