BOL: Perl subroutine to read genome/reads fasta file !

BioScripts
Rahul Nayak
Perl subroutine to read genome/reads fasta file !

Perl subroutine to read genome/reads fasta file !

By Rahul Nayak 2334 days ago

sub readSeqFromFasta{
	my $file = $_[0];
	my (%map,$id,$seq);
	open(IN,$file) or die("Cannot open file for reading $file:$!\n");
	while(<IN>){
		chomp;
		if($_ =~ /^>/){
			if(defined $id && defined $seq){
				$map{$id} = $seq;
				$seq="";
			}
			($id) = split(' ',$_);
			$id=~s/>//;
		}
		else {
			$seq=$seq.$_;
		}
	}
	$map{$id} = $seq;
	close(IN);
	return \%map;

}