#!/usr/bin/perl

sub read_fasta {
	my $filename = $_[0];
	my @LINES;
	if ( defined ( $filename ) ) {
		open FASTA, $filename or die("Unable to open FASTA.\n");
		while (<FASTA>) {
			push @LINES , $_;
		}
		close FASTA;
	} else {
		while (<STDIN>) {
			push @LINES , $_;
		}
	}
	my @fasta;
	my $seqentry = -1;
	foreach my $line ( @LINES ) {
		chomp $line;
		if ($line=~ m/^>(.*)/) {
			$seqentry++;
			my $id = $1 if $line =~ /^>(\S+)/;
			my $comment = $1 if $line =~ /^>\S+\s+(.*)/;
			$fasta[$seqentry]{comment} = $comment if defined $comment;
			$fasta[$seqentry]{seqentry} = $seqentry;
			$fasta[$seqentry]{id} = $id;
		} elsif ($line =~ m/^([A-Za-z\-]+)/) {
				$fasta[$seqentry]{seq} .= uc ( $1 );
		}
	}
	return @fasta;
}

1;