Fasta 读写

InputAndOutputFa.pl

### Read Fa sequence ###
sub ReadFaSeq {

    my ( $file, $fa ) = @_;

    my ( $refId, $seq );
    open I, $file or die "Cannot open file : $file\n";

    $/ = ">"; <I>; $/ = "\n";
    while ( <I> ) {
        chomp;
        $refId = ( split /\s+/ )[0];
        $/ = ">"; chomp( $seq = <I> ); $/ = "\n";
        $seq =~ s/\s+//g;
        $$fa{$refId} = $seq;
    }
    close I;
}

### Output Fa Sequence ####
sub OutputFa {

    my ( $id, $lineLength, $seq ) = @_;

    my $i= 0;
    print "$id\n";
    for (; $i < length( $$seq ); $i += $lineLength ) {

        print substr($$seq, $i, $lineLength );
        print "\n";
    }
}