perl_ver

#!/usr/bin/perl
use strict;

open( IN_P1, "/Users/John/Desktop/ENCFF001LCU.fq" ) or die "File not found";
$| = 1;
my $yup = 0;
my $barcode1 = 'AATTCCGGAATT';
my $barcode1_regex = make_barcode_fragments( $barcode1 );

while ( defined( my $firstp1 = <IN_P1> ) ) {
    my $p1_first_line  = $firstp1;
    my $p1_second_line = <IN_P1>;
    my $p1_third_line  = <IN_P1>;
    my $p1_fourth_line = <IN_P1>;
    chomp( $p1_first_line, $p1_second_line, $p1_third_line, $p1_fourth_line, );
    my $matched_R1 = "$p1_first_line\n$p1_second_line\n$p1_third_line\n$p1_fourth_line\n";
    if ( $p1_second_line =~ /$barcode1_regex/i ) { $yup++; }
}

# make two mismatch patterm of barcode
sub make_barcode_fragments {
    my ($in1) = @_;
    my @subpats;
    for my $i ( 0 .. length($in1) - 1 ) {
        for my $j ( $i + 1 .. length($in1) - 1 ) {
            my $subpat = join( '',
                substr( $in1, 0, $i ),
                '\\w', substr( $in1, $i + 1, $j - $i - 1 ),
                '\\w', substr( $in1, $j + 1 ),
            );
            push @subpats, $subpat;
        }
    }
    my $pat = join( '|', @subpats );

    #print $pat;
    return "$pat";
}
print $yup;
exit;