Raku script to find SSRs in fastq file !

LEGE — Sun, 14 Jan 2024 12:05:24 -0600

sub find-ssrs(Str $sequence) {
    my @ssrs;

    for 2..$sequence.chars -> $min-repeats {
        for $sequence.chars...$min-repeats -> $max-repeat {
            my $repeat = $sequence.substr($min-repeats - 1, $max-repeat - $min-repeats + 1);
            my $repeat-length = $max-repeat - $min-repeats + 1;

            if $sequence.substr($max-repeat).index($repeat) == 0 {
                push @ssrs, {
                    start   => $min-repeats,
                    end     => $max-repeat,
                    length  => $repeat-length,
                    sequence => $repeat
                };
            }
        }
    }

    return @ssrs;
}

sub process-fastq-file(Str $filename) {
    my $fh = open $filename, :r;

    my $line-number = 0;
    while $fh.readline -> $header {
        $line-number++;
        my $sequence = $fh.readline.chomp;

        # Skipping the next two lines (comment and quality lines)
        $fh.readline;
        $fh.readline;

        my @ssrs = find-ssrs($sequence);

        if @ssrs {
            say "SSRs found in sequence at line $line-number:";
            for @ssrs -> $ssr {
                say "  Start: $ssr, End: $ssr, Length: $ssr, Sequence: $ssr";
            }
        }
    }

    $fh.close;
}

# Replace 'your_fastq_file.fastq' with the path to your FASTQ file
process-fastq-file('your_fastq_file.fastq');

BOL: Raku script to find SSRs in fastq file !

Raku script to find SSRs in fastq file !