import gzip
import argparse
def extract_gene_names(input_fastq_gz, output_file):
    with gzip.open(input_fastq_gz, 'rt') as fastq_gz, open(output_file, 'w') as out_file:
        line_count = 0
        for line in fastq_gz:
            line_count += 1
            if line_count % 4 == 1:
                gene_name = line.strip().split()[0]
                out_file.write(gene_name + '\n')
def main():
    parser = argparse.ArgumentParser(description='Extract gene names from a gzipped fastq file.')
    parser.add_argument('input_fastq_gz', help='Path to the input fastq.gz file')
    parser.add_argument('output_file', help='Path to the output file containing gene names')
    args = parser.parse_args()
    extract_gene_names(args.input_fastq_gz, args.output_file)
if __name__ == '__main__':
    main()

use Bio::SeqIO;
use Bio::Seq;
use Term::ProgressBar;

if (@ARGV == 3) {
    my ($id_file, $fq1_file, $out1_file) = @ARGV;

    filter_fastq($id_file, $fq1_file, $out1_file);

} elsif (@ARGV == 5) {
    my ($id_file, $fq1_file, $fq2_file, $out1_file, $out2_file) = @ARGV;

    filter_fastq($id_file, $fq1_file, $out1_file, $fq2_file, $out2_file);

} else {
    die "Usage: perl $0 <id> <fq1> [<fq2>] <OUT1> [<OUT2>]\n";
}

sub filter_fastq {
    my ($id_file, $fq1_file, $out1_file, $fq2_file, $out2_file) = @_;

    my %keep;
    open my $ID, $id_file or die "Cannot open ID file: $id_file\n";
    while (<$ID>) {
        chomp;
        next if /^#/;
        my @tmp = split(/\s+/);
        my ($cleaned_id) = $tmp[0] =~ /([^@]+)/; # 移除 "@" 符号
        $keep{$cleaned_id} = 1;
    }
    close($ID);

    process_fastq_file($fq1_file, $out1_file, \%keep, "Read 1");

    if (defined $fq2_file && defined $out2_file) {
        process_fastq_file($fq2_file, $out2_file, \%keep, "Read 2");
    }
}

sub process_fastq_file {
    my ($input_file, $output_file, $keep_ref, $read_label) = @_;

    open my $FQ, "zcat $input_file |" or die "Cannot open input file: $input_file\n";
    open my $GZ, "| gzip >$output_file" or die "Cannot open output file: $output_file\n";

    my $fq_in  = Bio::SeqIO->new(-fh => $FQ, -format => 'fastq');
    my $fq_out = Bio::SeqIO->new(-fh => $GZ, -format => 'fastq');

    my $total_seqs = `zcat $input_file | grep -c "^@"`; # Count total sequences in the input file
    chomp($total_seqs);

    my $progress = Term::ProgressBar->new({name => $read_label, count => $total_seqs, ETA => 'linear'});
    $progress->minor(0); # Disabling minor updates for better performance

    my $count = 0;

    while (my $seq_obj = $fq_in->next_seq()) {
        my $id = $seq_obj->id;
        my ($cleaned_id) = $id =~ /([^@]+)/; # 移除 "@" 符号

        if (exists $keep_ref->{$cleaned_id}) {
            $fq_out->write_seq($seq_obj);
        }

        $count++;
        $progress->update($count);
    }

    $progress->update($total_seqs); # Ensure the progress bar reaches 100%

    close($FQ);
    close($GZ);
}