53 lines
1.2 KiB
Perl
53 lines
1.2 KiB
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use FindBin;
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use lib ("$FindBin::RealBin/../../PerlLib");
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use Fastq_reader;
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my $usage = "\n\nusage: $0 interleaved.fq [left_output_filename.fq right_output_filename.fq]\n\n";
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my $interleaved_fq = $ARGV[0] or die $usage;
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my $left_out_filename = $ARGV[1] || "unweaved.left.$$.fq";
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my $right_out_filename = $ARGV[2] || "unweaved.right.$$.fq";
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main: {
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my $fastq_reader = new Fastq_reader($interleaved_fq);
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open (my $left_ofh, ">$left_out_filename") or die "Error, cannot write to $left_out_filename";
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open (my $right_ofh, ">$right_out_filename") or die "Error, cannot write to $right_out_filename";
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while (my $fq = $fastq_reader->next()) {
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my $read_name = $fq->get_full_read_name();
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my $record = $fq->get_fastq_record();
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if ($read_name =~ m|/1$|) {
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print $left_ofh $record;
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}
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elsif ($read_name =~ m|/2$|) {
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print $right_ofh $record;
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}
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else {
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die "Error, cannot decipher left or right read from name: $read_name";
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}
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}
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close $left_ofh;
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close $right_ofh;
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print "Done.\n";
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exit(0);
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}
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