20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,77 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 inputFile out.cleanReads out.malformedReads\n\n";
+
+my $inputFile = $ARGV[0] or die $usage;
+my $cleanReads = $ARGV[1] or die $usage;
+my $malformedReads = $ARGV[2] or die $usage;
+
+
+open (my $ofh_clean, ">$cleanReads") or die "Error, can't write to $cleanReads";
+open (my $ofh_malformed, ">$malformedReads") or die "Error, cannot write to $malformedReads";
+
+open (my $fh, $inputFile) or die "Error, cannot open $inputFile";
+
+my $counter = 0;
+my $num_clean = 0;
+my $num_dirty = 0;
+
+my @rec;
+
+my $line = <$fh>;
+
+while ($line) {
+
+	if ($line =~ /^\@/) {
+		$counter++;
+		
+		print STDERR "\r[$counter] [$num_clean clean] [$num_dirty dirty]       " if ($counter % 10000 == 0);
+		
+		push (@rec, $line);
+		
+		$line = <$fh>;
+		for (1..3) {
+			push (@rec, $line);
+			$line = <$fh>;
+		}
+		
+		my $record_text = join("", @rec);
+
+		my $header = shift @rec;
+		my $seq = shift @rec;
+		my $qual_header = shift @rec;
+		my $qual_line = shift @rec;
+				
+		chomp $header;
+		chomp $seq if $seq;
+		chomp $qual_header if $qual_header;
+		chomp $qual_line if $qual_line;
+		
+		if ($header && $seq && $qual_header && $qual_line && 
+			$qual_header =~ /^\+/ && length($seq) == length($qual_line)) {
+			
+			# can do some more checks here if needed to be sure that the lines are formatted as expected.
+			print $ofh_clean join("\n", $header, $seq, $qual_header, $qual_line) . "\n";
+			$num_clean++;
+		}
+		else {
+			print $ofh_malformed $record_text;
+			$num_dirty++;
+		}
+		@rec = ();
+	} else {
+		$line = <$fh>;
+	}
+	
+}
+
+exit(0);
+
+
+		
+		
+		
+