20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,143 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Carp;
+use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
+
+use FindBin;
+use lib("$FindBin::Bin/../../PerlLib");
+use Fastq_reader;
+use Data::Dumper;
+
+my $help_flag;
+
+my $usage = <<__EOUSAGE__;
+
+#############################################################################################
+#
+# --samples_file <string>      samples.txt
+#
+# --output_prefix <string>     outputs will be named <string>.left.fq and <string>.right.fq
+#
+#############################################################################################
+
+
+
+__EOUSAGE__
+
+    ;
+
+
+my $samples_file;
+my $output_prefix;
+
+&GetOptions ( 'h' => \$help_flag,
+              'samples_file=s' => \$samples_file,
+              'output_prefix=s' => \$output_prefix,
+    );
+
+unless ($samples_file && $output_prefix) {
+    die $usage;
+}
+
+main: {
+    
+    my @samples = &parse_samples_file($samples_file);
+
+    # init fq readers    
+    foreach my $sample (@samples) {
+        my $left_fq = $sample->{left_fq};
+        my $left_fq_reader = new Fastq_reader($left_fq);
+        $sample->{left_fq_reader} = $left_fq_reader;
+
+        my $right_fq = $sample->{right_fq};
+        my $right_fq_reader = new Fastq_reader($right_fq);
+        $sample->{right_fq_reader} = $right_fq_reader;
+    }
+
+    # open output files:
+    my $left_fq_outfile = "$output_prefix.left.fq";
+    open(my $left_ofh, ">$left_fq_outfile") or die "Error, cannot write to $left_fq_outfile";
+
+    my $right_fq_outfile = "$output_prefix.right.fq";
+    open(my $right_ofh, ">$right_fq_outfile") or die "Error, cannot write to $right_fq_outfile";
+    
+    my $samples_remaining = scalar(@samples);
+
+    my $counter = 0;
+    while($samples_remaining != 0) {
+                
+        $samples_remaining = 0;
+        
+        foreach my $sample (@samples) {
+
+            if ($sample->{done}) { next; }
+            
+            my $sample_name = $sample->{sample_name};
+            
+            my $left_fq_reader = $sample->{left_fq_reader};
+            my $left_fq_entry = $left_fq_reader->next();
+
+            my $right_fq_reader = $sample->{right_fq_reader};
+            my $right_fq_entry = $right_fq_reader->next();
+
+            if ($left_fq_entry xor $right_fq_entry) {
+                confess "Error, found left_fq entry but not right_fq entry: " . Dumper([$sample, $left_fq_entry, $right_fq_entry]);
+            }
+            elsif ($left_fq_entry && $right_fq_entry) {
+                                
+                print $left_ofh $left_fq_entry->get_fastq_record();
+                print $right_ofh $right_fq_entry->get_fastq_record();
+                
+                $samples_remaining = 1;
+                
+                $counter++;
+                
+                if ($counter % 100000 == 0) {
+                    print STDERR "\r[$counter]        ";
+                }
+                
+            }
+            else {
+                $sample->{done} = 1;
+                $sample->{left_fq_reader}->finish();
+                $sample->{right_fq_reader}->finish();
+            }
+            
+        }
+
+    } # end of while samples remaining
+
+    close $left_ofh;
+    close $right_ofh;
+
+    print STDERR "\n\nDone. Output $counter fastq records per file.\n";
+    
+    exit(0);
+    }
+
+
+
+
+####
+sub parse_samples_file {
+    my ($samples_file) = @_;
+
+    my @samples;
+    
+    open(my $fh, $samples_file) or die "Error, cannot open file: $samples_file";
+    while(<$fh>) {
+        chomp;
+        my ($sample_name, $left_fq, $right_fq) = split(/\t/);
+        push (@samples, { sample_name => $sample_name,
+                          left_fq => $left_fq,
+                          right_fq => $right_fq,
+              } );
+    }
+
+    close $fh;
+
+    return(@samples);
+}
+