20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,111 @@
+#!/usr/bin/env perl
+
+## util/fastQ_rand_subset.pl
+## Purpose: Extracts out a specific number of random reads from an
+##   input file, making sure that left and right ends of the selected
+##   reads are paired
+## Usage: $0 left.fq right.fq num_entries
+##
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use Fastq_reader;
+use File::Basename;
+use List::Util qw(shuffle);
+use Data::Dumper;
+
+my $usage = "usage: $0 left.fq right.fq num_entries num_total_records\n\n";
+
+my $left_fq = $ARGV[0] or die $usage;
+my $right_fq = $ARGV[1] or die $usage;
+my $num_entries = $ARGV[2] or die $usage;
+my $num_total_records = $ARGV[3] or die $usage;
+
+
+main: {
+
+    srand();
+    my @selected_indices = &get_random_indices($num_entries, $num_total_records);
+    
+    if (scalar(@selected_indices) != $num_entries) {
+        die "Error, get_random_indices returned "  . scalar(@selected_indices) . " instead of $num_total_records";
+    }
+    else {
+        print STDERR "-selected  $num_entries indices. Now outputting selected records\n";
+    }
+    
+    my %selected = map { + $_ => 1 } @selected_indices;
+
+    @selected_indices = ();
+    
+    print STDERR "Selecting $num_entries entries...";
+    
+    my $left_fq_reader = new Fastq_reader($left_fq) or die("unable to open $left_fq for input");
+    my $right_fq_reader = new Fastq_reader($right_fq) or die("unable to open $right_fq for input");;
+    
+    my $num_M_entries = $num_entries/1e6;
+    $num_M_entries .= "M";
+    my $base_left_fq = basename($left_fq);
+    my $base_right_fq = basename($right_fq);
+
+    
+    open (my $left_ofh, ">$base_left_fq.$num_M_entries.fq") or die $!;
+    open (my $right_ofh, ">$base_right_fq.$num_M_entries.fq") or die $!;
+    
+    my $counter = 0;
+    while (my $left_entry = $left_fq_reader->next()) {
+        my $right_entry = $right_fq_reader->next();
+        
+        unless ($left_entry && $right_entry) {
+            die "Error, didn't retrieve both left and right entries from file ($left_entry, $right_entry) ";
+        }
+        unless ($left_entry->get_core_read_name() eq $right_entry->get_core_read_name()) {
+            die "Error, core read names don't match: "
+                . "Left: " . $left_entry->get_core_read_name() . "\n"
+                . "Right: " . $right_entry->get_core_read_name() . "\n";
+        }
+        
+        if ($selected{$counter}) {
+            
+            print $left_ofh $left_entry->get_fastq_record();
+            
+            print $right_ofh $right_entry->get_fastq_record();
+        
+            delete($selected{$counter});
+
+        }
+
+        $counter++;
+        if ($counter % 100000 == 0) {
+            print STDERR "\r[$counter]   ";
+        }
+    }
+    
+    print STDERR "\n\ndone.\n";
+    
+    close $left_ofh;
+    close $right_ofh;
+    
+    if (%selected) {
+        die "Error, missing indices: " . Dumper(\%selected);
+    }
+    else {
+        print STDERR "-all records located and output.\n";
+    }
+    
+    exit(0);
+}
+
+
+
+####
+sub get_random_indices {
+    my ($num_entries, $num_total_records) = @_;
+
+    return( (shuffle 0..$num_total_records)[0..($num_entries-1)]);
+
+}
+