perl/etc/justonce/readsCount_threads.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4 use threads;
   5
   6 my $maxthreads = 8;
   7
   8 my %file;
   9 while (<>) {
  10   chomp;
  11   my $a = $_;
  12   s/\w+\///;
  13   if (open $file{$_}, "-|", "gzip -dc $a") {
  14     print STDERR "open $a was succesful!\n";
  15   } else {
  16     print STDERR "open $a failed!\n";
  17   }
  18 }
  19 print STDERR "Read file list complete!\n";
  20
  21 my (%thread,%count);
  22 my $t = 0;
  23 foreach (sort keys %file) {
  24   ++$t;
  25   if ($t > $maxthreads ) {
  26         for (sort keys %thread) {
  27                 $count{$_} = $thread{$_}->join;
  28                 print STDERR "$t: Count $_ complete!\n";
  29                 delete $thread{$_};
  30         }
  31         $t = 0;
  32   }
  33   if (/sam.gz$/) {
  34     $thread{$_} = threads->new(\&countsam, $file{$_});
  35   } elsif (/fq.gz$/) {
  36     $thread{$_} = threads->new(\&countfq, $file{$_});
  37   }
  38 }
  39
  40 foreach (sort keys %thread) {
  41   $count{$_} = $thread{$_}->join;
  42   print STDERR "Count $_ complete!\n";
  43 }
  44
  45 foreach (sort keys %count) {
  46   print $_, "\t", join( ',',@{$count{$_}} ), "\n";
  47 }
  48
  49 sub countfq {
  50   my $in = shift;
  51   my ($lc,$f)=(0,0);
  52   while (<$in>) {
  53     ++$lc;
  54     if (/^\@[^ ]+ [12]:([YN]):/) {
  55         ++$f if $1 eq 'N';
  56     }
  57   }
  58   close $in;
  59   return [$lc/4,$f];
  60 }
  61
  62 sub countsam {
  63   my $in = shift;
  64   my $lc;
  65   while (<$in>) {
  66     next if /^@/;
  67     ++$lc;
  68   }
  69   close $in;
  70   return [$lc/2];
  71 }