perl/etc/WoodyMiaoLin/Tiger/75_1458coverage.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 my $in1 = shift;
   6 my $in2 = shift;
   7 open I1, "<", "$in1";
   8 open I2, "-|", "gzip -dc $in2";
   9
  10 my @notN;
  11 while (<I1>) {
  12   chomp;
  13   push @notN, $_;
  14 }
  15 close I1;
  16 #print STDERR "read $in1 complete!\n";
  17
  18 my $n75 = 0;
  19 my $n1458 = 0;
  20 my (@cover, @line, @depth);
  21 while (<I2>) {
  22   chomp;
  23   my @a = split /\t/;
  24   $line[$a[1]] = $_;
  25   my $c = 0;
  26   my @d;
  27   foreach (9..11) {
  28     my @b = split /:/, $a[$_];
  29     push @d, $b[1];
  30     if ($b[1] >= 3) {
  31       ++$c;
  32     }
  33   }
  34   $depth[$a[1]] = join ",", @d;
  35   $cover[$a[1]] = 1 if $c == 3;
  36 }
  37 close I2;
  38 #print STDERR "read $in2 complete!\n";
  39
  40 foreach (@notN) {
  41   $line[$_] = "N/A" unless defined $line[$_];
  42   $depth[$_] = "0,0,0" unless defined $depth[$_];
  43   print "$_\t$depth[$_]\t$line[$_]\n" unless defined $cover[$_];
  44 }