released/pIRS.old/bwasam/snpmerge.pl

   1 #!/bin/env perl
   2 #use lib "/ifs1/ST_ASMB/USER/huxuesong/public/lib";
   3 use strict;
   4 use warnings;
   5 use Time::HiRes qw ( gettimeofday tv_interval );
   6 use Galaxy::ShowHelp;
   7
   8 $main::VERSION=0.0.1;
   9 our $opts='o:';
  10 our($opt_o);
  11
  12 #our $desc='';
  13 our $help=<<EOH;
  14 \t-o output prefix (./matrix).{mcount,mratio}
  15 EOH
  16 our $ARG_DESC='{sam,soap}pe_files';
  17
  18 ShowHelp();
  19 $opt_o='./mchrpos.lst' if ! $opt_o;
  20
  21 print STDERR "From [@ARGV] to [$opt_o]\n";
  22 my $start_time = [gettimeofday];
  23 #BEGIN
  24 my %Dat;
  25 while(<>) {
  26     chomp;
  27     my ($chr,$pos)=split /\s+/;
  28     ++$Dat{$chr}{$pos};
  29 }
  30 open O,'>',$opt_o or die "Error: $!\n";
  31 my %Stat;
  32 for my $chr (sort keys %Dat) {
  33     for my $pos (sort {$a<=>$b} keys %{$Dat{$chr}}) {
  34         print O "$chr\t$pos\t$Dat{$chr}{$pos}\n";
  35         ++$Stat{$Dat{$chr}{$pos}};
  36     }
  37 }
  38 print "Stat:\n";
  39 print "$_\t$Stat{$_}\n" for sort {$a<=>$b} keys %Stat;
  40 #END
  41 my $stop_time = [gettimeofday];
  42
  43 print STDERR "\nTime Elapsed:\t",tv_interval( $start_time, $stop_time )," second(s).\n";
  44 __END__
  45