perl/etc/justonce/countmsam.pl

   1 #!/bin/env perl
   2 =pod
   3 Author: Hu Xuesong @ BIOPIC <galaxy001@gmail.com>
   4 Version: 1.0.0 @ 20120330
   5 =cut
   6 use strict;
   7 use warnings;
   8 #use Data::Dump qw(ddx);
   9
  10 die "Usage: $0 <fq_base_list> <genome_list> <sam_path> <out>\n" if @ARGV<1;
  11 my $fqlst=shift;
  12 my $reflst=shift;
  13 my $sampath=shift;
  14 my $outf=shift;
  15
  16 sub openfile($) {
  17     my ($filename)=@_;
  18     my $infile;
  19     if ($filename=~/.xz$/) {
  20             open( $infile,"-|","xz -dc $filename") or die "Error opening $filename: $!\n";
  21     } elsif ($filename=~/.gz$/) {
  22         open( $infile,"-|","gzip -dc $filename") or die "Error opening $filename: $!\n";
  23     } else {open( $infile,"<",$filename) or die "Error opening $filename: $!\n";}
  24     return $infile;
  25 }
  26
  27 open L,'<',$fqlst or die;
  28 my @fqpres;
  29 while (<L>) {
  30         chomp;
  31         push @fqpres,$_;
  32 }
  33 close L;
  34
  35 open L,'<',$reflst or die;
  36 my @refs;
  37 while (<L>) {
  38         chomp;
  39         push @refs,$_;
  40 }
  41 close L;
  42
  43 my %FH;
  44 for my $fq (@fqpres) {
  45         for my $ref (@refs) {
  46                 my $fh = openfile("$sampath/${fq}_$ref.sam.gz");
  47                 push @{$FH{$fq}},$fh;
  48                 #$FH{$fq}{$ref}=$fh;
  49         }
  50 }
  51
  52
  53 __END__
  54 ./countmsam.pl fqbase.lst genomes.lst ./check pigv2.stat