tools/linkage/fmt.pl

   1 #!/bin/env perl
   2 use strict;
   3 use warnings;
   4
   5 my $minMAF=0.2;
   6 my $minCOV=0.5;
   7
   8 unless (@ARGV > 0) {
   9     print "perl $0 <In_file> <Out_File> <ChrID>\n";
  10     exit 0;
  11 }
  12
  13 open I,'<',$ARGV[0] or die $!;
  14 open O,'>',$ARGV[1] or die $!;
  15 my $t=<I>;
  16 $t=~s/^#//;
  17 print O "#ChrID\tPos\t$t";
  18 while (<I>) {
  19     chomp;
  20     my ($Pos,$D)=split /\s+/,$_,2;
  21     my @Dat=split / /,$D;
  22     my ($cvg,%cnt)=(0);
  23     for (@Dat) {
  24         ++$cnt{$_} if /\d/;
  25         ++$cvg if /\d/;
  26     }
  27     next if $cvg < @Dat * $minCOV;
  28     ($cvg)=sort {$a<=>$b} values %cnt;
  29     next if $cvg < @Dat * $minMAF;
  30     print O "$ARGV[2]\t$Pos\t$D\n"
  31 }
  32 close O;
  33 close I;
  34 __END__
  35 ./fmt.pl ./p15/Chr01 Chr01.15 Chr01
  36 cat chrorder | while read a; do ./fmt.pl ./p15/$a $a.15 $a;done &
  37