perl/bsim/overlapVF.pl

   1 #!/usr/bin/env perl
   2 use strict;
   3 use warnings;
   4
   5 die "Usage: $0 <SimLst> <AnalyseRes> [Shift=10]\n" if @ARGV <2;
   6
   7 my $total=shift;
   8 my $result=shift;
   9 my $shift=shift;
  10 $shift = 10 unless defined $shift;
  11 open TT,$total or die $!;
  12 open RT,$result or die $!;
  13 my %hash;
  14
  15 while(<TT>){
  16         chop;
  17         my @a=split;
  18         #print $a[3]."\n";
  19         next unless(/\w/);
  20         for( my $kk=$a[3]-$shift;$kk<$a[3]+$shift;$kk++){
  21                 $hash{$kk}=1;
  22         }
  23
  24 }
  25 close TT;
  26
  27 sub docheck($$$) {
  28         my ($chr,$start,$end) = @_;
  29         my $ret = 0;
  30         ($start,$end) = sort {$a <=> $b} ($start,$end);
  31         for my $p ($start .. $end) {
  32                 if (exists $hash{$p}) {
  33                         $ret = 1;
  34                         last;
  35                 }
  36         }
  37         return $ret;
  38 }
  39
  40 while(<RT>){
  41         chomp;
  42         my @a=split;
  43         my ($chr,$start,$end)=split /_/,$a[3];
  44         my $ret = docheck($chr,$start,$end);
  45         print "$_\n" if $ret;
  46 }
  47 close RT;
  48
  49 __END__
  50 grep \> simout_*.Ref.fa | sed 's/^simout_m//'|sed 's/.Ref.fa:>/\t/'|sed 's/Ref_/Ref:/g'|sed 's/Vir_/Vir:/'|sed 's/R_/R:/'|sed 's/_/ /g'|cat -n >simed.lst
  51
  52 $ wc VirusFinder2/results-virus-loci.txt
  53      630    9450   58915 VirusFinder2/results-virus-loci.txt
  54
  55 $ ./overlapVF.pl simed.lst VirusFinder2/results-virus-loci.txt |wc
  56      408    6120   38407