bin/replace_accessions_in_vcf.pl

   1
   2 use strict;
   3
   4 my $vcf_file = shift;
   5 my $equivalence_file = shift;
   6
   7
   8 open(my $E, "<", $equivalence_file) || die "Can't open $equivalence_file\n";
   9
  10 my %ids;
  11 while (<$E>) {
  12     chomp;
  13
  14     my ($original_id, $modified_id, $new_id, $match_type, $stock_type) = split /\t/;
  15     $ids{$original_id} = $new_id;
  16 }
  17
  18 close($E);
  19
  20 open(my $V, "<", $vcf_file) || die "Can't open $vcf_file\n";
  21
  22 while (<$V>) {
  23     chomp();
  24
  25     if ($_ =~ m/^\#CHROM/) {
  26         print STDERR "Parsing ids in vcf file...\n";
  27         my @F = split /\t/;
  28         my $count = 0;
  29         foreach my $f (@F) {
  30             $count++;
  31             if (exists($ids{$f}) && ($ids{$f} ne $f)) {
  32                 print STDERR "replace $f with $ids{$f} ($count), ";
  33                 $f = $ids{$f};
  34             }
  35         }
  36         my $line = join("\t", @F);
  37         print "$line\n";
  38     }
  39     else {
  40         print $_."\n";
  41     }
  42 }
  43
  44