Mercurial > repos > yusuf > miseq_bam_variants

comparison split_hgvs_by_confidence @ 0:1a23ea467feb default tip

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intial commit
author Yusuf Ali <ali@yusuf.email>
date Thu, 26 Mar 2015 09:36:17 -0600
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-1:000000000000 0:1a23ea467feb
1 #!/usr/bin/env perl
2
3 @ARGV > 3 or die "Usage: $0 <input.combined.hgvs.txt> <confident_out.hgvs.txt> <marginal_out.hgvs.txt> <min num sources> [alt min regex]\n";
4
5 my $infile = shift @ARGV;
6 my $confident_outfile = shift @ARGV;
7 my $marginal_outfile = shift @ARGV;
8 my $min_sources = shift @ARGV;
9 my $alt_regex = @ARGV ? shift @ARGV : undef;
10
11 open(IN, $infile)
12 or die "Cannot open $infile for reading: $!\n";
13 open(CONFIDENT, ">$confident_outfile")
14 or die "Cannot open $confident_outfile for writing: $!\n";
15 open(MARGINAL, ">$marginal_outfile")
16 or die "Cannot open $marginal_outfile for writing: $!\n";
17
18 my $header = <IN>;
19 print CONFIDENT $header;
20 print MARGINAL $header;
21 chomp $header;
22 my @headers = split /\t/, $header;
23 my $srcs_column;
24 for(my $i = 0; $i <= $#headers; $i++){
25 if($headers[$i] eq "Sources"){
26 $srcs_column = $i;
27 }
28 }
29 die "Cannot find Sources column in header of $infile, aborting.\n" if not defined $srcs_column;
30
31 while(<IN>){
32 my @F = split /\t/, $_;
33 my @sources = split /; /, $F[$#F];
34 if(@sources >= $min_sources or defined $alt_regex and $F[$#F] =~ /$alt_regex/o){
35 print CONFIDENT $_;
36 }
37 else{
38 print MARGINAL $_;
39 }
40 }
41 close(CONFIDENT);
42 close(MARGINAL);