Mercurial > repos > dereeper > sniplay3

comparison VCFToolsStats/VCFToolsStats.pl @ 24:21d878747ac6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Mon, 23 Mar 2015 05:53:20 -0400
parents 7ba803afa41b
children
comparison
equal deleted inserted replaced
23:a1ab979f4551 24:21d878747ac6
1
2 #!/usr/bin/perl
3
4 use strict;
5 use Switch;
6 use Getopt::Long;
7 use Bio::SeqIO;
8
9 my $usage = qq~Usage:$0 <args> [<opts>]
10
11 where <args> are:
12
13 -i, --input <VCF input>
14 -o, --out <output basename>
15 ~;
16 $usage .= "\n";
17
18 my ($input,$out);
19
20 GetOptions(
21 "input=s" => \$input,
22 "out=s" => \$out
23 );
24
25
26 die $usage
27 if ( !$input);
28
29
30
31 my $nb_gene = `grep -c mRNA $input`;
32 $nb_gene =~s/\n//g;
33 my $nb_intergenic = `grep -c INTERGENIC $input`;
34 $nb_intergenic =~s/\n//g;
35
36 my $nb_intron = `grep -c INTRON $input`;
37 $nb_intron =~s/\n//g;
38 my $nb_UTR = `grep -c UTR $input`;
39 $nb_UTR =~s/\n//g;
40 my $nb_exon = $nb_gene - $nb_intron - $nb_UTR;
41
42 my $nb_ns = `grep -c NON_SYNONYMOUS_CODING $input`;
43 $nb_ns =~s/\n//g;
44 my $nb_s = $nb_exon - $nb_ns;
45
46
47
48
49 #system("$VCFTOOLS_EXE --vcf $input --remove-filtered-all --out $out --hardy >>vcftools.log 2>&1");
50 system("vcftools --vcf $input --remove-filtered-all --out $out --het >>vcftools.log 2>&1");
51 system("vcftools --vcf $input --remove-filtered-all --out $out --TsTv-summary >>vcftools.log 2>&1");
52 system("vcftools --vcf $input --remove-filtered-all --out $out --missing-indv >>vcftools.log 2>&1");
53
54 open(my $G,">$out.annotation");
55 print $G "Genic $nb_gene\n";
56 print $G "Intergenic $nb_intergenic\n";
57 print $G "========\n";
58 print $G "Intron $nb_intron\n";
59 print $G "Exon $nb_exon\n";
60 print $G "UTR $nb_UTR\n";
61 print $G "========\n";
62 print $G "Non-syn $nb_ns\n";
63 print $G "Synonym $nb_s\n";
64 close($G);
65
66
67
68
69
70
71