Mercurial > repos > dereeper > sniplay3
comparison VCFToolsStats/VCFToolsStats.pl @ 18:7ba803afa41b draft
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author | dereeper |
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date | Thu, 26 Feb 2015 16:02:46 -0500 |
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17:f21d05b9d3fe | 18:7ba803afa41b |
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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 |