1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
#!/usr/bin/env perl
################################################################################
#
# FILE: analyser.pl
#
# USAGE: perl analyser.pl
#
# DESCRIPTION: Filter relevant insertions from a VCF file.
#
################################################################################
use strict;
use warnings;
# Some variables.
my $count = 0;
my $count_val = 0;
my $count_ins = 0;
my $count_homo_zyg = 0;
my $line_sz = 0;
my $shr = 0;
# Test for input arguments from command line.
if ( @ARGV ) {
my $vcf = $ARGV[0];
# Test input existence.
die "ERROR: Non existent file \"$vcf\"" unless -f $vcf;
open my $fh, '<', $vcf or die "Can't open file $vcf";
while ( <$fh> ) {
$count++;
# Skip header lines.
next if /^#/;
chomp;
my @line = split;
$count_val++;
# Skip Unknown chromosomes.
next if (length($line[0]) < 4)
or (length($line[0]) > 5)
or ($line[6] ne "PASS");
$count_ins++;
$line_sz = @line - 9;
my $ct = 0;
# Test haplotype.
foreach ( 9 .. $#line ) {
$ct++ if (split(":", $line[$_]))[0] =~ /1/;
$count_homo_zyg++ if $line[$_] =~ /^1\/1:/;
}
$shr++ if $ct > 1;
}
close $fh;
# Print results.
my $str = <<" EOS";
GENERAL STATISTICS: $vcf
================================================================================
Total number of lines in file: $count
Total non header lines: $count_val
Total valid insertions: $count_ins
Number of shared insertions: $shr
Ratio of homozygous insertions in all samples: $count_homo_zyg / ($count_ins*$line_sz)
================================================================================
EOS
print $str;
}
else {
# Print an usage for help.
die "ERROR: No input arguments";
}
|
