/usr/bin/vcf-indel-stats is in vcftools 0.1.14+dfsg-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Vcf;
my $opts = parse_params();
do_stats($opts);
exit;
#--------------------------------
sub error
{
my (@msg) = @_;
if ( scalar @msg )
{
croak @msg;
}
die
"About: Currently calculates in-frame ratio.\n",
"Usage: vcf-indel-stats [OPTIONS] < in.vcf > out.txt\n",
"Options:\n",
" -h, -?, --help This help message.\n",
" -e, --exons <file> Tab-separated file with exons (chr,from,to; 1-based, inclusive)\n",
" -v, --verbose\n",
"\n";
}
sub parse_params
{
my $opts = { };
while (my $arg=shift(@ARGV))
{
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
if ( $arg eq '-e' || $arg eq '--exons' ) { $$opts{exons}=shift(@ARGV); next; }
if ( $arg eq '-v' || $arg eq '--verbose' ) { $$opts{verbose}=1; next; }
error("Unknown parameter \"$arg\". Run -h for help.\n");
}
return $opts;
}
sub init_regions
{
my ($opts) = @_;
my $exname = $$opts{exons}=~/\.gz$/i ? "gunzip -c $$opts{exons} |" : "<$$opts{exons}";
open(my $exfh, $exname) or error("$exname: $!");
my %regs;
while (my $line=<$exfh>)
{
my ($chr,$from,$to) = split(/\t/,$line);
chomp($to);
push @{$regs{$chr}}, [$from,$to];
}
close($exfh);
for my $chr (keys %regs)
{
$regs{$chr} = [ sort { if ($$a[0]==$$b[0]) {return $$a[1]<=>$$b[1]} else {return $$a[0]<=>$$b[0]} } @{$regs{$chr}} ];
}
$$opts{regs} = \%regs;
$$opts{iregs} = {};
}
sub do_stats
{
my ($opts) = @_;
init_regions($opts);
my $vcf = Vcf->new(fh=>\*STDIN);
$vcf->parse_header;
$$opts{in_frame} = $$opts{out_frame} = 0;
my ($prev_chr,$prev_pos);
my $ntot=0;
while (my $line=$vcf->next_line)
{
if ( substr($line,0,1) eq '#' ) { next; }
my $i=0;
my $j;
$j=index($line,"\t",$i); my $chr=substr($line,$i,$j-$i); $i=$j+1;
$j=index($line,"\t",$i); my $pos=substr($line,$i,$j-$i); $i=$j+1;
$j=index($line,"\t",$i); $i=$j+1;
$j=index($line,"\t",$i); my $ref=substr($line,$i,$j-$i); $i=$j+1;
$j=index($line,"\t",$i); my $alt=substr($line,$i,$j-$i); $i=$j+1;
if ( defined $prev_chr && $prev_chr eq $chr && $prev_pos>$pos ) { error("The VCF file must be sorted"); }
$prev_chr = $chr;
$prev_pos = $pos;
if ( $alt eq '.' ) { next; }
#print "[$chr] [$pos] [$ref] [$alt]\n";
my $is_indel;
$i=0;
while (($j=index($alt,',',$i))!=-1)
{
my ($type,$len,$ht) = $vcf->event_type($ref,substr($alt,$i,$j-$i));
if ( $type eq 'i' or $type eq 'o' ) { check_csq($opts,$chr,$pos,$len); }
$i = $j+1;
}
my ($type,$len,$ht) = $vcf->event_type($ref,substr($alt,$i));
if ( $type eq 'i' or $type eq 'o' )
{
$ntot++;
check_csq($opts,$chr,$pos,$len);
}
}
printf "total\t%d\n", $ntot;
printf "in-frame\t%d\n", $$opts{in_frame};
printf "frameshift\t%d\n", $$opts{out_frame};
printf "ratio\t%f\n", ($$opts{out_frame}+$$opts{in_frame})?$$opts{out_frame}/($$opts{out_frame}+$$opts{in_frame}) : 0;
}
sub check_csq
{
my ($opts,$chr,$pos,$len) = @_;
my $opos = $pos;
if ( !exists($$opts{regs}{$chr}) ) { return; }
my $regs = $$opts{regs}{$chr};
my $ir = exists($$opts{iregs}{$chr}) ? $$opts{iregs}{$chr} : 0;
while ( $ir<@$regs && $$regs[$ir][1] <= $pos ) { $ir++; }
$$opts{iregs}{$chr} = $ir;
if ( $ir>=@$regs ) { return; }
my $reg_to = $$regs[$ir][1];
if ( $reg_to<=$pos ) { return; }
my $reg_from = $$regs[$ir][0];
my $to = $len<0 ? $pos-$len : $pos+1;
if ( $to<$reg_from ) { return; }
$pos++;
if ( $pos<$reg_from ) { $len += $reg_from-$pos; $pos = $reg_from; }
if ( $reg_to<$to && $len<0 ) { $len += $to-$reg_to; }
#print "\tinside $$regs[$ir][0] - $$regs[$ir][1] ($pos,$to,$len)\n";
#if ( $len%3 || ($pos-$reg_from)%3 ) { $$opts{out_frame}++; }
if ( $len%3 ) { $$opts{out_frame}++; }
else { $$opts{in_frame}++; }
if ( $$opts{verbose} )
{
print "$chr\t$opos\t$$regs[$ir][0]\t$$regs[$ir][1]\t", ($len%3 ? 'frameshift':'inframe') ,"\n";
}
}
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