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|
#!/usr/bin/env perl
use strict;
use warnings;
# TODO:
# getopt
# better messaging
# usage
# pod...
my $fn = shift || die "No input file";
my %to_alt = (
"AR" => "G", "GR" => "A",
"CY" => "T", "TY" => "C",
"CS" => "G", "GS" => "C",
"AW" => "T", "TW" => "A",
"GK" => "T", "TK" => "G",
"AM" => "C", "CM" => "A"
);
open(FH, "$fn") || die "Could not open '$fn' for reading.\n";
print STDOUT "##fileformat=VCFv4.1\n";
print STDOUT "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSample\n";
my $type = -1; # 1 - SUB, 2 - INS, 3 - DEL
my $prev_name = -1;
my $prev_pos = -1;
my $del_n = 0;
my $del_name = "";
my $del_pos = -1;
my $del_ref = "";
my $del_s = -1;
my $line_n = 0;
while(defined(my $line = <FH>)) {
if($line =~ m/^(.+)\t(\d+)\t(.+)\t(.+)\t(\d+)$/) {
$line_n++;
my $name = $1;
my $pos = $2;
my $ref = $3;
my $alt = $4;
my $s = $5;
if($prev_name ne $name) {
if(0 < $del_n) {
printf(STDOUT "%s\t%d\t.\t%s\t.\t100\tPASS\tpl=%d\n",
$del_name, $del_pos, $del_ref, $del_s);
}
# reset
$prev_pos = -1; $del_n = 0; $del_s = -1;
$del_name = ""; $del_pos = -1; $del_ref = "";
}
if("-" eq $alt) { # DEL
if(0 < $del_n && $del_pos + $del_n == $pos && $s == $del_s) {
$del_n++;
$del_ref .= $ref;
}
else {
if(0 < $del_n) {
printf(STDOUT "%s\t%d\t.\t%s\t.\t100\tPASS\tpl=%d\n",
$del_name, $del_pos, $del_ref, $del_s);
}
$del_n = 1;
$del_name = $name;
$del_pos = $pos;
$del_ref = $ref;
$del_s = $s;
}
}
else {
# print deletion, if it exists
if(0 < $del_n) {
printf(STDOUT "%s\t%d\t.\t%s\t.\t100\tPASS\tpl=%d\n",
$del_name, $del_pos, $del_ref, $s);
# reset
$prev_pos = -1; $del_n = 0; $del_s = -1;
$del_name = ""; $del_pos = -1; $del_ref = "";
}
if("-" eq $ref) { # INS
printf(STDOUT "%s\t%d\t.\t.\t%s\t100\tPASS\tpl=%d\n",
$name, $pos, $alt, $s);
}
else { # SUB
if(3 != $s) {
if(!defined($to_alt{"$ref"."$alt"})) {
die "Could not convert $ref$alt"." on $line_n.\n";
}
$alt = $to_alt{"$ref"."$alt"};
}
printf(STDOUT "%s\t%d\t.\t%s\t%s\t100\tPASS\tpl=%d\n",
$name, $pos, $ref, $alt, $s);
}
}
$prev_name = $name;
$prev_pos = $pos;
}
else {
die "Input file is not in the proper format.\n";
}
}
# print deletion, if it exists
if(0 < $del_n) {
printf(STDOUT "%s\t%d\t.\t%s\t.\t100\tPASS\tpl=%d\n",
$del_name, $del_pos, $del_ref, $del_s);
}
close(FH);
|
