hmp2cmpositions.pl

#!/bin/perl

use warnings;
use strict;

my $map = $ARGV[0]; #lg.ALL.bronze14.path.txt
my $snp = $ARGV[1]; #SNP file in hmp format

my $tmp;
my %hash;
open MAP, $map;
while(<MAP>){
	chomp;
	my @a = split(/\t/,$_);
	if ($. ne "1"){
		if ($a[2] ne "NA"){
			my $chrom = $a[0];
			if ($chrom =~ m/^0/){
				my @tmp = split(//, $chrom);
				$chrom = "Ha$tmp[1]";
			}else{
				$chrom = "Ha$chrom";
			}
			$hash{$chrom}{$a[1]} = $a[2];
			$tmp = $chrom;
		}
	}
}

close MAP;

open SNP, $snp;
while(<SNP>){
	chomp;
	my $line = $_;
	my @a = split(/\t/,$line);
	if ($. eq "1"){
		foreach my $i(0..3){
			print "$a[$i]\t";
		}
		print "cM";
		foreach my $i(4..$#a){
			print "\t$a[$i]";
		}
	}else{
		my $chrom = $a[2];
		my $bp = $a[3];
		my $previous_site;
		my $before_site;
		my $after_site;
		my $loci_cM;
		foreach my $site (sort  {$a <=> $b} keys %{$hash{$chrom}}){
			if ($site > $bp){
				if ($previous_site){
					$before_site = $previous_site;
					$after_site = $site;
					goto FOUNDPOS;
				}else{
					$loci_cM = "NA";
					goto BADSITE;
				}
			}
			$previous_site = $site;
		}
		$loci_cM = "NA";
		goto BADSITE;
		FOUNDPOS:
		my $cM_range = $hash{$chrom}{$after_site} - $hash{$chrom}{$before_site};
		my $bp_range = $after_site - $before_site;
		my $percent_of_range = ($bp - $before_site)/$bp_range;
		$loci_cM = ($percent_of_range * $cM_range) + $hash{$chrom}{$before_site};
		
		BADSITE:
		print "\n";
		foreach my $i(0..3){
                        print "$a[$i]\t";
                }
                print "$loci_cM";
                foreach my $i(4..$#a){
                        print "\t$a[$i]";
		}
	}
}