fmappositions

#!/usr/bin/perl

use warnings;
use strict;
use Getopt::Long;
use fralib;
use File::Basename;
use POSIX qw(ceil floor);
use File::Path;
use Pod::Usage;

=head1 NAME

fmappositions

=head1 SYNOPSIS

 fmappositions
    
  -h           help
  -map         mapping file
               a)snp-id
               b)position
  mk-file      marker file ...

 example: fmappositions --map mapping.mk pscalare.mk ...
 
 Maps positions.

=head1 DESCRIPTION

=cut

#option variables
my $help;
my $mapFile;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions('h'=>\$help, 'map=s'=>\$mapFile, ) 
   || scalar(@ARGV)<1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

my $mkFile;
my $headerProcessed;
my %label2Column;
my $colNo;
my %SNP;

open(MAP_MK, $mapFile) || die "Cannot open $mapFile";
     		
while(<MAP_MK>)
{
    s/\r?\n?$//;
    
    if(!$headerProcessed)
    {
        $colNo = s/\t/\t/g + 1;
        
        my @fields = split('\t', $_, $colNo);
         
        SEARCH_LABEL: for my $label ('snp-id', 'position')
        {
            for my $col (0 .. $#fields)
            {
                if ($fields[$col] eq $label)
                {           
                    $label2Column{$label}=$col;
                    next SEARCH_LABEL;
                }
            }

                die "Cannot find '$label' in $mapFile";
        }
        
        $headerProcessed = 1;
    }
    else
    {
        my @fields = split('\t', $_, $colNo);
        my $snpID = $fields[$label2Column{'snp-id'}];
        my $position = $fields[$label2Column{'position'}];
        
    	$SNP{$snpID} = $position;
	} 
}

close(MAP_MK);

my $positionColumn;

for $mkFile (@ARGV)
{
	open(MK, $mkFile) || die "Cannot open $mkFile";
	open(NEW_MK, ">modified-$mkFile") || die "Cannot open modified-$mkFile";
	        
	$headerProcessed = 0;  		
	while(<MK>)
	{
	    s/\r?\n?$//;
	    
	    if(!$headerProcessed)
	    {
	        $colNo = s/\t/\t/g + 1;
	        
	        my @fields = split('\t', $_, $colNo);
	         
	        SEARCH_LABEL: for my $label ('SNP', 'Position')
	        {
	            for my $col (0 .. $#fields)
	            {
	                if ($fields[$col] eq $label)
	                {           
	                    $label2Column{$label}=$col;
	                    next SEARCH_LABEL;
	                }
	            }
	
	                die "Cannot find '$label' in $mkFile";
	        }
	        
	        print NEW_MK "$_\n";
	        
	        $positionColumn = $label2Column{"Position"};
	        $headerProcessed = 1;
	    }
	    else
	    {
	        my @fields = split('\t', $_, $colNo);
	        my $snpID = $fields[$label2Column{'snp-id'}];
	        my $position = $fields[$label2Column{'position'}];
	        
	        if(exists($SNP{$snpID}))
	        {
	        	$fields[$positionColumn] = $SNP{$snpID};
	        
	        	print NEW_MK join("\t", @fields) . "\n";
	        }
		} 
	}
	
	close(MK);
	close(NEW_MK);
}