#!/usr/local/bin/perl -w

# Example 5: lia_lung.pl
#       Creating a liability class column in LINKAGE pedigree file. 
#	Case 1: Lung Cancer: Two files are needed, which share the
#	first 6 columns in common (pedID,personID,father,mother, gender,
#	affectionstatus). The rest of the first file stores the 
#	marker information, whereas the rest of the second file contains 
#	two columns: age and daily packs of cigarette one consumes
#
# Ref: Li and Haghighi, "Perl as a tool for linkage analysis",
# Am J Hum Genet, suppl,65: A260 (1999)
#
# Contact: perl@linkage.rockefeller.edu
#
# Last update: October 17, 1999
#
# Usage: lia_lung.pl 
#       [marker file]
#       [extra phenotype file] 
#	[age threshold]
#	[# of packs of cig threshold]

$usage ="Usage: lia_lung.pl [marker file] [extra phenotype file] [age thre] [cig threshol]";

if($#ARGV != 3 ){ print "$usage\n"; exit; }

$marker_file=$ARGV[0];
$pheno_file=$ARGV[1];
$age_thre =$ARGV[2];
$pack_thre =$ARGV[3];

open(MIN,"< $marker_file"); 
@mdata= grep(/\n/,<MIN>); 
close(MIN);
open(PIN,"< $pheno_file"); 
@phdata= grep(/\n/,<PIN>); 
close(PIN);

if($#mdata != $#phdata){        # check the two files have same num. of lines
 print "unequal size between $marker_file and $pheno_file\n"; 
 exit; 
}

foreach $i (0..$#mdata){
 $mdata[$i] =~ s/^\s+//; 
 $phdata[$i] =~ s/^\s+//;
 @mline= split(/\s+/,$mdata[$i]); 
 @phline= split(/\s+/,$phdata[$i]);

 if( $mline[0] == $phline[0] && $mline[1]==$phline[1]){
   if($phline[6] < $age_thre){         # age information
    # daily cigarettes consumption: -1 for no info
    if($phline[7] <0){ 
	$lia=1; 
    }
    elsif($phline[7] < $pack_thre){ 
	$lia=2; 
    } 
    else{ 
	$lia=3; 
    }
   }
   else{
    if($phline[7] <0){
	$lia=1; 
    }
    elsif($phline[7] < $pack_thre){ 
	$lia=4; 
    }else{ 
	$lia=5; 
    }
   }
   for($j=0;$j<=4;$j++){ 
	print "$mline[$j] "; 
   }
   print "$phline[5] ";         # affection status
   print " $lia  ";             # the liability class determined vt age/cig cons
   for($j=5; $j<=$#mline;$j++){ 
	print "$mline[$j] ";
   }
   print "\n";
 }
 else{ 
	print "$marker_file and $phenoe_file don't match\n"; 
	exit;
 }
}