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

# Example 6: ehplus_cc.pl
#	Run fpmp in FASTEH+ for each marker
#
# 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: November 27, 2001
#
# Usage: ehplus_cc.pl [.dat file]
#
# Format for .dat file:
# 	col1: person ID
#	col2: affection status ( unaffected and 1 affected)
#	col3,4: genotype of marker 1
#	col5,6: genotype of marker 2
#	....
#
# Format for .par file
#	line1: (# markers) (case-control study?) (if case-control, permute label?) 
#		(# label permutations)
#	line2: (# alleles for marker1) (# allele for marker2)...
#	line3: (.dat contains "single genotype identifier"?) 
#		(print "single genotype identifier"?)
#	line4: (use marker 1?) (use marker 2?)....
#	line5: (permute marker 1 within a block?) (permute marker 2 in a block?)...
#	line6: (disease allele D freq) (penetrance for ++) (penetrance for +D) (..for DD)
#

$usage="Usage: ehplus_cc.pl [.dat file]";

if( $#ARGV != 0){ print "$usage\n"; exit; }
$datafile=$ARGV[0];

$nmarkers=38;	# number of markers (for this data set)

$m1=1;		# starting marker. can be changed
$m2=$nmarkers;	# ending marker. can be changed

for($i=$m1; $i<=$m2; $i++){

 $parfile= "m".$i."."."par";
 open(PAR, "> $parfile");	# preparing .par file for each marker

 # particular information (e.g. total number of markers, number of
 # alleles for each marker...) is used here. for your own data,
 # change accordingly.

 print PAR <<"EOF";
38 1 1 500 << num markers, case-control?, label-permutation? how many times?
13 13 12 13  3 9 15 8 8 16 17 5  16  7 14 3  3 7 8 20 12 12 12 8 6 13 6 11 9 27 5 13 9 11 10 16 20 5 << number of alleles for each marker
0 0 << something on printing output
EOF

 # marker selection. 1 if the marker is selected, 0 not.

 for($j=1; $j<=$nmarkers; $j++){
  if($j != $i){ print PAR "0 ";}
  else{ print PAR "1 ";}
 }
 print PAR "\n";

 # 0 for all because we are not doing marker-marker LD analysis

 for($j=1; $j<=$nmarkers; $j++){ print PAR "0 "; }
 print PAR "\n";

 # this particular line doesn't matter, because fpmp carries out
 # model-free analysis.

 print PAR "0.001 0.05 0.2 0.8 << disease all-freq, 3 penetrances\n";
close(PAR);

 $arg=" ".$parfile." ".$datafile." m".$i."."."out"; 

 system("fpmp  $arg");
}

exit;