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

# Example 4: no_lcp.pl
#	Setting up two-point analysis with LINKAGE without LCP 
#
# 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 15, 1999
#
# Usage: no_lcp.pl 
#	[chromosome number]
#	[starting marker] (e.g. 1,2...)
#	[ending marker] 
#

$usage ="Usage: no_lcp.pl [chr #] [starting marker] [ending marker]";

if($#ARGV != 2 ){ print "$usage\n"; exit; }

$chr=$ARGV[0];
$start_marker=$ARGV[1];
$end_marker=$ARGV[2];

$start_marker++;  # use the convention 1,2,...N
$end_marker++;

$prog="mlink"; 
$ukn="unknown";
$lsp="lsp";

$pedfile="chr".$chr.".ped";    # the name of the pedigree file
$datfile="chr".$chr.".dat";    # the name of the parameter file

$first_4_lines="$prog\n $pedfile\n $datfile\n 2\n";
$last_6_lines="0\n 0\n 1\n 0.05\n 0.4\n 0\n";

for($i=$start_marker;$i<=$end_marker;$i++){
   $arg= "$first_4_lines"."1 $i\n".$last_6_lines;
   open(INPUT, "| $lsp >/dev/null");
   print INPUT $arg;            # feed inputs to LSP program
   close(INPUT);

   system("cat lsp.log >> final.out");
   system("cat lsp.stm>> stream.out");
   system($ukn);          # run UNKNOWN program
   system($prog);         # run MLINK program
   system("cat outfile.dat>> final.out");
   system("cat stream.dat>> stream.out");
 }