fpeek

#!/usr/bin/perl

use warnings;
use strict;
use fralib;
use Getopt::Long;

#option variables
my $verbose;
my $debug;

#variables
my $genotypeFile;
my $colNo;
my $colElement;
my $rowElement;
my $selectedRow;
my $selectedCol;

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

if(!GetOptions ('v'=>\$verbose, 'd'=>\$debug) || scalar(@ARGV)!=3)
{
	print <<HELP;
usage: fpeek -[vd] <1> <2> <genotype-file>	
	
	   v - verbose
	   d - debug
	
	   example: fpeek snpA sampleA pscalare.geno
	
	   Gets the value at a row, column entry of a table file.
	
HELP

	exit(1);
}

#look for genotype file
for my $i (0..$#ARGV)
{
	if (-e $ARGV[$i])
	{
		$genotypeFile = $ARGV[$i];
		#isGeno($genotypeFile) || die "$genotypeFile not a genotype file";	
		splice(@ARGV, $i, 1);
	}
}

$rowElement = $ARGV[0];
$colElement = $ARGV[1];

open(GENO, $genotypeFile) || die "Cannot open $genotypeFile";

while(<GENO>)
{		
	if ($.==1)
	{
		$colNo = s/\t/\t/g + 1;

		my @fields = split('\t', $_, $colNo);
		
		for my $col (1..$#fields)
		{
			if ($fields[$col] eq $colElement)
			{
				$selectedCol = $col;
			}
		}
	}
	else
	{
		my @fields = split('\t', $_, 2);
		
		if ($fields[0] eq $rowElement)
		{
			my @selectedRowFields = split('\t', $_, $selectedCol+2);
			print "$selectedRowFields[$selectedCol]\n";
			close(GENO);
			exit(0);
		}
	}
}

close(GENO);