TestBimFileHandler.pl

#!/usr/bin/perl -w

use strict;
use warnings;

use BimFileHandler;

my $selectedOption;
my $methodCounter = 0;
my $maxMethodCounter = 2;

print "Which methods to do you want to test? PLEASE Enter one of TWO Valid Options ((1,A)):";

$selectedOption = <STDIN>;
chomp($selectedOption);

while($selectedOption !~ /[1Aa]/){
	print "Entered Option Is Illegal. PLEASE Enter one of TWO Valid Options ((1,A)):";
	$selectedOption = <STDIN>;
	chomp($selectedOption);
}

if($selectedOption =~ /1/){
	$maxMethodCounter = $selectedOption;
}

print "TEST::: Instantiating BimFileHandler\n";

my $bfh = BimFileHandler->new();

# 1000 Genes ----> "../imputation/plink/chr7From1000Genes/chr7From1000Genes.bim";
# Metabo Chip ---> "../imputation/plink/CAP838metabochipChr7ForJoe/CAP838metabochipChr7ForJoe.bim"
# Illumina Chip -> "../imputation/plink/CAP300and610Kchr7forJoe/CAP300and610Kchr7forJoe.bim"

print "TEST::: Extracting SNPs From BIM files\n";

my %snpMap1 = $bfh->getSNPsFromBimFile();
++$methodCounter;

if($methodCounter >= $maxMethodCounter){
	exit;
}

my %snpMap2 = $bfh->getSNPsFromBimFile();

my @keys1 = keys %snpMap1;
my @keys2 = keys %snpMap2;

print "TEST::: Finding Difference Between SNP sets\n";

my @diff = $bfh->findDifferenceBetweenSnpSets(\%snpMap1, \%snpMap2);

my @snps1 = keys %snpMap1;
my @snps2 = keys %snpMap2;

print "TEST::: Writing to File\n";

$bfh-> writeFile(\@diff);

print "TEST::: ENDING TEST EXECUTION: $#snps1\t$#snps2\t$#diff\n";