#!/usr/bin/perl
$inputFile = $ARGV[0];
chomp($inputFile);
open(IN,"$inputFile");
unless(open(IN, $inputFile)){
	print "Error: Cannot open file \"$inputFile\".\n\n";
	exit;
}
@genes=<IN>;
delete($Dna[0]);
close IN;
$i=1;
foreach $geneLine(@genes){
	#$geneLine = "ENSG00000204873	TAAATAGTGGTCATAACAAATATATTATCTAATAAG";
	@gl = split('\t', $geneLine);
	#print "\n".$gl[0]." - ".$gl[1];
	#for($i=1; $i<2; $i++){
		$chrFile = "human_chromosomes/chr".$i.".fa";
		chomp($chrFile);
		open(CHR,"$chrFile");
		unless(open(CHR, $chrFile)){
			print   "Error: Cannot open file \"$snpFile\".\n\n";
			exit;
		}
		@chr = <CHR>;
		delete($chr[0]);
		close CHR;
		$chrSeq = join('', @chr);
		$chrSeq =~s/\s//g;					# Remove white space
		$chrSeq =~ s/($chrSeq)/\U$1/gi;	
		@chrFrags = split/$gl[1]/,$chrSeq;
		$count = @chrFrags;
		if($count>1){
			$n = length($chrFrags[0]);
			$startPos = $n;
			$length = length($gl[1]);

			$snpFile = "SNP_CHROMOSOMES/chr".$i.".subst.fa";
			chomp($snpFile);
			open(SNP,"$snpFile");
			unless(open(SNP, $snpFile)){
				print   "Error: Cannot open file \"$snpFile\".\n\n";
				exit;
			}
			@snp = <SNP>;
			delete($snp[0]);
			close SNP;
			$snpSeq = join('', @snp);
			$snpSeq =~s/\s//g;					# Remove white space
			$snpSeq =~ s/($snpSeq)/\U$1/gi;	
			$seqMatch = substr($snpSeq,$startPos,$length);
			print "Gene ID: $gl[0]\nStart position = $startPos \nLength = $length\n";
			print "Choromosome $i.\n";
			print "\nGene : ".$gl[1]."\nSNP  : $seqMatch\n";
			($snpMatch1=$seqMatch)=~s/[ATGC]/-/g;
			($snpMatch2=$snpMatch1)=~s/[\w]/+/g;
			#$snpMatch2=~s/[-]/0/g;
			print "Match: $snpMatch2\n\n#######################################################################################################\n\n";
		}
		else{
			#print "match not found\n";
		}
	#}
}