ths script has matching the gene id with human chromosome and also with snp file then gives output but the problem s its takng lots of time n unabl 2 get d desired op please help me out!!!!!! 

#!/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    TAAATAGTGGTCATAACAAATATATTATCTAAT
+AAG";
    @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 \nLengt
+h = $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";
        }
    #}
}

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In reply to perl script to sort out the genes which i have in the human chromosome by anisha3

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