HI Monks, I would like to check whether the keys of two hashes are same and work on them. The hashes should be in the same order as the input file. Since, we cant compare the hashes directly and have to loop over the key and value pair the larger files are taking very long to be finished.
I have attached my piece of code Could you please give suggestions to imporve it please
Thanks
#!/usr/local/bin/perl  -w


use strict;
use Getopt::Long;
use Tie::IxHash;

my ($bpfile , $intfile, $out);

my $usage = " USAGE: perl beadpool_int.pl  -bpfile <file with snp,chr,
+beadpoolid> -int <intensities file from b2i>\n";

GetOptions("bp=s" =>\$bpfile,
       "int=s" =>\$intfile,
       "out=s" =>\$out) || warn "Error $!\n";
       
if(!$bpfile) {die "\n$usage\n"};

my %beads;

tie my %ints,"Tie::IxHash";
open BP, "<$bpfile" or die $!;
open INT, "<$intfile" or die $!;
open OUT, ">$out"or die $!;

while (my $line= <BP>) {

  chomp $line;
  my @bp = split(/,/,$line);
  $beads{$bp[0]} = $bp[2];

}

close BP;

#my ($snp, @array)
my @intensities;
while (my $line = <INT>){

  chomp $line;
  my $LABELS_REGEX =qr(^SNP\s+Coor);
  if ($line !~ $LABELS_REGEX) {
   
   my ($snp, $coor, $allele,@array) = split(/\t/,$line);
   $ints{$snp} = \@array;
   @intensities = @array;
   
   }
   
}

close INT;

foreach my $snp(keys %ints) {

    foreach my $snpbs(keys %beads){
    
      if($snp eq $snpbs){
      
         my @ints;
         for(my $i = 0;$i<scalar(@intensities);$i++) {
     
      push @ints, $ints{$snp}[$i] ;
     
     } 
         
    print OUT "$beads{$snpbs}\t$snp\t", join("\t",@ints), "\n";
    
      }
      #print OUT "\n";
    }
    
    
}

[download]

Thanks for your time and suggestions

In reply to To make the comparison work faster by Anonymous Monk

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