Hi All, I am new to perl so please be gentle. I am trying to compare two hashes. I have a reference text file (1) and another text file (2) i would like to compare (Eventually i have another 19 to compare to reference) what i want to do is compare the two text files and if there is a key (representing position) eg 245 in both text file 1 and 2 to keep the value from text file 2. Then i want to compare the next line in the files, if the position in text file 1 is missing in textfile 2 i want it to add that position and value to text file two. I hope this makes sense, i have pasted the script that i have written below (but the problem is when i run it i get an identical copy of text file 1 saved as text file two. Hope you can help Thanks Gemma : 

#! /usr/bin/perl -w

use 5.010;

open (REF, "ref_snp.txt");
open (GENOTYPE, "$ARGV[0]");
open (OUT, ">$ARGV[1]");


my %genotype;
my %ref;
while(<GENOTYPE>) 

{
if (/(\d+)\t\w\t(\w)/) 
{
%genotype=($1=>$2,);
my @position=keys %genotype;
   #foreach $position (sort keys %genotype) 
   # {
   
# print OUT "$position\t$genotype{$position}\n";   
   # }
}
else 
{
print "It doesn'y match!$_ not match!\n\n";
}
   

}

while (<REF>)
{
if (/(\d+)\t(\w)/)
{
%ref = ($1=>$2,);
my @position_ref = keys %ref;
foreach $position_ref (sort keys %ref)
{
if (exists $genotype{$position_ref}) 
{
print OUT "$position_ref\t$genotype{$position_ref}\n";
}
else 
{
$genotype{$position_ref}=$ref{$position_ref};
print OUT "$position_ref\t$genotype{$position_ref}\n";
}
}
}

}

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In reply to Comparing two hashes-help by Gemchal

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