perl script to find matching lines in two files - perl

Question

I have two files that look like (below) and want to find the fields from the first in the second file, but print every field of the second.
#rs116801199 720381
#rs138295790 16057310
#rs131531 16870251
#rs131546 16872281
#rs140375 16873251
#rs131552 16873461
and
#--- rs116801199 720381 0.026 0.939 0.996 0 -1 -1 -1
#1 rs12565286 721290 0.028 1.000 1.000 2 0.370 0.934 0.000
#1 rs3094315 752566 0.432 1.000 1.000 2 0.678 0.671 0.435
#--- rs3131972 752721 0.353 0.906 0.938 0 -1 -1 -1
#--- rs61770173 753405 0.481 0.921 0.950 0 -1 -1 -1
My script looks like:
#! perl -w
my $file1 = shift#ARGV;
my #filtered_snps;
open (IN, $file1) or die "couldn't read file one";
while(<IN>){
my#L=split;
#next if ($L[0] =~ m/peak/);
push #filtered_snps,[$L[0],$L[1]];
}
close IN;
my $file2 = shift#ARGV;
my #snps;
open (IN, $file2);
while (<IN>){
my#L=split;
foreach (#filtered_snps){
if (($L[1] eq ${$_}[0]) && ($L[2] == ${$_}[1])) {
print "#L\n";
next;
}
}
}
I am getting no output, when I should be finding every line from file 1. I've also tried grep with no success.

Answer 1

In first while you are assigning to wrong array, you meant #L here.
Then you have pretty different strings in your first array (from first file) and in other. Try to print them both out in your for-iteration. You'll see they can't match.

Answer 2

Create a hash table of the items from the first file, then iterate over the second file and check if that rs-name exists... I'm also confirming that the number matches the name.
use strict;
use warnings;
my %hash;
my $regex = qr/#.* *(rs\d+) (\d+) *.*/;
open my $file1, '<', shift #ARGV;
while (<$file1>) {
my ($name, $num) = $_ =~ $regex;
$hash{$name} = $num;
}
close $file1;
open my $file2, '<', shift #ARGV;
while (<$file2>) {
my ($name, $num) = $_ =~ $regex;
print if (exists $hash{$name} and $hash{$name} = $num)
}
close $file2;