Thank you very much! I am using the first suggestion, as I don't really understand the binary search yet, and so far it doesn't seem to have problems with searching the 500,000 rows.

I am now running into the problem of the results being output on different lines in the resulting CSV file for each print command. Here is my code: 

#!/usr/bin/perl
use warnings;
use strict;

open my $GENES,     '<', 'chr1data.csv'     or die $!;
open my $LOCATIONS, '<', 'chr1snps.csv' or die $!;

chomp(my @locations = map { (split ',')[2] } <$LOCATIONS>);
# If IDs are not already sorted, uncomment the following line:
# @locations = sort { $a <=> $b } @locations;

for (<$GENES>) {
    my ($chromosome, $start, $end) = split ',';
    print "$chromosome,$start,$end";
    my $idx = 0;        # For $end, start searching where you left for
+ $start.
    my $correction = 0; # Needed for Start(-) == Start and End(+) == E
+nd.
    for my $pos ($start, $end) {
        $idx++ while $locations[$idx] <= $pos - $correction
                     and $idx <= $#locations;
        die "No numbers around $pos ($idx) \n"
            if $idx == 0 or $idx > $#locations;
        print ",$locations[$idx-1],$locations[$idx]";
        $correction = 1;
    }
    print "\n";
}

[download]

Printing print ",$locations[$idx-1],$locations[$idx]"; puts this information on a new line. I'd like it to come out on the same line as print "$chromosome,$start,$end"; for each search. Do I have a \n in the wrong place?

In reply to Re^2: Reading values from one .csv, searching for closest values in second .csv, returning results in third .csv? by pickleswarlz
in thread Reading values from one .csv, searching for closest values in second .csv, returning results in third .csv? by pickleswarlz

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