A large part of the trick is to only make one pass through each file and to use a lookup in some in-memory structure to perform the test. If your data gets too big for that to work then you need to think about using a database, but for only a few million entries a hash works well. Consider:

use strict;
use warnings;
 
my $snpFile = <<SNP;
snp_rs              log_1_pval
rs3749375    11.7268615355335
rs10499549    10.4656064706897
rs7837688    9.85374546064131
rs4794737    9.41576680248523
rs10033399    9.36407447191822
rs4242382    9.22809709356544
rs4242384    8.91767075801336
rs9656816    8.61480602028324
rs982354    8.40833878650415
rs31226            8.38047936810042
SNP

my $mapFile = <<MAP;
rs10904494    NP_817124    17881
rs7837688    NP_817124    39800
rs4881551    ZMYND11    21567
rs7909028    ZMYND11    5335
rs10499549    ZMYND11    0
rs12779173    ZMYND11    0
rs2448370    ZMYND11    0
rs2448366    ZMYND11    0
rs2379078    ZMYND11    0
rs3749375    ZMYND11    0
MAP

my %snpLookup;

# Populate the hash
open my $snpIn, '<', \$snpFile or die "Can't open snp file: $!";
/^(\w+)\s+(\d+\.\d+)/ and $snpLookup{$1} = $2 while <$snpIn>;
close $snpIn;

# Perform the search and report
open my $mapIn, '<', \$mapFile or die "Can't open map file: $!";
/^(\w+)\s+(\w+)/ and exists $snpLookup{$1} and print "$1    $2\n"
    while <$mapIn>;
close $mapIn;

[download]

Prints:

rs7837688    NP_817124
rs10499549    ZMYND11
rs3749375    ZMYND11

[download]

The output is in a different order than specified in the OP. If the order is important there are various ways of fixing the problem with very little extra performance cost.

Perl is environmentally friendly - it saves trees

In reply to Re: Searching Huge files by GrandFather
in thread Searching Huge files by biomonk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.