There is a pile of stuff that can be tidied up there. First off, always use strictures (use strict; use warnings;).

Use chomp instead of chop.

Use the three parameter version of open and check the result. Use lexical file handles:

open my $inFile, '<', "MOUSE_TF1.txt" or die "Failed to open MOUSE_TF1
+.txt: $!";

[download]

Instead of using "parallel" data structures that have to be handled piecemeal, group common data using a hash:

use warnings;
use strict;

open my $inFile, '<', "MOUSE_TF1.txt" or die "Failed to open MOUSE_TF1
+.txt: $!";

my %families;
my @fields = qw(chr start end symbol strand);

while (<$inFile>) {
    my $line = $_;
    chomp ($line);

    my @Gene_Info = split "\t", $line;
    my $id = shift @Gene_Info;

    @{$families{$id}}{@fields} = @Gene_Info;
}
close $inFile;

# select Gene Symbols belonging to "Hox" family and print
foreach my $key (keys %families) {
    if ($key =~ /Hox/) {
        print join ("\t", $key, @{$families{$key}}{@fields}), "\n";
    }
}

[download]

untested

Perl reduces RSI - it saves typing

In reply to Re: If Statements and Regular Expressions by GrandFather
in thread If Statements and Regular Expressions by TempAcolyte

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.