G'day TJCooper,

I've provided an example script below which shows some techniques that you might use for this. I've assumed your IN2 file just contains headers (your description wasn't 100% clear on that). If you're going to be reusing IN2, you may want to consider running the first part of the script separately, and storing the @all_order data: a database, Storable, or other serialisation methods are all possible candidates (depends on your requirements and what you have available). 

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

use Data::Dump;

my @all_order; 

{
    open my $in2_fh, '<', 'pm_1204589_IN2';

    while (<$in2_fh>) {
        chomp;
        push @all_order, $_;
    }
}

for my $range ([0..0], [0..2], [1..3], [3..3]) {
    my %wanted = map { $_ => 1 } @all_order[@$range];

    {
        open my $in1_fh, '<', 'pm_1204589_IN1';

        local $/ = "\n>";

        while (<$in1_fh>) {
            chomp;
            substr $_, 0, 1, '' if $. == 1;
            my ($head, $seq) = split;
            $wanted{$head} = $seq if $wanted{$head};
        }
    }

    print "Range: @$range\n";
    dd \%wanted;
}

[download]

With these dummy files (yes, I know, the sequences are totally bogus — just used for demonstration purposes): 

$ cat pm_1204589_IN1
>Z
ABC
>Y
DEF
>X
GHI
>W
JKL

[download]
$ cat pm_1204589_IN2
W
X
Y
Z

[download]

I get this output: 

Range: 0
{ W => "JKL" }
Range: 0 1 2
{ W => "JKL", X => "GHI", Y => "DEF" }
Range: 1 2 3
{ X => "GHI", Y => "DEF", Z => "ABC" }
Range: 3
{ Z => "ABC" }

[download]

See also: Data::Dump.

— Ken

In reply to Re: Loading only portions of a file at any given time by kcott
in thread Loading only portions of a file at any given time by TJCooper

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.