My general approach in this type of situation is to build a hash, or more specifically a hash of lists. I am not familiar with your particular input, and figuring out the patterns and how to parse them is usually where most of the effort in writing a script of this type falls. Taking the input from your original post: 

HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1    -    1449586    1449619
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2    -    1449544    1449577
HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1    -    4744083    4744113
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1    -    4867122    4867157
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2    -    4866942    4866977
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1    +    1930232    1930266
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2    +    1930354    1930389

[download]

And fitting the most general pattern that seems to match, I would use code like 

#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV;

my @result;
my $csv = Text::CSV->new ( { sep_char => "\t" } )  # should set binary
+ attribute.
                or die "Cannot use CSV: ".Text::CSV->error_diag ();
 
my %result;
while ( my $row = $csv->getline( *DATA ) ) {
    my ($key, $index) = $row->[0] =~ m{^(.+)/([12])$}
        or die "Line did not match pattern: @$row";
    
    if ($index == 1) {
        $result{$key}[0] = $row->[2];
    } elsif ($index == 2) {
        $result{$key}[1] = $row->[2];
    } else {
        die "Index was not 1 or 2: @$row"
    }
}
$csv->eof or $csv->error_diag();

# Output results:
for my $key (keys %result) {
    next unless $result{$key}[1];
    print "$key:\t$result{$key}[0]\t$result{$key}[1]\n";
}

__DATA__
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1    -    1449586    1449619
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2    -    1449544    1449577
HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1    -    4744083    4744113
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1    -    4867122    4867157
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2    -    4866942    4866977
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1    +    1930232    1930266
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2    +    1930354    1930389

[download]
to get the output 

HWUSI-EAS95L_0025_FC:3:1:6539:1083#0:    4867122    4866942
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0:    1449586    1449544
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0:    1930232    1930354

[download]

Note that because of how tabs get mangled on this site, you'll need to click the download link in order to get the proper formatting in your clipboard.

In reply to Re^8: compare lines within a file by kennethk
in thread compare lines within a file by garyboyd

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.