As your input file looks a lot like a variant on CSV (with spaces and newlines as delimiters), I would suggest using one of the modules for parsing these types of files off of . My usual choice is Text::CSV, but the search results for CSV will give you an idea of how many solutions are out there for this parsing problem. The above module will generate an array of arrays for you - let us know if you have difficulty dealing with Perl references.

Your code may end up looking something like this (adapted from the documentation):

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

my @result;
my $csv = Text::CSV->new ( { sep_char => ' ' } )  # should set binary 
+attribute.
                or die "Cannot use CSV: ".Text::CSV->error_diag ();
 
open my $fh, "<", "test.csv" or die "test.csv: $!";
while ( my $row = $csv->getline( $fh ) ) {
    if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0/\E}) {
        if (@result) {
            $result[1] = $row->[3];
        } else {
            $result[0] = $row->[2];
        }
    }
}
printf "%s\t%s\n", @result;
$csv->eof or $csv->error_diag();
close $fh;
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As you did not wrap your input text in <code> tags, it's possible the files were mangled during posting. For example, if your file is actually tab delimited, you would need to specify "\t" as your delimiter, not " ".

Update: Fixed typo in code

Thanks for helping out with this I really appreciate the input from you guys.

I tried the above code but I get an error:

Use of uninitialized value in printf at parse_result.txt.pl line 23, <$fh> line 45.

The code I used was practically the same as yours except for changing the name of the input file to results.txt and changing the " " to "\t"

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


my @result;
my $csv = Text::CSV->new ( { sep_char => '\t ' } )  # should set binar
+y +attribute.
                or die "Cannot use CSV: ".Text::CSV->error_diag ();

open my $fh, "<", "result.txt" or die "result.txt: $!";

while ( my $row = $csv->getline( $fh ) ) {
    if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0//E}) {
        if (@result) {
            $result[1] = $row->[3];
        } else {
            $result[0] = $row->[2];
        }
    }
}
#printf "%s\t%s\n", @result;
printf  @result;
$csv->eof or $csv->error_diag();
close $fh;
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oops, shouldn't have included the printf @result; in the code, but it still doesn't work with the

#printf "%s\t%s\n", @result;

uncommented........

use strict;

my @last;
my $lastKey;
while (<DATA>) {
    my @rec = /(\S+)/;
    my ($key) = $rec[0] =~ m/([^#]+)/;

    if ($key eq $lastKey) {
        print "matching $key\n";
    }

    @last = @rec;
    $lastKey = $key;
}

__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]