in reply to Bioinformatics- Use of uninitialized value

I'm not a bio-guy, so just some general thoughts.

... error: Use of uninitialized value $_ in pattern match (m//) at /Users/.../Triple.pl line 66.

This is not an error, but a warning. Warnings are enabled by use-ing the warnings pragma, which the script you posted does not do. I don't see how you could get the quoted warning from the posted code (update: unless you're using the  -w command-line switch to invoke your script — Ah-ha, I see it now in the shebang invocation: strike this comment). 

c:\@Work\Perl\monks>perl -MData::Dump -le
"use strict;
 ;;
 my $rx = 'x';
 my @ra = grep !/$rx/, undef;
 dd \@ra;
"
[undef]

c:\@Work\Perl\monks>perl -MData::Dump -le
"use strict;
 use warnings;
 ;;
 my $rx = 'x';
 my @ra = grep !/$rx/, undef;
 dd \@ra;
"
Use of uninitialized value $_ in pattern match (m//) at -e line 1.
[undef]

[download]
my @third_fragments = grep !/$rsite3/, $second_fragments[$i];

grep operates on a list, but this statement has a list consisting only of the  $second_fragments[$i] scalar, i.e., a single item. The  @third_fragments array can then be initialized with only zero or one elements. I don't know if this was intended. Further, I don't offhand see any reason the  @second_fragments array must contain  $i + 1 elements; thus, you may be accessing an element that's "off the end" of the array and therefore undefined.

Update: Finally saw  -w in shebang invocation, so strike entire first 'thought'.

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