G'day lairel,

"I keep getting errors about uninitialized variables and needing explicit declaration."

Those error messages should tell you the variable involved and other information: use this to track down your problem. If you need help with any particular error message(s), you'll need to show us the text also.

"I have tried so many things that I am lost and confused ..."

You need to understand fundamental constructs, such as while loops. I suggest you read "perlintro -- a brief introduction and overview of Perl".

Consider this technique for accessing fasta files for this type of work: 

#!/usr/bin/env perl

use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        $_ = substr $_, 1 if $. == 1;

        my ($head, $data) = split /\n/;

        if ($head eq $ARGV[0]) {
            print "Found! Head: '$head'; Data: '$data'\n";
            last;
        }
    }
}

__DATA__
>head1
data1
>head2
data2
>head3
data3

[download]

Some test runs:

$ pm_1159403_fasta.pl head1
Found! Head: 'head1'; Data: 'data1'
$ pm_1159403_fasta.pl head2
Found! Head: 'head2'; Data: 'data2'
$ pm_1159403_fasta.pl head3
Found! Head: 'head3'; Data: 'data3'

[download]

See also: $/ - input record separator; $. - input line number.

— Ken

In reply to Re: While loop with nested if statements by kcott
in thread While loop with nested if statements by lairel

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