Dear Monks,
I came up with a script for parsing 2 files but it is giving
me many warning and error messages. I am not getting howto
debug. Can somebody help ?

My File 1 looks like this:- 
155369268 300
169212695 200

My File 2 looks like this:-
>gi|155369268|ref|NM_802300917.1| Homo sapiens ewqeqwaspanin 19 (USUAN
+23), mRNA
CCTGCTCTCGATTCTAATGTGATGCGAACGCAGCATTTCAGGGACTGGATGAGGAGCTTACGGTTTTTT
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
CTTAATCTCATTAATGGAGCTTTCTTGGTTCTTGGACTTTTATTCATGGGATTTGGTGCATGGCTCTTAT
TAGATAGAAATAATTTTTTAACAGCTTTTGATGAAAATAATCACTTCATAGTACCTATTTCTCAAATTTT
GATTGGAATGGGATCTTCTACTGTTCTTTTTTGTCTATTGGGTTATATAGGAATTCACAACGAAATCAGA
TGGCTCCTAATTGTGTATGCAGTATTGATAACATGGACCTTTGCTGTTCAGGTTGTACTTTCAGCATTCA
TCATCACAAAGAAAGAGGAGGTTCAGCAACTATGGCATGACAAAATTGATTTTGTCATTTCTGAGTATGG
ATCTAAAGATAAGCCTGAAGATATAACCAAGTGGACTATTCTGAATGCCTTACAGAAAACATTACAGTGT
TGTGGCCAACATAATTACACAGACTGGATAAAGAATAAGAACAAAGAAAATTCAGGACAGGTGCCATGTT
CTTGCACAAAGTCAACTTTAAGAAAATGGTTTTGTGATGAGCCACTGAATGCAACTTACCTTGAGGGTTG
TGAAAATAAAATCAGTGCATGGTATAATGTTAATGTGTTAACCTTAATCGGAATTAACTTTGGACTTTTA
ACTTCAGAGGTTTTCCAAGTCTCATTAACAGTTTGTTTCTTCAAAAACATCAAGAATATAATCCATGCAG
AAATGTGACCTTTGGATTTCAATTTGTTCAGAAGAAACCAGTTAATTCTTAAAAAATCACATTA
>gi|169212695|ref|XM_96216884.1| PREDICTED: Homo sapiens hypothetical 
+protein UJI1001326087 (YHC1001326768), mRNA
ATGTGTGTATATATATATATGCATATATATGTGTGTGTATATATATATACACATATATATGTGTGTGTAT
ATATATACACATATATATGTGTGTGTATATATATATACACATATATATGTGTGTATATATATATACACAC
ACATATATATGTATACATATACATGTATATGTATATATGTATACATATACATATATATGTATATATGTAT
ACATATACATATATACGTATATATACATATATGTATATATGTAAGTATACGTATATATACATATATGTAT
ATGTATGTACATATATATGCATGCACATATATATGTATTTATATATATGCATGTATATGTATATGCATGT
ACATATGGATGTATATATGCACGCATGTCTGTACATATGCATGTATGTATGTACATATAAATGTATATAT
ATGTATACATACATGTGTATATATACATGTATATGTATGTATACGTACATACATATGTATGTATACGTGT
ATGTATACATACATATGTATGTATGCGTACATACATATGTATACGTACATACATATGTATGCTTACACAC
ATGTATGCTTACACACATATGTATGTACGTGTACATACATATGTACACGTACATACATATGTACACGTAC
ATACATATGTTCCAGAGGAAGAAGAAACAAGTGTCTGGTGCCCAGAGACGACCAGATGCCCCACCAGTTC
TGATCCATAGGAGAATGATCGTTCCACATGGCCAACTCCATCCTCATGCAGCAATTCCTCCACAAGCACA
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
TGTGGCCTAACCATGGTCGTGTTGTGCTGGACGTCACAGCAGAGGAGGAGGCGCAGAACAAAGGCTGC
[download]

The error or warning messages are :-

I am getting this error /warning:-
Substr outside of the string at line 42. <$fh> line 2.
Use of Uninitialized value in concatenation or string at line 42. <$fh
+> line 4.
Use of uninitialized value in hash element at line 34. <$fh> line 4. 
...................................
[download]

My code is :-

#!/usr/bin/perl

use strict;
use warnings;

my $qfn1 = "File1.txt";
my $qfn2 = "File2.txt";

my %positions;
{
   open(my $fh, '<', $qfn1)
      or die("Cannot open file \"$qfn1\": $!\n");

   while (<$fh>) {
      my ($key, $pos) = split /\s+/;
      $positions{$key} = $pos;
   }
}

{
   open(my $fh, '<', $qfn2)
      or die("Cannot open file \"$qfn2\": $!\n");

   for (;;) {
      defined( my $key = <$fh> )
         or last;
      defined( my $text = <$fh> )
         or last;
      chomp($key);
      chomp($text);

      $key = (split(/\|/,$key,3))[1];

      defined( my $pos = $positions{$key} ) ##line 34
         or next;

      my $index = rindex($text, "ATG", $pos);
      next if ( $index < 0 );

      $index += 3 while ( ($index + 3) < $pos);

      print "$key $pos " . substr($text, $index, 3) . "\n";  ##line 42

   }
}
[download]

20081224 Janitored by Corion: Restored content

---

---

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! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

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:
	&		&
	<		&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.