Dear Monks,

Hi I have written a program using hash of hashes type of data structure. I am using the keys in File 1 to parse the file 2.
I am unable to get the correct output. I have got many multiple values for the single key in my File 1.
I am getting this error / warning in my program

Use of uninitialized value in hash element at TEST.pl line 17, <$fh> l
+ine 4.
Use of uninitialized value in hash element at TEST.pl line 18, <$fh> l
+ine 4.
Use of uninitialized value in hash element at TEST.pl line 17, <$fh> l
+ine 5.
Use of uninitialized value in hash element at TEST.pl line 20, <$fh> l
+ine 5.
KEY  in File1 not found in File2
KEY  in File1 not found in File2
KEY 155369268: File2 string length too short for File1 position value
KEY 155369268: File2 string length too short for File1 position value
KEY 269212605: File2 string length too short for File1 position value
[download]

Here is my code

#!/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>) {

   chomp;

   my ($key, $pos) = split /\s+/;

   if (!$positions{$key}) {

     $positions{$key} = [$pos];

   } else {

     my $ref = $positions{$key};

     push @$ref,$pos;

   }

}

}



my %sequences;

{

   open(my $fh, '<', $qfn2)

      or die("Cannot open file \"$qfn2\": $!\n");



   my $key;

   while (<$fh>) {

       if ( s/^>// ) {

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

       }

       else {

           chomp;

           $sequences{$key} .= $_;

       }

   }

}



for my $key ( sort keys %positions ) {

   my $ref = $positions{$key};

   foreach my $value (@$ref) {

    if ( ! exists( $sequences{$key} )) {

        warn "KEY $key in File1 not found in File2\n";

        next;

    }

    if ( length( $sequences{$key} ) < $positions{$key} ) {

        warn "KEY $key: File2 string length too short for File1 positi
+on value\n";

        next;

    }

    my $index = rindex( $sequences{$key}, "ATG", $positions{$key} );

    if ( $index < 0 ) {

        warn sprintf( "KEY %s: No ATG in File2 string prior to positio
+n %d\n",

                      $key, $positions{$key} );

        next;

    }

    $index += 3 while ( ($index + 3) < $positions{$key} );

    print "$key $positions{$key} " . substr($sequences{$key}, $index, 
+3) . "\n";

}



}
[download]

My Input file looks like this:-

 
File 1:-
155369268 17 A 
155369268 70 G
269212605 75 T

File 2:-
>gi|155369268|ref|NM_001100917.1| some text
AAACAATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGAATGGGAGCTTACGGTTTTTTACG
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
>gi|269212605|ref|XM_401716884.1| some text 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCTATGAC
CTAATTGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
[download]

I want my Output should be like this:-

155369268 17 CTA 
155369268 70 CGA
269212605 120 TTG
[download]

good bye

20081224 Janitored by Corion: Restored content

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