Eliminating unitialized values in my Perl hash of arrays - arrays

Question

I successfully create a hash of arrays, and I am using it to calculate log-odds scores for each DNA sequence from a file (Creating a hash of arrays for DNA sequences, Perl has input file format). I get a score for each sequence, but I get a warning for each calculation. Naturally, I want to clear up the warning. The warning is: Use of uninitialized value in string eq at line 148.
Here is a summarized version of the code (I can post the full code if necessary):
use strict;
use warnings;
use Data::Dumper;
#USER SPECIFICATIONS
print "Please enter the filename of the fasta sequence data: ";
my $filename1 = <STDIN>;
#Remove newline from file
chomp $filename1;
#Open the file and store each dna seq in hash
my %id2seq = ();
my %HoA = ();
my %loscore = ();
my $id = '';
open (FILE, '<', $filename1) or die "Cannot open $filename1.",$!;
my $dna;
while (<FILE>)
{
if($_ =~ /^>(.+)/)
{
$id = $1; #Stores 'Sequence 1' as the first $id, for example
}
else
{
$HoA{$id} = [ split(//) ]; #Splits the contents to allow for position reference later
$id2seq{$id} .= $_; #Creates a hash with each seq associated to an id number, used for calculating tables that have been omitted for space
$loscore{$id} .= 0; #Creates a hash with each id number to have a log-odds score
}
}
close FILE;
#User specifies motif width
print "Please enter the motif width:\n";
my $width = <STDIN>;
#Remove newline from file
chomp $width;
#Default width is 3 (arbitrary number chosen)
if ($width eq '')
{
$width = 3;
}
#Omitting code about $width<=0, creation of log-odds score hash to save space
foreach $id (keys %HoA, %loscore)
{
for my $pos (0..($width-1))
{
for my $base (qw( A C G T))
{
if ($HoA{$id}[$pos] eq $base) #ERROR OCCURS HERE
{
$loscore{$id} += $logodds{$base}[$pos];
}
elsif ( ! defined $HoA{$id}[$pos])
{
print "$pos\n";
}
}
}
}
print Dumper(\%loscore);
The output I get is:
Use of uninitialized value in string eq at line 148, <STDIN> line 2.
2
(This error repeats 4 times for each position - most likely due to matching to each $base?)
$VAR1 = {
'Sequence 15' => '-1.27764697876093',
'Sequence 4' => '0.437512962981119',
(continues for 29 sequences)
}
To summarize, I want to calculate the log-odds score of each sequence. I have a log-odds score hash %loscore that contains the score of a base at each location within a motif. The log-odds score is calculated by summing the referenced values. For example, if the log-odds table was
A 4 3 2
C 7 2 1
G 6 9 2
T 1 0 3
The log-odds score of the sequence CAG would be 7+3+2=12.
At the moment, I believe that the error occurs because of the way I split the strings of DNA to be put into the hash of arrays. As I previously stated, if you want all the code so you can copy-paste, I can provide it. I think the solution is pretty simple, and I just need someone to point me in the right direction. Any and all help is appreciated, and I can clarify as questions arise. Also, any tips that could help me to post more concise questions are appreciated (I know this one is lengthy, I just want to provide enough background information).

Answer 1

Here is the code that I am using to iterate through the `%HoA. It calculates a log-odds score for each sequence, then works through each sequence to find a maximum score for each sequence. Big thanks to everyone for helping out!
foreach $id (keys %HoA)
{
for my $pos1 (0..length($HoA{$id})-1)
{
for my $pos2 ($pos1..$pos1+($width-1))
{
for my $base (qw( A C G T))
{
if ($HoA{$id}[$pos2] eq $base)
{
for my $pos3 (0..$width-1)
{
$loscore{$id} += $logodds{$base}[$pos3];
if ($loscore{$id} > $maxscore{$id})
{
$maxscore{$id} = $loscore{$id};
}
}
}
elsif ( ! defined $HoA{$id}[$pos2])
{
print "$pos2\n";
}
}
}
}
}