what is the correct loop/conditional option for not finding a variable? - perl

Question

I am searching through three text files for one of four specific gene names (stored in $var#). When it is found, it takes the value found after the gene name and adds it to a count. We then average the value by taking total $count_exp# and dividing by the number of appearances within all files.
What is the proper way to let the user know when a gene name is not found in each file? I'm having difficulties handling the flow of this loop/conditional.
Here is a snippet of code that handles one of the three text files....
foreach $hyperosmotic(#hyperosmotic)
{
#hyperosmotic1=split(/\t/,$hyperosmotic);
$name=$hyperosmotic1[0];
$exp=$hyperosmotic1[1];
chomp $name;
chomp $exp;
if ($name eq $var1)
{
$count_exp1 = $count_exp1 + $exp;
$count_var1 = ++$count_var1;
}
elsif ($name eq $var2)
{
$count_exp2 = $count_exp2 + $exp;
$count_var2 = ++$count_var2;
}
elsif ($name eq $var3)
{
$count_exp3 = $count_exp3 + $exp;
$count_var3 = ++$count_var3;
}
elsif ($name eq $var4)
{
$count_exp4 = $count_exp4 + $exp;
$count_var4 = ++$count_var4;
}
}

Answer 1

You basically want to use arrays:
(and use strict; use warnings;)
my #count_var = (0)x4;
my #count_exp = (0)x4;
my #var = ($var1, $var2, ...);
HYPEROSMOTIC:
for my $hyperosmotic (#hyperosmotic) {
my ($name, $exp) = split /\t/, $hyperosmotic;
for my $i (0 .. $#var) {
if ($name eq $var[$i]) {
$count_exp[$i] += $exp;
$count_var[$i]++;
next HYPEROSMOTIC; # jump into next iteration of the labeled loop
}
}
# this code is only reached if no var matched:
die qq[I don't have a var for name "$name"];
# That just threw a fatal error. You may want to do something different.
}
You could improve efficiency by using hashes:
my %counts = (
$var1 => {exp => 0, var => 0},
$var2 => {exp => 0, var => 0},
$var3 => {exp => 0, var => 0},
$var4 => {exp => 0, var => 0},
);
for my $hyperosmotic (#hyperosmotic) {
my ($name, $exp) = split ...;
if (my $count = $counts{$name}) {
$count->{exp} += $exp;
$count->{var}++;
} else {
die qq[I don't have a var for name "$name"];
}
}