how can I choose particular lines from a file by using a second file - perl

Question

I am trying to filter a file (trying to find the best blast hits) by using a second file.
The file that I want to filter looks like this:
conserved1 chr22 100.00 92 0 0 1 92 19679676 19679767 2e-44 182
.....................
The second file (which is the first input in my script) that I’m using is like this:
conserved1 92
conserved2 76
.....................
(the first column is the name of my ‘item’ which is exactly with the first column of the previous file, and the second column is the size).
I stored the second file in a hash in order to connect the first file with the sizes of the conserved elements and to filter only the lines which the size (4th column) be the 70% of the size (from the 2nd file).
I wrote this script for that purpose, it works but it prints each chosen line more than once.
How can I fix this?
my $size_file = $ARGV[0];
my $alignment_file = $ARGV[1];
open my $con_info, $size_file or die "Could not open $size_file: $!";
my %hash;
while (<$con_info>)
{
chomp;
my ($key, $val) = split /\t/;
$hash{$key} .= exists $hash{$key} ? "$val" : $val;
}
#print "# %hash\n", Dump \%hash;
#print %hash;
#print "#{[%hash]}";
close $con_info;
open my $al_info, $alignment_file or die "Could not open $alignment_file: $!";
while (my $line = <$al_info>) {
chomp;
my#data = split('\t', $line);
my $con_name = $data[0];
my $evalue = $data[10];
my $percent = $data[2];
my $length = $data[3];
# print $con_name. "\n";
foreach my $key (keys %hash) {
if ($key == $con_name) {
#print "key: $key, value: $hash{$key}\n";
if ($evalue <= 1e-4 && $length >= 0.70 * $hash{$key}) {
print $line;
}
}
}
}
The output should be the first file (the file which is at the first code box) but with less lines, the lines that passes through the last if condition.
Thank you very- very much for your help!!!

Answer 1

if ($key == $con_name)
should be
if ($key eq $con_name)
as this should be string comparison.
And you don't really need foreach loop, just to pick one particular key:
while (my $line = <$al_info>) {
chomp($line);
my #data = split('\t', $line);
# my $con_name = $data[0];
# my $percent = $data[2];
# my $length = $data[3];
# my $evalue = $data[10];
my ($con_name, $percent, $length, $evalue) = #data[0,2,3,10];
# print $con_name. "\n";
if ($evalue <= 1e-4 && $length >= 0.70 * $hash{$con_name}) {
print $line;
}
}