perl script not giving output

Question

[bioinfo355]

The following program is suppose to read rs ID's of SNPs from the file 'testID' and then search them from file 'testSNP' and sends the output to testSNP.out. I through multiple print statements have debugged the program and found no error but it is not generating the output. what is the problem with this code?

#!/usr/bin/perl 
use warnings;
use strict;

my $rs_id;
open (my $id_file, '<testID') or die "Could not open the file: $!\n";
while ($rs_id = <$id_file>) {
findVariants($rs_id); }

close $id_file;
print "Done\n";

sub findVariants {
my ($rs_num) = @_;
open (my $in_file, '<testSNPs') or die "Could not open the file: $!\n";
my @snp = <$in_file>;
my @result= grep /$rs_num/, @snp; 
print @result;
open (my $out_file, '>>testSNPs.out');

print $out_file @result;

close $out_file;
close $in_file; 
}

[lakhujanivijay]

Share the contents of testID so that I can run the same at my end and troubleshoot. Will be happy to assist

[bioinfo355]

I have added the 'chomp' statement and now it is working fine.

[Jean-Karim Heriche]

One thing to look for is that when reading from a file, the variable includes the end of line character(s), so in your case $rs_id contains the whole line including the \n character (assuming Linux), e.g. $rs_id contains 'rs1234\n'. So later when trying to match, you still have this end-of-line character. Try:

while ($rs_id = <$id_file>) {
  chomp($rs_id);
  ....

[bioinfo355]

yes it works fine now. Thank you