The following code is working fine with the file 'testID' but when this program gets the input from 'piSNPs' file instead of 'testID' then it produces wrong input. The following program is suppose to get IDs from 'testID' file and then search for those IDs in testSNPs file. 'testID' has some IDs that get match and some do not get match and the program gives correct output and shows those IDs which get match. but when I use 'piSNPs' as an input file which has all those IDs none of which are present in 'testSNPs' then program gives wrong output. it shows all the data of testSNPs while it was suppose to give no output as none of the ID got matched. I have shown a line from my testSNPs file to give the idea as the file is large.

!/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>) {

chomp($rs_id);

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;

open (my $out_file, '>>testSNPs.out');

print $out_file @result;

close $out_file;

close $in_file; }

rs559388654

rs528510043

rs551517067

rs201326893_ Y152OCH

rs147422954

rs568103159

rs683

rs1805008

rs1805009

N29insA

rs1110400

rs11547464

rs1805005

rs1805006

rs1805007

rs1805008

rs1805009

rs201326893_ Y152OCH

rs2228479

rs885479

rs2378249

CHROM POS ID REF ALT QUAL FILTER INFO

1 10505 rs548419688 A T 100 PASS AC=1;AF=0.000199681;AN=5008;NS=2504;DP=9632;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS _AF=0;AA=.|||;VT=SNP