dear all, i am having a weird problem. i am comparing a specific column between two large files. file1 is a database text file. and file2 is a query text file. i want to compare a particular column (which has alphabets) from file2 to file1. final results should have all the lines in file2, with an extra added column from file1. for example.

file1.db:
zm811463    1190    31050    -    A/G/T/C
zm811462    1190    31051    -    C/T
zm1829427    1190    31789    +    A/G
zm445312    1190    31883    -    A/G
zm5377419    1190    32419    +    A/C
zm1052506    1190    32829    +    C/G
zm1052507    1190    32886    +    A/C/T
zm9115338    1190    33832    +    A/G/CC

file2.query
1190    31277    A > T    1    0    0
1190    31607    C > A    0    3    1
1190    31629    C > T    0    2    0
1190    31789    A > G    1    2    5
1190    31882    A > C    0    4    0
1190    31883    T > A    0    4    0
1190    31883    T > C    2    2    5
1190    32199    C > T    0    1    1
1190    32487    T > C    0    1    1
1190    32496    A > G    0    3    0

output which i am getting now:
1190    31277    A > T    1    0    0    -
1190    31607    C > A    0    3    1    -
1190    31629    C > T    0    2    0    -
1190    31789    A > G    1    2    5    zm1829427
1190    31882    A > C    0    4    0    -
1190    32199    C > T    0    1    1    -
1190    32487    T > C    0    1    1    -
1190    32496    A > G    0    3    0    -

Total number of HITS: 1

BUT, i want my output look like:

1190    31277    A > T    1    0    0    -
1190    31607    C > A    0    3    1    -
1190    31629    C > T    0    2    0    -
1190    31789    A > G    1    2    5    zm1829427
1190    31882    A > C    0    4    0    -
1190    31883    T > A    0    4    0    -
1190    31883    T > C    2    2    5    -
1190    32199    C > T    0    1    1    -
1190    32487    T > C    0    1    1    -
1190    32496    A > G    0    3    0    -

Total number of HITS: 1
[download]

if you notice keenly, these two lines are missing in my output:

1190    31883    T > A    0    4    0       -
1190    31883    T > C    2    2    5       -
[download]

why is this happening? the program so far looks like this:

use strict;
use warnings;
use DB_File;


my $myhashfile = "hash.$$";
tie my %hash1, "DB_File", $myhashfile, O_RDWR|O_CREAT, 0666, $DB_HASH
    or die "cannot open file $myhashfile: $!";


open(OUT,">output.out")or die "can not open";
open(my $fh1, "<", "file1.db") or die "file1.db: $!";


foreach (<$fh1>){
    chomp;
    my @dbinfo = split(/\s+/);
    $hash1{"$dbinfo[1]#$dbinfo[2]"} = "$dbinfo[4]##$dbinfo[0]";
}
close($fh1);


my $c=0;
open(my $fh2, "<", "file2.query") or die "file2.query: $!";
my @snplist;
foreach (<$fh2>) {
chomp($_);@snplist=();

    my @queryinfo = split(/[\s>]+/);
    my $values = $hash1{"$queryinfo[0]#$queryinfo[1]"};
    my ($variant,$rs)=split("##",$values);

    my $flag_left=0;my $flag_right=0;
    @snplist=split("/",$variant);

    if(defined($variant)){ 
    foreach my $lis(@snplist){
        if($queryinfo[2] eq $lis){$flag_left=1;}
        elsif($queryinfo[3] eq $lis){$flag_right=1;}
    }

        if(($flag_left == 1) && ($flag_right == 1)){
        print OUT "$_\t$rs\n";
        $c++;
        $flag_left=0;$flag_right=0;
        }
  }

  else{
    print OUT "$_\t-\n";
  }
}


print OUT "\nTotal number of HITS: $c\n";
close($fh2);

untie %hash1;
unlink($myhashfile);
$myhashfile=();
[download]

using hash tie, because am dealing with large files.using @snplist because, there can be more alphabets to compare and only if both(seperated by ">") the alphabets in file2 third column is present in file1 5th column(which has many seperated by "/"), its considered as hit. plz help.thank you very much.

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