Table matching and concatenation

[kumarboston]

Hi All,
I have 2 tables:
tab1: has 4 columns tab separated- id,ac,start,end.
tab2: has 3 columns tab separated- id, seq, desc.

what i am trying to do, when id of tab1 matches with id of tab2 then program should take start and end coordinates from tab1 and pool out seq from tab2 and trying to make a third table with id, ac, seq(with only start and end coordinate).

my code is given below but its giving me some uninitialized errors.

#!/usr/bin/perl
use strict;
use warnings;
 
my ($start,$end,$sequence,$se,@se,$id,$acc,$seq);
my $cnt=0;
my %hash;
open(FH,"test1");
while(<FH>)
{
    my @temp = split(/\t/,$_);
        $id    = $temp[0];
        $acc   = $temp[1];
        $start = $temp[2];
        $end   = $temp[3];
        $hash{$acc} = $id;
    #print "$temp[1]\t$temp[2]\t$temp[3]\n";
}
while ( ($acc,$id) = each %hash ) {
    #print "$acc => $id\n";
}
close(FH);
 
open(TH,"test2");
while(<TH>)
{
    chomp $_;
    my @temp1=split(/\t/,$_);
 
    if(exists $hash{$temp1[0]})
    {
        #print "$hash{$temp1[0]}\n";
        @se=split("",$temp1[2]);
        do{
            if($start eq @se)
            {
                $seq .=$temp1[2];
            }
        } while($end eq @se);
    print "$seq\n";
    }
 
 
    #print "$se[0]\n";
    #$cnt++;
 
    #print "$temp1[2]\n";
}
#print $cnt;
close(TH);
 
 

thanks for any help.
Kumar

[numberwhun]

Well, to start with, can you post the "uninitialized errors"? We will want you to have those worked out first.

Regards,

Jeff

[KevinADC]

even if he gets that worked out, this is not correct usage/syntax, although I am unsure what the OP is trying to do with this condition:

while($end eq @se);

and there is is no hash here:

while ( ($acc,$id) = each %hash ) {
    #print "$acc => $id\n";
}

but I guess that loop isn't doing anything ayway. Probably more basic problems in the code.

Seing a sample of the data would also be nice.