perl search algorithm

[lilly07]

Hi, there are two text files as below:

test1.txt

53015910        53018079
53028477        53039398
53057449        53060200
53062918        53067636
53068725        53070903
53073104        53082405
53157340        53159848
53162114        53164278
53170778        53177010
53186077        53190880
 

test2.txt is a tab delimited file and I want to check whether col 13 and col 35 of this values (each line) lies between test1.txt columns. I am trying to search as below:

1. I am adding the contents of test1 into a hashname
2. For each line in the second file, I am checking whether col 13 and col 35 lies between (key and value) of hashname
3. I am trying to interrupt once if the status is set to 1 so that I can stop avoiding the whole of hashname.

#!/usr/bin/perl
 
$st_status;
$end_status;
 
#adding contents into a hash
 
$hashfile = 'test1.txt';
open (LIST1, $hashfile) || die "File not found\n";
     while (<LIST1>) {
                chomp $_;
          @v = split(/\t/, $_);
          $hashname{$v[1]} = $v[2];
     }
close(LIST1);
 
 
#Search in the second file
 
  while(<>) {
 
        $st_status = 0;
        $end_status = 0;
 
        chomp $_;
        @cols=split(/\t/,$_);
 
        while (($key, $value) = each(%hashname)){
                 if(($cols[12] >= $key) && ($cols[12] <= $value)) {
                        $st_status = 1;                        
                        last;
                } 
 
        }
 
        while (($key, $value) = each(%hashname)){
                 if((cols[34] >= $key) && (cols[34] <= $value)) {
                        $end_status = 1;                        
                        last;
                }
 
        }
 
        if (($st_status == 1 ) && ($end_status == 1)) {               
                print "$_\n";                
        } else { next; }
 
}
 
close FILE;
 

Is there any better way to do this? This is taking quite a long time. Thanks.

[numberwhun]

Can you please provide a sample of the second text file? Without it we would be guessing that the solution works.

Regards,

Jeff

[lilly07]

Hi Jeff,

my sample test2.txt contains the following in the 13th and 35th column.

57583225        57580491
57583262        57580492
58049166        58012648
57583215        57580442
59416357        59435981
56506459        56164151
63518481        63509149
58053224        58138139
59675405        60296224
59675408        60296279
 

Hence for every line in test2.txt, I have to check whether "57583225" lies between any on the test1.txt record (e.g 53015910 53018079.. ) as well as "57580491" lies in between any of the record on test1.txt.
Please let me know if u need any more info. Thanks.