Hi Monks, I have three tab-delim files.

mainfile 

START STOP TYPE MEAN

1456   5385   p  98
6739  5468    n  87
6543  7275    n  54
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file 1

NAME-WITH    START   STOP  
qqq            4202    8644
rrr              6399   3256
eee            6438   8456
….
…
ttt            1456   5385
ggg         6543   7275
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file 2

NAME-WITHOUT START STOP
ddd   3467   3284
bbb   6739   5468
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What I want is to input the first file and read in the following file 1 and file 2. So something like this should be happening, Checking the main file start and stop overlap with start and stop of first file 1 and second file 2.

Overlap of the starts and stops in each line of these files (file1 and file2) can be in following ways:

 start (file1/2)stop---- start(mainfile)stop----start(file1/2)stop

a. either the file1/2 stop is less than mainfile start ; then return 0
b. either the file1/2 start is less than mainfile stop; then return 0
or else if
a. the file1/2 stop is less than the mainfile start; then return 1 and say what name-without/with, start and stop (eg: qqq, 4202 8644)
b. the file1/2 start is less than mainfile stop; then return 1 and say what name-without/with, start and stop (eg: qqq, 4202 8644)
c. the file1/2 start and stop both is less than mainfile start stop; then return 1 and say what name-without/with, start and stop (eg: qqq, 4202 8644)
d. the file1/2 start and stop both is less than mainfile start stop; then return 1 and say what name-without/with, start and stop (eg: qqq, 4202 8644)

------------------------------

Is there any way to address this? I started working on the code but I am stuck as to how to proceed..Pardon if is difficult to understand what I am asking but I tried my best to describe the whole picture. Here is my code:

#!/usr/bin/perl

#Open the  mainfile with start, stop  

my $input_file = "/Users/myfolder/mainfile.txt";
die "Cannot open $input_file\n" unless (open(IN, $input_file));

my %start_stop_type;
while (chomp($line = <IN>))
{
    my (@columns) = split /\s+/, $line;
    my $type = $columns[3];
        my $start = $columns[1];
    my $stop = $columns[2];
        $type_and_start{$type} = $start;
        $type_and_stop{$type} = $stop;
}
close(IN);

#Now open both the files i.e file1 and file2 with respective start and
+ stops

open (MYFILE, "/Users/myfolder/file1.txt");
@file1 = <MYFILE>;
close MYFILE;
open (MYFILE2, "/Users/myfolder/file2.txt");
@file2 = <MYFILE2>;
close MYFILE2;

foreach $line (@file1,@file2){
###NOT SURE??

if $file1/2_start<mainfile_start;
return 0
???







#Open output file and write the start stops of each name-with/without
die "output.txt" unless(open(OUT,"> output.txt"));
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