Loop through file to create interval tree

[pinha]

Hi,

I have a series of tables with the following interval information:

start    end    ID
36701    40200    1
37901    39700    2
36701    39700    3

I want to find overlaps between the intervals of the IDs. Do different IDs have overlapping intervals? If so, what is the overlap and where?

I realise that the best way to approach my problem is to use an interval tree. I have been trying to use the module Set::IntervalTree but I am stuck.

Basically I am not sure how to loop through my file columns to fill the interval tree.

This is what I have so far:

#!/usr/local/bin/perl
use strict;
use warnings;
use Set::IntervalTree;
use Data::Dumper;

#get the scaffold file name from user input (@ARGV) and stores in $fil
+e
#opens the scaffold file so that it can be used to fill the empty inte
+rval tree
my $file = shift;
open my $fh, '<', $file or die "Cannot open $file: $!";


#create an empty interval tree
my $tree = Set::IntervalTree -> new();


#loop to the file, read each line and add objects to the empty interva
+l tree
#there will be as many objects in the interval tree as there are hits 
+for the specific file

my %overlap_table;

while (my $line=<$fh>){                      #while there are lines

      my @low = split("\t", $line);   #get the <code> value from the 1
+st column (start position = low BT)
                                print "$low[0]\n";
        $overlap_table{$low[0]}++;


        my @high = split("\t", $line);  #get the value from the 2nd co
+lumn (end position = high BT)
                              print "$high[1]\n";
      $overlap_table{$high[1]}++;


       my @ID = split ("", $line);     #ID information is the "value"
                              print "$ID[2]\n";
      $overlap_table{$ID[2]}++;
                       }

close($fh);
 print Dumper \%overlap_table;

I now want to use each one of the $low, $high and $ID to fill in the tree.

I would like to be able to loop through the file automatically.

I have lots of files with lots of lines and so entering the values manually is not a good option

To sum up, I would love if someone could help me understand how I loop through the lines of my $fh so that I can fill in the interval tree according to the following requirement:

 $tree->insert($ID, $low, $high) for each one of the lines.

Thank you so much in advance!

[Laurent_R]

Please fix your formatting to make your code readable. Put one opening <code> at the beginning of the code, one closing </code> tag at the end of your code, and no <code> tag in the middle of your comments.

Otherwise, your splitting is very inefficient. You could get your 3 variables in just one operation:

while (my $line=<$fh>){ 
     chomp $line;
     my ($low, $high, $id) = split /\t/, $line;
     # ...