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!
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