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Can find overlapping coordinates

 


oxydeepu
New User

Jul 11, 2013, 4:30 AM

Post #1 of 4 (5156 views)
Can find overlapping coordinates Can't Post
I have a file of exons like this where col1 is chromosome name col2 is orientation and rest are start and stop.

Contig0 + 127874 130761
Contig0 + 129936 129984
Contig0 + 130573 130607
Contig0 + 130630 130761
Contig0 + 130732 130767
Contig0 + 130784 130818
Contig0 + 130832 130866
Contig0 + 130832 130867
Contig0 + 130893 130928
Contig0 + 130970 131004
Contig0 + 130982 131017


The question is

how to get the overlapping coordinates pairs if there any? If yes take the smallest start position and largest stop position from overlapping coordinates and if no overlap for a pair, report as it is?

for example

Contig0 + 127874 130761
Contig0 + 129936 129984
Contig0 + 130573 130607
Contig0 + 130630 130761
Contig0 + 130732 130767

in this block the result will be

Contig0 + 127874 130767

So at last the result for the example block will be

Contig0 + 127874 130767
Contig0 + 130784 130818
Contig0 + 130832 130867
Contig0 + 130893 130928
Contig0 + 130970 131017

I hope the question is clear.
Can anyone please help me with this.
Thank you in advance,
Deepak


BillKSmith
Veteran

Jul 11, 2013, 8:28 PM

Post #2 of 4 (5145 views)
Re: [oxydeepu] Can find overlapping coordinates [In reply to] Can't Post
The following code demonstrates my method for a single chromosome. It assumes that all exons are in the order of their starting positions. (We can sort them first if necessary.)

If you provide a more realistic sample of your data, I can generalize the code to process it.

Note: I assume that orientation should be ignored in forming ranges.

Code
use strict; 
use warnings; 
my ($range_start, $range_end); 
my ($chrom      , $orientation); 
my @ranges; 
while (my $exon = <DATA>) { 
    my ($start_position, $end_position); 
    chomp $exon; 
    ($chrom, $orientation, $start_position, $end_position) = split /\s/, $exon; 
    if (!defined $range_start) { 
        ($range_start, $range_end) = ($start_position, $end_position); 
        next; 
    } 
    if ($start_position > $range_end) { 
        push @ranges, [$range_start, $range_end]; 
        ($range_start, $range_end) = ($start_position, $end_position); 
    } 
    elsif ($start_position <= $range_end and $end_position > $range_end) { 
        $range_end = $end_position; 
    } 
} 
push @ranges, [$range_start, $range_end]; 
 
print "$chrom $orientation $_->[0] $_->[1]\n" foreach @ranges; 
 
          
__DATA__ 
Contig0 + 127874 130761  
Contig0 + 129936 129984  
Contig0 + 130573 130607  
Contig0 + 130630 130761  
Contig0 + 130732 130767  
Contig0 + 130784 130818  
Contig0 + 130832 130866  
Contig0 + 130832 130867  
Contig0 + 130893 130928  
Contig0 + 130970 131004  
Contig0 + 130982 131017
OUTPUT:
Code
Contig0 + 127874 130767 
Contig0 + 130784 130818 
Contig0 + 130832 130867 
Contig0 + 130893 130928 
Contig0 + 130970 131017
Good Luck,
Bill


oxydeepu
New User

Jul 11, 2013, 10:41 PM

Post #3 of 4 (5142 views)
Re: [BillKSmith] Can find overlapping coordinates [In reply to] Can't Post
Thank you Bill,

The file need not to be sorted all the time, but you you don't need to worry about the orientation. We just need overlapping regions.

I am attaching a bigger part of my data.

Can you take a look at it.

Thanks once again.

Regards,
Deepak
Attachments: test.bed.txt (5.39 KB)


BillKSmith
Veteran

Jul 13, 2013, 7:09 AM

Post #4 of 4 (5125 views)
Re: [BillKSmith] Can find overlapping coordinates [In reply to] Can't Post
Try the attached program. Please report any errors that your find. I know that there are minor errors in the documentation that are not worth fixing until the program is finalized.

Perhaps in the future, I will have time to do the sorting in the main program.
Good Luck,
Bill
Attachments: ranges.pl (4.73 KB)
  range_sort.pl (0.20 KB)
  ranges.html (5.84 KB)
  test.bed.txt (5.39 KB)
  test.bed.sorted.txt (5.61 KB)

 
 


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