Unique bases from .gff file

[Khanjan]

Hey all,

I want to find the unique number of bases from the gff file. My problem here is the exons might be overlapping. I tried one algorithm but it failed.

For example -
Start Stop
8 11
9 14
10 18
15 20

1. I took each Set A and compared with all the others
2. if Set A overlapped with Set B, I took the minimum start point and maximum end point and marked the Set B as 'Done' ( i.e. do not consider them again ).
3. After comparing Set A to all the coordinates, I found the bases in Set A. ( End - Start ) ( zero based )

I repeated the process for all the co-ordinates.

However, this fails.

Can anyone please tell me some other way to do this.

Thanks in advance,
K

[westerman]

Hey all,

I want to find the unique number of bases from the gff file. My problem here is the exons might be overlapping. I tried one algorithm but it failed.

For example -
Start Stop
8 11
9 14
10 18
15 20

The memory intensive but straight-forward way is to put all of the bases into one large array. E.g., something like this (sort of perlish code):

@array=();
foreach $line (@lines) {
($begin, $end) = split /\s+/, $line;
$array[$base] = 1 foreach ($begin ... $end);
}

$count = 0;
for $pos (0..$#array) {
$count++ if $array[$pos] == 1
}

print "count is $count\n";

----
I am sure there is better code (and I didn't test the above). And your language will vary. But the idea is dead simple.

[Khanjan]

Thanks !

Khanjan