Re: Help the counting!

[jethro]

What is bp?

Without exactly knowing what you want I can tell you that your script seems to have 3 loops nested into each other which will make the running time of your script unbearable for non-trivial data. And your problem doesn't seem to need that.

How about this algorithm: Sort the ranges in ascending start position (you need to use a more complex data structure like Array-of-Arrays for this). Store the range of the first cluster into $xstart and $xend. For each new cluster (outer loop) test if the new cluster overlaps and if yes, count the overlap (inner loop) and update $xend with the end of the range

[g-alone]

I guess Easiest way is to show you what my data looks like in simpler way bp = basepair I have data of different chromosomes with start and end point of cluster tags in each of chromosomes it looks like :

columns = 1: chr  2: start 3:end 4: info(X) 5: info(X) 6:strand 

chr1    101  105   X     X     -
chr1    102  108   X     X     -
chr1    106  111   X     X     -
chr1    112  113   X     X     -
chr1    113  115   X     X     -
chr2    114  118   X     X     -  
chr2    119  121   X     X     -
chr2    120  123   X     X    -
chr3    125  130   X     X    -
chr3    131  132   X     X   -

I need column 1 - 2 -3 - 6 

I want to count the overlappes with 2 basepair overlappes for each cor
+dinates in each chromosome and give ID number for those over laps tog
+ether like in chr1 there are 4 cordinates and 3 of them have overlapp
+ed 
except the last cordinate  : so I will need to first count those 3 ove
+rlappes 
and give them ID_1 then ID_2 will give to last cordinate in chr1 which
+ is not have overlapped with others .
then Counting is became zero for the chr2 and check inside the chr2 co
+rdinates for overlap and give ID from ID_1 for chr2 again and countin
+g and so on for all chromosomes and give the out put like this :

TSSD_ID        chr       start        end      strand      count
  ID_1         1          101          111       -           3
  ID_2         1          112          113       -           1
  ID_3         1          113          115       -           1
  ID_1         2          114          118       -           1   
  ID_2         2          119          123       -           2 
  ID_1         3          125          132       -           1

this the output I want to get but Mine is not working well !

[jethro]

I think you made a mistake with chromosom 3 in your example output

Here is a working solution:

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

my @chrom;

while (<>) {
    my ($chr, $start,$end,$c,$d,$strand)= split;
    push @chrom, {'chrom'=>$chr, 'start'=>$start, 'end'=>$end, 'strand
+'=>$strand };

}
my @chroms= sort { $a->{start} <=> $b->{start} } @chrom;

#print Dumper(\@chroms);

exit(0) if (@chroms==0);
my $coord= shift @chroms; #use first coordinate as range counter
my $overlap=1;
my $id= 1;

while( my $co= shift @chroms ) {
    if ($co->{chrom} ne $coord->{chrom}) {
    printresults($coord,$overlap,$id);
    $coord= $co;
    $overlap=1;
    $id=1;
    }
    else {
    if ($co->{start}>=$coord->{end}) {
        printresults($coord,$overlap,$id);
        $coord= $co;
        $overlap=1;
        $id++;
    }
    else {
        $overlap++;
        $coord->{end}= $co->{end};
    }
    }
}

printresults($coord,$overlap,$id);



#-------------

sub printresults {
    my ($coord,$overlap,$id)= @_;
    print "ID_$id       $coord->{chrom}      $coord->{start}     $coor
+d->{end}    $coord->{strand}      $overlap\n";
}

prints

ID_1       chr1      101     111    -      3
ID_2       chr1      112     113    -      1
ID_3       chr1      113     115    -      1
ID_1       chr2      114     118    -      1
ID_2       chr2      119     123    -      2
ID_1       chr3      125     130    -      1
ID_2       chr3      131     132    -      1

You can remove the '#' in front of the 'print Dumper' line if you want to see how the data in @chroms looks like