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";
}

[download]
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

[download]

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

In reply to Re^3: Help the counting! by jethro
in thread Help the counting! by g-alone

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