Hello,
I need to count elements within every 100k range along a chromosome. I understand
how to parse the file and get the columns that I want to work on. What I don't get
is how to count each numeric value that falls in each 100k range. Each value in column
two represents is to be counted within a 100k range. Then I repeat this until I have recorded
the number of values in column two per 100k range. 

#!/usr/bin/perl -w
# examine the value. When the value reaches 100k
# print out the count of the word "gene" in the keys for 1..100k range
+.
# Then increment and perform the same operation for the range 101k..20
+0k.
# Do this until you reach the final 100k increment.        
use strict;
#Open the file. Use indexes 2 and 4.
open( my $in, "chr8.txt" );
open( my $out, ">/Users/mgavibrathwaite/Desktop/genecoord.txt");
my %genes_per_100k;
while(<DATA>) {
    next if /\#\#.+/;
    chomp;
    my @fields = split /\t/;
    my ($genes,$gene_end) = ($fields[2], $fields[4]); 
    #print $out "$genes\t$gene_end\n";
#=cut    
    if($genes =~ /gene/){
        print $out "$genes\t$gene_end\n";
        #$genes_per_100k{$gene_end};
        }
}
close($in);
close($out);



__DATA__    
gene    3936
gene    7591
gene    13082
gene    23200
gene    32518
gene    45123
gene    57330
gene    62384
gene    66839
gene    71715
gene    83427
gene    90948
gene    87510
gene    96042
gene    106380
gene    108247
gene    109395
gene    120121
gene    138410
gene    143225
gene    147455
gene    152452
gene    155580
gene    158939
gene    163483
gene    167583
gene    178450
gene    181546
gene    184301
gene    193505
gene    190880
gene    199431
gene    202844

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In reply to Howto count elements within an interval by lomSpace

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