Find highest value

[linseyr]

Hi, I have a file like this:

chr        nr        begin        end         c1      total_c1      
chr10    1         10             20          15          2

where the first column describes the chromosome nr, second column nr of peak, third column begin position, fourth column end position, and in total there are 20 columns for (10x class, total_class) so in total 10 classes. I want to find out which class had the highest total, and write a file with "$chr $begin $end $class". There are some classes for which the highest total equals the total of an other class. This line will be "undefined". I wrote a script to find the highest column (probably not the easiest way to do it), but how can I find the undefined lines? So for example this line would be undefined:

chr      nr      begin   end      c1      total_c1   c2    total_c2   
+ c3    total_c3
chr1    2     30      50      10      9         8        9           7
+        2

Because it had two times a 9 as total, which is the highest total in the line. My code looks like this now:

open(classFile,'<',"Results/Classification/classesNormal.txt") or die 
+$!;
my @classes = <classFile>;
close(classFile);


for my $line(@classes){
    my($chr,$nr,$begin,$end,$c1,$total_c1,$c2,$total_c2,$c3,$total_c3,
+$c4,$total_c4,$c5,$total_c5,$c6,$total_c6,$c7,$total_c7,$c8,$total_c8
+,$c9,$total_c9,$c10,$total_c10) = split("\t",$line);
    if ($total_c1 > $total_c2 && $total_c1 > $total_c3 && $total_c1 > 
+$total_c4 && $total_c1 > $total_c5 && $total_c1 > $total_c6 && $total
+_c1 > $total_c7 && $total_c1 > $total_c8 && $total_c1 > $total_c9 && 
+$total_c1 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c1,"\n");
            }
    if ($total_c2 > $total_c1 && $total_c2 > $total_c3 && $total_c2 > 
+$total_c4 && $total_c2 > $total_c5 && $total_c2 > $total_c6 && $total
+_c2 > $total_c7 && $total_c2 > $total_c8 && $total_c2 > $total_c9 && 
+$total_c2 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c2,"\n");
    }
    if ($total_c3 > $total_c1 && $total_c3 > $total_c2 && $total_c3 > 
+$total_c4 && $total_c3 > $total_c5 && $total_c3 > $total_c6 && $total
+_c3 > $total_c7 && $total_c3 > $total_c8 && $total_c3 > $total_c9 && 
+$total_c3 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c3,"\n");
    }
    if ($total_c4 > $total_c1 && $total_c4 > $total_c2 && $total_c4 > 
+$total_c3 && $total_c4 > $total_c5 && $total_c4 > $total_c6 && $total
+_c4 > $total_c7 && $total_c4 > $total_c8 && $total_c4 > $total_c9 && 
+$total_c4 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c4,"\n");
    }
    if ($total_c5 > $total_c1 && $total_c5 > $total_c2 && $total_c5 > 
+$total_c3 && $total_c5 > $total_c4 && $total_c5 > $total_c6 && $total
+_c5 > $total_c7 && $total_c5 > $total_c8 && $total_c5 > $total_c9 && 
+$total_c5 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c5,"\n");
    }
    if ($total_c6 > $total_c1 && $total_c6 > $total_c2 && $total_c6 > 
+$total_c3 && $total_c6 > $total_c4 && $total_c6 > $total_c5 && $total
+_c6 > $total_c7 && $total_c6 > $total_c8 && $total_c6 > $total_c9 && 
+$total_c6 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c3,"\n");
    }
    if ($total_c7 > $total_c1 && $total_c7 > $total_c2 && $total_c7 > 
+$total_c3 && $total_c7 > $total_c4 && $total_c7 > $total_c5 && $total
+_c7 > $total_c6 && $total_c7 > $total_c8 && $total_c7 > $total_c9 && 
+$total_c7 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c7,"\n");
    }
    if ($total_c8 > $total_c1 && $total_c8 > $total_c2 && $total_c8 > 
+$total_c3 && $total_c8 > $total_c4 && $total_c8 > $total_c5 && $total
+_c8 > $total_c6 && $total_c8 > $total_c7 && $total_c8 > $total_c9 && 
+$total_c8 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c8,"\n");
    }
    if ($total_c9 > $total_c1 && $total_c9 > $total_c2 && $total_c9 > 
+$total_c3 && $total_c9 > $total_c4 && $total_c9 > $total_c5 && $total
+_c9 > $total_c6 && $total_c9 > $total_c7 && $total_c9 > $total_c8 && 
+$total_c9 > $total_c10){
        print ($chr,"\t",$begin,"\t",$end,"\t",$c9,"\n");

    }
}

Could somebody help me? :)

[choroba]

Naming variables c1 .. c10 suggests you need an array.

To find a maximum, you can use List::Util.

The following code returns "$chr $begin $end $class" if the class has the maximal total, or 'undefined' instead of the class number if there are more classes having the same maximum. Tweak it to serve your needs:

#!/usr/bin/perl
use warnings;
use strict;
use List::Util qw/max/;

<>; # skip header
for my $line (<>){
    my ($chr, $nr, $begin, $end, @values) = split ' ', $line;

    my %total;
    while (@values) {
        my $class = shift @values;
        my $total = shift @values;
        $total{$class} = $total;
    }
    my $max = max values %total;
    my @maxes = grep $total{$_} == $max, keys %total;
    if (@maxes == 1) {
        print "$chr $begin $end $maxes[0]\n";
    } else {
        print "$chr $begin $end undefined\n";
    }
}

Updated code.

[linseyr]

Thank you for your answer. But the last columns are classes and totals of classes, so I only want to find the maximum of the totals of classes. I should select only subset of the @values and put in array then, but this doesn't work:

push(@totals, values[1], values[3], values[5], values[7]);

Is there a way to do this? I want to find the class for which the total of class is the highest, and print the class name..

[Tux]

Looking at your example code, the .txt file is TAB seperated. You could read it with DBD::CSV if you are slightly acquinted with SQL commands, that might be handy. Here's a start:

use DBI;

my $dbh = DBI->connect ("dbi:CSV:", undef, undef, {
    f_dir        => "Results/Classification",
    f_ext        => ".txt/r",

    csv_sep_char => "\t",

    RaiseError   => 1,
    PrintError   => 1,
    }) or die $DBI::errstr;

my $sth = $dbh->prepare ("select max (begin) from classesNormal where 
+nr = 2");
   $sth->execute;
my ($max) = $sth->fetchrow_array;

[nemesdani]

Consider:
• read a line into an array
• split it by whitespace
• make a slice from the totals (the 5th, 7th, etc. element)
• select the maximum with e.g. List::Util, use a flag is more maxes are found
• write out the elements you need


Optionally the last 3 steps can be implemented in a subroutine, thus making your code more readable.