On Mon, 17 Sep 2012 18:29:34 +0000
"Wang, Li" <li.w...@ttu.edu> wrote:
> Dear List members
>
> I have three columns of a table. The example is as follows:
>
> DBS R^2 genename
> 801 0.27807486057281494 POPTR_0002s00200
> 1903 1.0 POPTR_0002s00200
> 1103 0.25852271914482117 POPTR_0002s00200
> 3215 0.03134157508611679 POPTR_0002s00200
> 2415 0.010018552653491497 POPTR_0002s00200
> 1313 0.03134157508611679 POPTR_0002s00200
> 3442 1.0 POPTR_0002s00200
> 2642 0.25852271914482117 POPTR_0002s00200
> 1540 1.0 POPTR_0002s00200
> 228 0.03134157508611679 POPTR_0002s00200
> 3099 0.026160990819334984 POPTR_0002s00210
> 7555 0.800000011920929 POPTR_0002s00210
> 4457 0.014814814552664757 POPTR_0002s00210
> 7564 5.232862313278019E-4 POPTR_0002s00210
> 4466 0.0018315018387511373 POPTR_0002s00210
> 10 0.0036630036775022745 POPTR_0002s00210
> 7565 5.232862313278019E-4 POPTR_0002s00210
> 4467 0.0018315018387511373 POPTR_0002s00210
> 11 0.0036630036775022745 POPTR_0002s00210
> 2 1.0 POPTR_0002s00210
>
> I would like to calculate the average value of column 2 while the
> content of column three is the same. In this case, I would like the
> output of my result be as follows: R^2 genename 0.3899163577
> POPTR_0002s00200 0.2314956035 POPTR_0002s00210
>
> I donot know how to deal with columns in Perl. I thought about using
> the idea of hash. But the key of a hash could not be the same.
You'd probably want to use a hash where the key is the genename in the
third column of your input, and the value is an arrayref of each value
you saw - so you can collate values against genenames, then calculate
the average at the end.
Something along the lines of:
use strict;
use List::Util;
# For each row, record the value against the genename in question:
my %values_by_genename;
while(my $line = <>) {
chomp $line;
next if $genename eq 'genename'; # skip header row
my ($dbs, $r2, $genename) = split /\s+/, $line;
push @{ $values_by_genename{$genename} }, $r2;
}
# Now, for each genename, calculate the average value
for my $genename (keys %values_by_genename) {
my $avg = List::Util::sum(
@{ $values_by_genename{$genename} }
) / scalar @{ $values_by_genename{$genename} };
print "$avg,$genename\n";
}
Of course, you'd be better off parsing the input using Text::CSV, but
the above should give you something to start from.
--
David Precious ("bigpresh") <dav...@preshweb.co.uk>
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