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Re: Population of HoAoA based on file contents

by state-o-dis-array (Hermit)
on May 09, 2012 at 20:57 UTC ( #969707=note: print w/replies, xml ) Need Help??

in reply to Population of HoAoA based on file contents

So, if I understand correctly, you want your results to look something like:
$data{"HG00553"}[162][16287215] = "0 0" $data{"HG00553"}[162][16287226] = "0 0" ... $data{"HG00638"}[162][16287851] = "1 1" ...
First, I'd suggest you do a little debug work to understand what your code is doing. Specifically:
while (<$in_file>) { print "$_"; chomp; my @snp_bins; if (/^SAMPLE/) { my ( $placeholder, @coords ) = split /,/; foreach my $coord (@coords) { push @snp_bins, int( $coord / 100_000 ); } } else { my ( $id, @snps ) = split /,/; push @individuals, $id; foreach my $individual (@individuals) { print "working on $individual\n"; foreach my $snp (@snps) { my $snp_bin = shift @snp_bins; print "snp_bin $snp_bin\n"; $data{$individual}[ [ $snp_bin ] ] = $snp; } } print "snp_bins: @snp_bins\n"; } }
I think that you'll find some things which you didn't expect. Also, I think that you might be better off using HoHoH instead. I believe that doing:
$data{$individual}[162] = "something"
will result in:
even though you are only concerned with the former. So it would probably be better to:
$data{$individual}{162}{16287215} = "0 0"

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