Re^2: Population of HoAoA based on file contents

[state-o-dis-array]

in reply to Re: Population of HoAoA based on file contents
in thread Population of HoAoA based on file contents

I'm going to deal with just this section, I think once you understand/update what is happening here, everything else you have will work.

my $id;   # ??
foreach my $window ( @{ $data{$id} } ) {

  # only pass windows with > min number of stats (i.e. >1 for now), an
+d
  # of course we also ignore any 'undef' windows.
  next unless scalar @{ $data{$id} }[$window] >= 2;

    foreach my $individual ( keys(%data) ) {

First, I think that you understand that having an undefined $id as a hash key won't work. And to fix this, you want to just rearrange your for loops.

foreach my $id ( keys %data ){
  foreach my $window ( @{$data{$id}} ){

Just this will get you much further. There is still a problem with the second loop though, at least in how you use $window in the subsequent code. You are attempting to use $window as an index, but it's not an index. Since you have experience using Data::Printer, I suggest going ahead and checking out what $window is.

Now, the way to fix things with the fewest number of overall edits is to change the second for loop.

foreach my $id ( keys %data ){
  foreach my $window ( 0 .. $#{$data{$id}} ){
    next unless scalar @{ $data{$id}[$window] } >= 2;

Then in your method calls, just change those to align with the scalar test above:

\@{ $data{$id}[$window] }

I hope that helps.

[iangibson]

Thanks for your further help on this. I feel like I'm almost there, but not quite.. I made the changes you suggested, but I'm still getting errors starting at the line

next unless scalar @{ $data{$id}[$window] } >= 2;

The error is:

Can't use an undefined value as an ARRAY reference 

Is this referring to $window? Regarding the way I was using it above, was $window the outer array that holds all the smaller arrays? Even if this is true, I don't see why I'm getting the error messages I'm getting.

[state-o-dis-array]

Hmm, based on your expectation for your data, I'm guessing what you probably need is to add:

next unless ref( $data{$id}[$window] ) eq "ARRAY";

just before the line getting the error.

[iangibson]

That appears to have fixed that problem. However, now I'm getting errors from the module:

Can't call method "isa" on unblessed reference at /usr/local/share/per
+l/5.14.2/Bio/PopGen/Statistics.pm line 901, <GEN0> line 182.

I went back and re-ran my simpler code from earlier (i.e. where I just passed a file without building windows), and I'm now getting a similar error on this too, whereas before it successfully gave me output.

This is very strange, so I'll have to investigate further to see how to proceed.