Re^6: Population of HoAoA based on file contents

Hi again. I don't know if anyone can give me suggestions on this. I've been trying to work out what's going on here.

I'm getting the following error message.. :

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.
[download]

..when I re-run my earlier, smaller, no-windows script. I am 99% certain that I successfully ran this script earlier, and got some statistics back.

When I run my new, larger script with the 100kb windows, that you guys helped me with, I get a different error:

Can't call method "isa" without a package or object reference at /usr/local/share/perl/5.14.2/Bio/PopGen/Statistics.pm line 901.

Is this a problem with my own code, or with the module that the errors are originating from?

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Re^7: Population of HoAoA based on file contents by iangibson (Scribe) on Jun 11, 2012 at 16:43 UTC
I don't know if anyone is still reading this thread, but I think that the problem that's making the program crash is the undef values in the data structure I've written some code to attempt to replace each undef with some fake data that flags a window as undef, but what I've written doesn't seem to be modifying the output. Perhaps someone can tell me how to fix this: while (<$in_file>) { chomp; if (/^SAMPLE/) { my ( $placeholder, @coords ) = split /,/; foreach my $coord (@coords) { push @snp_bins, int( $coord / 100_000 ); } } else { my ( $id, @snps ) = split /,/; foreach my $snp (@snps) { # (@snps[0..$#snps-1] $snp =~ s/$snp/$snp,/ # put commas back in (preserve cs +v format) } foreach my $index ( 0 .. $#snp_bins ) { if ( $snps[$index] ) { push( @{ $data{$id}[ $snp_bins[$index] ] }, $snps[$index] +); # see note [1] } else { # replace 'undef' elements with f +lag data my @ones_array; foreach ( 1 .. 100) { push @ones_array, "1 1,"; } push( @{ $data{$id}[ $snp_bins[$index] ] }, @ones_arra +y ) } } } } [download] I am assuming that the problem lies with the line `if ( $snps[$index] )` [download] Is this the case, and if so how can I fix it? Help appreciated.	[reply] [d/l] [select]

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Re^7: Population of HoAoA based on file contents
by iangibson (Scribe) on Jun 11, 2012 at 16:43 UTC

I don't know if anyone is still reading this thread, but I think that the problem that's making the program crash is the undef values in the data structure

I've written some code to attempt to replace each undef with some fake data that flags a window as undef, but what I've written doesn't seem to be modifying the output. Perhaps someone can tell me how to fix this:

while (<$in_file>) {
    chomp;

    if (/^SAMPLE/) {
        my ( $placeholder, @coords ) = split /,/;
        foreach my $coord (@coords) {
            push @snp_bins, int( $coord / 100_000 );
        }
    }

    else {
        my ( $id, @snps ) = split /,/;
        foreach my $snp (@snps) {    # (@snps[0..$#snps-1]
            $snp =~ s/$snp/$snp,/    # put commas back in (preserve cs
+v format)
        }

        foreach my $index ( 0 .. $#snp_bins ) {
            if ( $snps[$index] ) {
            push( @{ $data{$id}[ $snp_bins[$index] ] }, $snps[$index] 
+);  # see note [1]
            }

            else {                   # replace 'undef' elements with f
+lag data
                my @ones_array;
                foreach ( 1 .. 100) {
                    push @ones_array, "1 1,";
                }
                push( @{ $data{$id}[ $snp_bins[$index] ] }, @ones_arra
+y )
            }
        }
    }
}
[download]

I am assuming that the problem lies with the line

if ( $snps[$index] )
[download]

Is this the case, and if so how can I fix it? Help appreciated.

[reply]
[d/l]
[select]