BioPerl incompatibility

[cjfields]

Re: the Bioperl issue, if you can provide a test case or file a bug regarding the errors you have we can try to address them. Thanks!

[lakshwadeep]

There is a TestData directory included, which will show errors if Perl is using BioPerl 1.6.9.

[cjfields]

Ok, that helps. Based on the error reported in the README it seems like something that changed with Newick parsing. I'll create a ticket and link it here.

[wenqingchu]

I met one error.
perl Scripts/Phylotyping.pl -CPUs 2 > phylotype.result
I typed the command above and got the error message below.
Can't call method "id" on an undefined value at Scripts/Phylotyping.pl line 164, line 1.

159 for my $query (keys %support) {
160 $output .= "$query\t$marker";
161 for my $edge (keys %{$support{$query}}) {
162 my @Lineage = $tree_functions->get_lineage_nodes($ref_taxon{$edge});
163 for my $taxon (@Lineage, $ref_taxon{$edge}) {
164 $confidence{$query}{$taxon->id} += $support{$query}{$edge};
165 }
166 }