Check Newick tree exporter

[fog]

There was a complain by someone using the LTP in newick format. He tried to parse it with the Bioperl parser and it did not work.

Here is his report: The $node→id is written by ARB in the format: ‘spec_tax, accession, genus_tax’ to the newick . I am using:

my $treeio = new Bio::TreeIO(-format ⇒ 'newick', -file ⇒ $file);

to get the . if I examine $node→id when traversing the , it is like this ‘spec_tax

Bioperl

1) Does not recognize single quote as a quote, but rather as a part of id

2) Ergo, treats subsequent comma as a “newick” delimiter between branches If I replace single quote by double quote and comma by greater-than (>), it parses fine. (It does not like semicolon either, BTW) “>” is a little unorthodox, so if you are going to change the export, please use more conventional delimiter that is still parsable by BIOPERL

[fog]

see also Ticket #153: Problem with the ARB Newick Tree Exporter

[westram]

• fixed by [6066]
• added options for quoting style and char-removal