[Bioperl-guts-l] [BioPerl - Bug #3039] TreeIO::newick writes root node branch length incorrectly

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Sun Mar 27 14:21:43 EDT 2011


Issue #3039 has been updated by Jason Stajich.

Assignee changed from Bioperl Guts to Greg Jordan

Greg - any way you can help look this over too, it might be almost there, but just needs another pair of eyes.  Dave can you also report back whether the code is committed on a branch that can be tested out now?
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Bug #3039: TreeIO::newick writes root node branch length incorrectly
http://redmine.open-bio.org/issues/3039

Author: Dave Messina
Status: New
Priority: Normal
Assignee: Greg Jordan
Category: Core Components
Target version: main-trunk
URL: 


It seems that TreeIO::newick might not be properly writing root nodes which have a branch length — it omits the colon.

e.g.

If you read in

	(a:1,b:2):0.0;

It will be written out as

	(a:1,b:2)0.0;


In the latter case, 0.0 now looks like a node id, causing strict interpreters of newick (like PAML) to complain.

I'll attach a patch and a test in a moment.

I'm not sure I understand the code that well, though; could another dev or two take a look before I commit?


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