[Bioperl-guts-l] [Bug 2211] New: TreeIO::nexus parsing problem for taxa with spaces

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2211

           Summary: TreeIO::nexus parsing problem for taxa with spaces
           Product: BioPerl
           Version: main-trunk
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jason at open-bio.org
         QAContact: jason at open-bio.org
                CC: ffnt at uaf.edu


>From Naoki Takebayashi

1. When it is reading in tree with "translate" (numbers to actual taxon),
it had problem with the taxon names with space.

e.g.

#NEXUS
BEGIN TREES;

   TRANSLATE
   1   'Allium drummondii',
   2   'Allium cernuum',
   3    A.cyaneum
   ;
   TREE onion = [&R] ((1,2),3);
END;


The taxon names for the first two nodes become both 'Allium.  Also it
wasn't removing the trailing spaces for the last taxon, so it became
"A.cyaneum  ".


2. nexus format specifies that in the tree statement, it can have *
before the tree name to indicate that the tree is the default tree.
For example:

        TREE * onionGrp =  [&R]
(((((((((1,2,3),4),((5,6),7)),((8,9),10,11)),(((12,13),14),(((15,(16,17)),18),(19,((20,21),22))))),((((23,24),25),26),((27,28),29)),30),(31,32)),(33,34)),(35,36));

It had troubles reading the trees with *, and it was skipping them.


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