[Bioperl-guts-l] [Bug 1660] New: Bio::TreeIO::nexus not parsing out final ID in a Translate block

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jul 5 05:59:58 EDT 2004


http://bugzilla.open-bio.org/show_bug.cgi?id=1660

           Summary: Bio::TreeIO::nexus not parsing out final ID in a
                    Translate block
           Product: Bioperl
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: pda at sanger.ac.uk


The code in Bio::TreeIO::nexus contains code to cope with the Translate block 
in nexus files which allow for numeric ID (usually) to replace the taxon IDs 
in the trees.  The regular expression which parses out the numeric ID and the 
taxon name from the block requires a comma ',' to be present after the taxon 
name.  Unfortunately, this is not a requirement of nexus format, and PAUP* 
usually leaves the last taxon name unadorned (with a semi-colon to terminate 
the Translate block on the next line on its own.  This means that the final 
taxon name in the block is not parsed out, at the resulting node in the tree 
contains only the numeric ID.  I will upload a nexus file which illustrates 
the problem.  If you load with with a Bio::TreeIO object, the resulting trees 
with have a node with the ID 12 instead of Tarsius_syrichta.  This was 
produced from one of the sample nexus files that ships with PAUP*.



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