[Biopython-dev] [Bug 3047] New: PhyloXML, behavior on setting color and width doesn't match docstring or spec

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Apr 6 18:13:23 EDT 2010


           Summary: PhyloXML, behavior on setting color and width doesn't
                    match docstring or spec
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: joelb at lanl.gov

>From the Clade docstring:

"Both 'color' and 'width' elements apply for the whole clade unless
overwritten in-sub clades.

This information follows the PhyloXML doc.  However, that's not the way the
code works:

>>> tree = Phylo.read('Bacteria403.phyloxml', 'phyloxml')
>>> tree.clade[0].color
BranchColor(blue='0', green='76', red='41')
>>> tree = Phylo.read('bcl_2.xml', 'phyloxml')
>>> tree.clade[0].color
>>> tree.clade[0].color = Phylo.PhyloXML.BranchColor(255,0,255)
>>> tree.clade[0].color
BranchColor(blue='255', green='0', red='255')
>>> tree.clade[0][0].color
>>> tree.clade[0].width = 3
>>> tree.clade[0][0].width

Personally I'd prefer changing the docstring.  The Java code doesn't implement
the spec either, and its actually more complicated for the user to deal with
side-effects of setting at the entire clade at once than it is to iterate over
the clade.

Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list