[Biopython-dev] [Bug 2564] New: Bio.Clustalw parsing fails if CLUSTAL files omit version number

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2564

           Summary: Bio.Clustalw parsing fails if CLUSTAL files omit version
                    number
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


This bug report is based on an email discussion with Nick Matzke on the mailing
list.

Some third party tools like PROMALS3D can mimic the CLUSTAL file format, e.g.
http://prodata.swmed.edu/promals3d/promals3d.php

In this case the first line reads:

CLUSTAL format multiple sequence alignment by PROMALS3D

rather than for example:

CLUSTAL W (1.81) multiple sequence alignment
CLUSTAL W (1.83) multiple sequence alignment
CLUSTAL 2.0.9 multiple sequence alignment

In my testing using Bio.AlignIO directly, the parser is happy with the
PROMALS3D output - but naturally cannot record a version number.  However,
parsing via Bio.Clustalw expects the version number and fails (testing on CVS):

>>> from Bio import Clustalw
>>> from Bio.Alphabet import IUPAC, Gapped
>>> a = Clustalw.parse_file("promals3d.aln", Gapped(IUPAC.protein,"-"))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/xxx/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Clustalw/__init__.py",
line 59, in parse_file
    clustal_alignment._version = generic_alignment._version
AttributeError: Alignment instance has no attribute '_version'

I'll upload an example PROMALS3D alignment file, and look into fixing this.


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