[Biopython-dev] [Bug 3048] New: Bio.Blast.Applications.NcbitblastxCommandline

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3048

           Summary: Bio.Blast.Applications.NcbitblastxCommandline
           Product: Biopython
           Version: 1.53
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: gebauer-jung at ice.mpg.de


NcbitblastxCommandline._validate() uses a non-existing attribute in_pssm (if
query is set), raises an error and hence the commandline cannot be used as
suggested in the tutorial.

The module Bio.Blast.Applications.py is identical to the biopython 1.54b and
current github versions.


from Bio.Blast.Applications import NcbitblastxCommandline
>>> cline = NcbitblastxCommandline()
>>> cline.query = 'xxx'
>>> print cline

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "....../Bio/Application/__init__.py", line 256, in __str__
    self._validate()
  File
"....../biopython-1.53/build/lib.linux-i686-2.5/Bio/Blast/Applications.py",
line 929, in _validate
    if self.query and self.in_pssm:
AttributeError: 'NcbitblastxCommandline' object has no attribute 'in_pssm'


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