[Biopython-dev] [Bug 2328] New: NCBIStandalone.blastall chokes on integer argument

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2328

           Summary: NCBIStandalone.blastall chokes on integer argument
           Product: Biopython
           Version: 1.43
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: grunberg at embl.de
                CC: grunberg at embl.de


Unlike previous versions, the current NCBIStandalone.blastall and blastpgp
expect that the argument align_view is given as a string rather than an
integer. So the following call worked with previous versions but now fails::

   results, err = NCBIStandalone.blastall( settings.blast_bin,
                                           method, db, seqFile,
                                           expectation=e,
                                           align_view=7, ## XML output
                                           **kw)

The error is raised here::

  NCBIStandalone: 1788 (blastall) 
     w, r, e = os.popen3(" ".join([blastcmd] + params))

because align_view escapes the str conversion of the other parameters in this
line::

   params.extend([att2param['align_view'], align_view])

This line should rather look like this::

   params.extend([att2param['align_view'], str(align_view)])

I am going to attach a patch to this bugreport.

Greetings,
Raik


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