[Biopython-dev] [Bug 1764] New: Bio.Application _Option class

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1764

           Summary: Bio.Application _Option class
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: gvg500 at york.ac.uk
                CC: gvg500 at york.ac.uk


When building a commandline from the sub-classed abstractcommandline:
if more than one advanced options are parsed and they do not have a value, they
appear on the commandline with no space separating them.
                  |
                  V             
hmmbuild -F --amino--archpri=0.5 --binary
                               A
                               |
if they have an associated value then a space is inserted correctly

I have modified __str__ in the _Options class in the following manner:

def __str__(self):
        """Return the value of this option for the commandline.
        """
        # first deal with long options
        if self.names[0].find("--") >= 0:
            output = "%s" % self.names[0]
            if self.value is not None:
                output += "=%s " % self.value
            else:             <<<<
                output += " " <<<<



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