[Biopython-dev] [Bug 2841] New: SeqFeature constructor ignores qualifiers and sub_features arguments

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue May 26 17:32:34 UTC 2009


           Summary: SeqFeature constructor ignores qualifiers and
                    sub_features arguments
           Product: Biopython
           Version: 1.50
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: n.j.loman at bham.ac.uk

The constructor to Bio.SeqFeature.SeqFeature ignores qualifiers and
sub_features, although the prototype to the constructor allows these keyword
arguments to be specified.

I see in the code there is a reason for it to be ignored:
        # XXX right now sub_features and qualifiers cannot be set
        # from the initializer because this causes all kinds
        # of recursive import problems. I can't understand why this is
        # at all :-<
        self.qualifiers = {}
        self.sub_features = []

However, would it not be better to get rid of the keyword arguments from the
constructor prototype to stop people getting confused? I keep stumbling over
this problem myself and forgetting about it.

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