[Biopython-dev] [Bug 2578] The GenBank SeqRecord parser does not record molecule type or if circular

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2578


n.j.loman at bham.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |n.j.loman at bham.ac.uk




------- Comment #3 from n.j.loman at bham.ac.uk  2010-12-12 13:26 EST -------
I needed this functionality for my project, and I got what I needed through the
modified method definition in Bio.GenBank._FeaureConsumer:

    def residue_type(self, type):
        """Record the sequence type so we can choose an appropriate alphabet.
        """
        self._seq_type = type
        if 'circular' in type:
            self.data.annotations['molecule'] = 'circular'
        else:
            self.data.annotations['molecule'] = 'linear'

This obviously doesn't address the need to write GenBank files.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.