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Sourcecode: python-biopython version File versions

def Bio::GenBank::_FeatureConsumer::record_end (   self,

Clean up when we've finished the record.

Definition at line 934 of file __init__.py.

00934                                  :
        """Clean up when we've finished the record.
        from Bio import Alphabet
        from Bio.Alphabet import IUPAC
        from Bio.Seq import Seq
        # add the last feature in the table which hasn't been added yet

        # add the sequence information
        # first, determine the alphabet
        # we default to an generic alphabet if we don't have a
        # seq type or have strange sequence information.
        seq_alphabet = Alphabet.generic_alphabet

        if self._seq_type:
            # mRNA is really also DNA, since it is actually cDNA
            if self._seq_type.find('DNA') != -1 or \
               self._seq_type.find('mRNA') != -1:
                seq_alphabet = IUPAC.ambiguous_dna
            # are there every really RNA sequences in GenBank?
            elif self._seq_type.find('RNA') != -1:
                seq_alphabet = IUPAC.ambiguous_rna
            elif self._seq_type == "PROTEIN":
                seq_alphabet = IUPAC.protein  # or extended protein?
            # work around ugly GenBank records which have circular or
            # linear but no indication of sequence type
            elif self._seq_type in ["circular", "linear"]:
            # we have a bug if we get here
                raise ValueError("Could not determine alphabet for seq_type %s"
                                 % self._seq_type)

        # now set the sequence
        sequence = "".join(self._seq_data)
        self.data.seq = Seq(sequence, seq_alphabet)

class _RecordConsumer(_BaseGenBankConsumer):

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