annotate BIO_FIX_TOPO.py @ 2:8f5f2142fc2b draft default tip

planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

import Bio.GenBank


def record_end(self, content):
    """Clean up when we've finished the record."""
    # from Bio import Alphabet
    # from Bio.Alphabet import IUPAC
    from Bio.Seq import Seq, UnknownSeq

    # Try and append the version number to the accession for the full id
    if not self.data.id:
        assert "accessions" not in self.data.annotations, self.data.annotations[
            "accessions"
        ]
        self.data.id = self.data.name  # Good fall back?
    elif self.data.id.count(".") == 0:
        try:
            self.data.id += ".%i" % self.data.annotations["sequence_version"]
        except KeyError:
            pass

    # 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

    # now set the sequence
    sequence = "".join(self._seq_data)

    if (
        self._expected_size is not None
        and len(sequence) != 0
        and self._expected_size != len(sequence)
    ):
        import warnings
        from Bio import BiopythonParserWarning

        warnings.warn(
            "Expected sequence length %i, found %i (%s)."
            % (self._expected_size, len(sequence), self.data.id),
            BiopythonParserWarning,
        )
    """
    if self._seq_type:
        # mRNA is really also DNA, since it is actually cDNA
        if "DNA" in self._seq_type.upper() or "MRNA" in self._seq_type.upper():
            seq_alphabet = IUPAC.ambiguous_dna
        # are there ever really RNA sequences in GenBank?
        elif "RNA" in self._seq_type.upper():
            # Even for data which was from RNA, the sequence string
            # is usually given as DNA (T not U).  Bug 2408
            if "T" in sequence and "U" not in sequence:
                seq_alphabet = IUPAC.ambiguous_dna
            else:
                seq_alphabet = IUPAC.ambiguous_rna
        elif (
            "PROTEIN" in self._seq_type.upper() or self._seq_type == "PRT"
        ):  # PRT is used in EMBL-bank for patents
            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", "unspecified"]:
            pass
        # we have a bug if we get here
        else:
            raise ValueError(
                "Could not determine alphabet for seq_type %s" % self._seq_type
            )

        # Also save the chomosome layout
        if "circular" in self._seq_type.lower():
            self.data.annotations["topology"] = "circular"
        elif "linear" in self._seq_type.lower():
            self.data.annotations["topology"] = "linear"
    """
    if not sequence and self.__expected_size:
        self.data.seq = UnknownSeq(self._expected_size)  # , seq_alphabet)
    else:
        self.data.seq = Seq(sequence)  # , seq_alphabet)


Bio.GenBank._FeatureConsumer.record_end = record_end