diff cpt_renumber_gbk/BIO_FIX_TOPO.py @ 0:8cac332dbc77 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_renumber_gbk/BIO_FIX_TOPO.py	Fri Jun 17 13:13:47 2022 +0000
@@ -0,0 +1,85 @@
+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