Mercurial > repos > cpt > cpt_gbk_to_5col

comparison cpt_gbk_to_5col/BIO_FIX_TOPO.py @ 0:66143811fe8a draft

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author cpt
date Fri, 17 Jun 2022 12:45:08 +0000
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-1:000000000000 0:66143811fe8a
1 import Bio.GenBank
2
3
4 def record_end(self, content):
5 """Clean up when we've finished the record.
6 """
7 #from Bio import Alphabet
8 #from Bio.Alphabet import IUPAC
9 from Bio.Seq import Seq, UnknownSeq
10
11 # Try and append the version number to the accession for the full id
12 if not self.data.id:
13 assert "accessions" not in self.data.annotations, self.data.annotations[
14 "accessions"
15 ]
16 self.data.id = self.data.name # Good fall back?
17 elif self.data.id.count(".") == 0:
18 try:
19 self.data.id += ".%i" % self.data.annotations["sequence_version"]
20 except KeyError:
21 pass
22
23 # add the sequence information
24 # first, determine the alphabet
25 # we default to an generic alphabet if we don't have a
26 # seq type or have strange sequence information.
27
28 #seq_alphabet = Alphabet.generic_alphabet
29
30 # now set the sequence
31 sequence = "".join(self._seq_data)
32
33 if (
34 self._expected_size is not None
35 and len(sequence) != 0
36 and self._expected_size != len(sequence)
37 ):
38 import warnings
39 from Bio import BiopythonParserWarning
40
41 warnings.warn(
42 "Expected sequence length %i, found %i (%s)."
43 % (self._expected_size, len(sequence), self.data.id),
44 BiopythonParserWarning,
45 )
46 """
47 if self._seq_type:
48 # mRNA is really also DNA, since it is actually cDNA
49 if "DNA" in self._seq_type.upper() or "MRNA" in self._seq_type.upper():
50 seq_alphabet = IUPAC.ambiguous_dna
51 # are there ever really RNA sequences in GenBank?
52 elif "RNA" in self._seq_type.upper():
53 # Even for data which was from RNA, the sequence string
54 # is usually given as DNA (T not U). Bug 2408
55 if "T" in sequence and "U" not in sequence:
56 seq_alphabet = IUPAC.ambiguous_dna
57 else:
58 seq_alphabet = IUPAC.ambiguous_rna
59 elif (
60 "PROTEIN" in self._seq_type.upper() or self._seq_type == "PRT"
61 ): # PRT is used in EMBL-bank for patents
62 seq_alphabet = IUPAC.protein # or extended protein?
63 # work around ugly GenBank records which have circular or
64 # linear but no indication of sequence type
65 elif self._seq_type in ["circular", "linear", "unspecified"]:
66 pass
67 # we have a bug if we get here
68 else:
69 raise ValueError(
70 "Could not determine alphabet for seq_type %s" % self._seq_type
71 )
72
73 # Also save the chomosome layout
74 if "circular" in self._seq_type.lower():
75 self.data.annotations["topology"] = "circular"
76 elif "linear" in self._seq_type.lower():
77 self.data.annotations["topology"] = "linear"
78 """
79 if not sequence and self.__expected_size:
80 self.data.seq = UnknownSeq(self._expected_size)#, seq_alphabet)
81 else:
82 self.data.seq = Seq(sequence)#, seq_alphabet)
83
84
85 Bio.GenBank._FeatureConsumer.record_end = record_end