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from xml.sax import handler
from Martel import Dispatch
from Bio import SeqRecord, StdHandler, Std, DBXRef, Seq
from Bio import Alphabet, SeqFeature
from Bio.Alphabet import IUPAC
alphabet_table = {
"iupac-protein": IUPAC.protein,
"iupac-dna": IUPAC.unambiguous_dna,
"iupac-rna": IUPAC.unambiguous_rna,
"iupac-extended-protein": IUPAC.extended_protein,
"iupac-ambiguous-dna": IUPAC.ambiguous_dna,
"iupac-ambiguous-rna": IUPAC.ambiguous_rna,
"protein": Alphabet.generic_protein,
"dna": Alphabet.generic_dna,
"rna": Alphabet.generic_rna,
"unknown": Alphabet.single_letter_alphabet,
}
# Convert from the internal Feature data structure used by the parser
# into the standard Biopytho form
def convert_std_feature(feature):
f = SeqFeature.SeqFeature()
loc = feature.location
return feature
class BuildSeqRecord(Dispatch.Dispatcher):
def __init__(self):
Dispatch.Dispatcher.__init__(self)
self.acquire(StdHandler.Handle_dbid(self.add_dbid),
prefix = Std.NS)
self.acquire(StdHandler.Handle_dbxref(self.add_dbxref_dbids),
prefix = Std.NS)
self.acquire(StdHandler.Handle_description(self.add_description),
prefix = Std.NS)
self.acquire(StdHandler.Handle_sequence(self.add_sequence),
prefix = Std.NS)
self.acquire(StdHandler.Handle_features(self.add_features),
prefix = Std.NS)
self.acquire(StdHandler.Handle_dbxref(self.add_dbxref),
prefix = Std.NS)
def start_record(self, tag, attrs):
self.dbname = None
self.id_text = None
self.name_text = '<unknown name>'
self.description = None
self.alphabet = None
self.seq = None
self.features = None
self.dbxrefs = []
def add_dbid(self, text, attrs):
if attrs.get("type") == "primary":
self.dbname = attrs.get("dbname", "unknown")
self.id_text = text
# use the first accession/secondary id as the name
# this should be equivalent to what Biopython does
elif attrs.get("type") in ["accession", "secondary"]:
self.name_text = text
def add_dbxref_dbids(self, dbname_style, dbname, idtype, dbid, negate):
"""Handle setting name and id attributes from the dbxref ids.
Likely we'll either have a dbid or dbxref dbids to use. We default
to using the dbid if it exists.
"""
# first deal with the primary id: SeqFeature.id
# set the id if we haven't yet set an id (take the first id we get)
# and if we have a primary id
if (self.id_text is None and idtype == "primary"):
self.id_text = dbid
# now deal with secondary ids: SeqFeature.name
if idtype == "secondary":
self.name_text = dbid
def add_description(self, text):
self.description = text
def add_sequence(self, (alphabet, seq, gapchar, stopchar)):
alphabet = alphabet_table.get(alphabet,
Alphabet.single_letter_alphabet)
self.seq = Seq.Seq(seq, alphabet)
def add_dbxref(self, dbname_style, dbname, idtype, dbid, negate):
"""Store all id cross references.
"""
self.dbxrefs.append(DBXRef.from_parser(dbname_style, dbname, idtype,
dbid, negate))
def add_features(self, features):
# Brad -- I can't understand this assertion -- there is no
# self.features on the first call to add features and then you'll
# expect to have some on future calls
# assert self.features is None
#print [feature.location for feature in features]
self.features = map(convert_std_feature, features)
def end_record(self, tag):
self.document = SeqRecord.SeqRecord(
seq = self.seq,
id = self.id_text,
name = self.name_text,
description = self.description,
dbxrefs = self.dbxrefs,
features = self.features,
)
make_builder = BuildSeqRecord
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