def to_seqrecord(self):
"""Create a SeqRecord object from this Sequence instance.
The seqrecord.annotations dictionary is packed like so::
{ # Sequence attributes with no SeqRecord equivalent:
'id_ref': self.id_ref,
'id_source': self.id_source,
'location': self.location,
'uri': { 'value': self.uri.value,
'desc': self.uri.desc,
'type': self.uri.type },
# Sequence.annotations attribute (list of Annotations)
'annotations': [{ 'ref': ann.ref,
'source': ann.source,
'evidence': ann.evidence,
'type': ann.type,
'confidence': [ ann.confidence.value,
ann.confidence.type ],
'properties': [{ 'value': prop.value,
'ref': prop.ref,
'applies_to': prop.applies_to,
'datatype': prop.datatype,
'unit': prop.unit,
'id_ref': prop.id_ref }
for prop in ann.properties],
} for ann in self.annotations],
}
"""
def clean_dict(dct):
"""Remove None-valued items from a dictionary."""
return dict(
(key, val) for key, val in dct.items() if val is not None)
seqrec = SeqRecord(
Seq(self.mol_seq.value, self.get_alphabet()),
**clean_dict({
'id': str(self.accession),
'name': self.symbol,
'description': self.name,
# 'dbxrefs': None,
}))
if self.domain_architecture:
seqrec.features = [
dom.to_seqfeature() for dom in self.domain_architecture.domains
]
# Sequence attributes with no SeqRecord equivalent
seqrec.annotations = clean_dict({
'id_ref':
self.id_ref,
'id_source':
self.id_source,
'location':
self.location,
'uri':
self.uri and clean_dict({
'value': self.uri.value,
'desc': self.uri.desc,
'type': self.uri.type,
}),
'annotations':
self.annotations and [
clean_dict({
'ref':
ann.ref,
'source':
ann.source,
'evidence':
ann.evidence,
'type':
ann.type,
'confidence':
ann.confidence
and [ann.confidence.value, ann.confidence.type],
'properties': [
clean_dict({
'value': prop.value,
'ref': prop.ref,
'applies_to': prop.applies_to,
'datatype': prop.datatype,
'unit': prop.unit,
'id_ref': prop.id_ref
}) for prop in ann.properties
],
}) for ann in self.annotations
],
})
return seqrec
def to_seqrecord(self):
"""Create a SeqRecord object from this Sequence instance.
The seqrecord.annotations dictionary is packed like so::
{ # Sequence attributes with no SeqRecord equivalent:
'id_ref': self.id_ref,
'id_source': self.id_source,
'location': self.location,
'uri': { 'value': self.uri.value,
'desc': self.uri.desc,
'type': self.uri.type },
# Sequence.annotations attribute (list of Annotations)
'annotations': [{ 'ref': ann.ref,
'source': ann.source,
'evidence': ann.evidence,
'type': ann.type,
'confidence': [ ann.confidence.value,
ann.confidence.type ],
'properties': [{ 'value': prop.value,
'ref': prop.ref,
'applies_to': prop.applies_to,
'datatype': prop.datatype,
'unit': prop.unit,
'id_ref': prop.id_ref }
for prop in ann.properties],
} for ann in self.annotations],
}
"""
def clean_dict(dct):
"""Remove None-valued items from a dictionary."""
return dict((key, val) for key, val in dct.items()
if val is not None)
seqrec = SeqRecord(Seq(self.mol_seq.value, self.get_alphabet()),
**clean_dict({
'id': str(self.accession),
'name': self.symbol,
'description': self.name,
# 'dbxrefs': None,
}))
if self.domain_architecture:
seqrec.features = [dom.to_seqfeature()
for dom in self.domain_architecture.domains]
# Sequence attributes with no SeqRecord equivalent
seqrec.annotations = clean_dict({
'id_ref': self.id_ref,
'id_source': self.id_source,
'location': self.location,
'uri': self.uri and clean_dict({
'value': self.uri.value,
'desc': self.uri.desc,
'type': self.uri.type,
}),
'annotations': self.annotations and [
clean_dict({
'ref': ann.ref,
'source': ann.source,
'evidence': ann.evidence,
'type': ann.type,
'confidence': ann.confidence and [
ann.confidence.value,
ann.confidence.type],
'properties': [clean_dict({
'value': prop.value,
'ref': prop.ref,
'applies_to': prop.applies_to,
'datatype': prop.datatype,
'unit': prop.unit,
'id_ref': prop.id_ref })
for prop in ann.properties],
}) for ann in self.annotations],
})
return seqrec
