def as_annotation(self):
top = dendropy.Annotation(name="otherSeqIds",
value=None,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
for key, value in self.items():
sub = dendropy.Annotation(name=key,
value=value,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=False,
is_hidden=False,
label=None,
oid=None)
top.annotations.add(sub)
return top
def as_reference_annotation(self):
annote = dendropy.Annotation(name="source",
value=self.uri,
datatype_hint=None,
name_prefix="dcterms",
namespace="http://purl.org/dc/terms/",
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
return annote
def as_annotation(self):
annote = dendropy.Annotation(name=self.name,
value=self.value,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=False,
is_hidden=False,
label=None,
oid=None)
return annote
def as_annotation(self):
top = dendropy.Annotation(name="INSDSeq_feature-table",
value=None,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
for feature in self:
top.annotations.add(feature.as_annotation())
return top
def as_annotation(self):
top = dendropy.Annotation(name="INSDReference_reference",
value=None,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
for item in [
("number", "INSDReference_reference"),
("position", "INSDReference_position"),
("title", "INSDReference_title"),
("journal", "INSDReference_journal"),
("pubmed_id", "INSDReference_pubmed"),
("medline_id", "INSDReference_medline"),
]:
value = getattr(self, item[0])
if value is None:
continue
sub = dendropy.Annotation(name=item[1],
value=value,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=False,
is_hidden=False,
label=None,
oid=None)
top.annotations.add(sub)
return top
def as_annotation(self):
top = self.as_reference_annotation()
# top = dendropy.Annotation(
# name="source",
# value=None,
# datatype_hint=None,
# name_prefix="dcterms",
# namespace="http://purl.org/dc/terms/",
# name_is_prefixed=False,
# is_attribute=False,
# annotate_as_reference=True,
# is_hidden=False,
# label=None,
# oid=None)
# for item in [
# ("db", "db"),
# ("request_key", "requestKey")
# ]:
# value = getattr(self, item[0])
# if value is None:
# continue
# a = dendropy.Annotation(
# name=item[1],
# value=value,
# datatype_hint=None,
# name_prefix="dendropy",
# namespace="http://packages.python.org/DendroPy/",
# name_is_prefixed=False,
# is_attribute=False,
# annotate_as_reference=False,
# is_hidden=False,
# label=None,
# oid=None)
# top.annotations.add(a)
for item in [
("locus", "INSDSeq_locus"),
("length", "INSDSeq_length"),
("moltype", "INSDSeq_moltype"),
("topology", "INSDSeq_topology"),
("strandedness", "INSDSeq_strandedness"),
("division", "INSDSeq_division"),
("update_date", "INSDSeq_update-date"),
("create_date", "INSDSeq_create-date"),
("definition", "INSDSeq_definition"),
("primary_accession", "INSDSeq_primary-accesison"),
("accession_version", "INSDSeq_accession-version"),
("other_seq_ids", "INSDSeq_hter-seqids"),
("source", "INSDSeq_source"),
("organism", "INSDSeq_organism"),
("taxonomy", "INSDSeq_taxonomy"),
("references", "INSDSeq_references"),
("feature_table", "INSDSeq_feature-table"),
]:
value = getattr(self, item[0])
if hasattr(value, "as_annotation") and value:
a = value.as_annotation()
elif value is not None:
a = dendropy.Annotation(name=item[1],
value=value,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=False,
is_hidden=False,
label=None,
oid=None)
top.annotations.add(a)
return top
def as_annotation(self):
top = dendropy.Annotation(name="INSDSeq_feature",
value=None,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
for item in [
("key", "INSDFeature_key"),
("location", "INSDFeature_location"),
]:
value = getattr(self, item[0])
if not value:
continue
sub = dendropy.Annotation(name=item[1],
value=value,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=False,
is_hidden=False,
label=None,
oid=None)
top.annotations.add(sub)
if self.intervals:
intervals_annote = dendropy.Annotation(
name="INSDSeq_intervals",
value=None,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
top.annotations.add(intervals_annote)
for interval in self.intervals:
interval_annote = dendropy.Annotation(
name="INSDInterval",
value=None,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=True,
is_hidden=False,
label=None,
oid=None)
intervals_annote.annotations.add(interval_annote)
for item in [
("begin", "INSDInterval_from"),
("end", "INSDInterval_to"),
("accession", "INSDInterval_accession"),
]:
value = getattr(self, item[0])
if not value:
continue
sub = dendropy.Annotation(
name=item[1],
value=value,
datatype_hint=None,
name_prefix=GENBANK_ANNOTATION_PREFIX,
namespace=GENBANK_ANNOTATION_NAMESPACE,
name_is_prefixed=False,
is_attribute=False,
annotate_as_reference=False,
is_hidden=False,
label=None,
oid=None)
interval_annote.annotations.add(interval_annote)
if self.qualifiers:
top.annotations.add(self.qualifiers.as_annotation())
return top
