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