def get_reader(self, name, **kwargs):
## hack to avoid confusing users ##
# if name.lower() == "fasta":
# raise error.UnsupportedSchemaError("FASTA data needs to be specified as 'dnafasta', 'rnafasta', or 'proteinfasta'")
if name not in self.formats:
raise error.UnsupportedSchemaError(
"'%s' is not a recognized data schema name" % name)
return self.formats[name].get_reader(**kwargs)
def get_tree_source_iter(self, stream, **kwargs):
if self.tree_source_iter is None:
raise error.UnsupportedSchemaError(
"Iteration over source trees not currently supported for data schema '%s'"
% self.name)
return self.tree_source_iter(stream, **kwargs)
def tree_source_iter(self, stream, name, **kwargs):
if name not in self.formats:
raise error.UnsupportedSchemaError(
"'%s' is not a recognized data schema name" % name)
return self.formats[name].get_tree_source_iter(stream, **kwargs)
def get_writer(self, **kwargs):
if self.writer_type is None:
raise error.UnsupportedSchemaError(
"Writing is not currently supported for data schema '%s'" %
self.name)
return self.writer_type(**kwargs)
def get_writer(self, name, **kwargs):
if name not in self.formats:
raise error.UnsupportedSchemaError(
"'%s' is not a recognized data schema name" % name)
return self.formats[name].get_writer(**kwargs)