def write(self, stream, schema, **kwargs):
"""
Writes this `DataSet` object to the file-like object `stream`
in `schema`. `schema` must be a recognized and supported
phylogenetic data file schema. If writing is not implemented for
the schema specified, then a `UnsupportedSchemaError` is raised.
The following optional keyword arguments are also recognized:
- `exclude_trees` if True skips over tree data
- `exclude_chars` if True skips over character data
Additional keyword arguments may be handled by various writers
specialized to handle specific data formats.
"""
from dendropy.utility.iosys import require_format_from_kwargs
from dendropy.dataio import get_writer
kwargs["dataset"] = self
# if self.attached_taxon_set is not None:
# if "taxon_set" not in kwargs:
# kwargs["taxon_set"] = self.attached_taxon_set
# elif kwargs["taxon_set"] is not self.attached_taxon_set:
# raise TypeError("DataSet object is already attached to a TaxonSet, but different TaxonSet passed using 'taxon_set' keyword argument")
writer = get_writer(schema=schema, **kwargs)
writer.write(stream)
def _format_and_write_to_stream(self,
stream,
schema,
exclude_trees=False,
exclude_chars=False,
**kwargs):
"""
Writes out ``self`` in ``schema`` format to a destination given by
file-like object ``stream``.
Parameters
----------
stream : file or file-like object
Destination for data.
schema : string
Must be a recognized character file schema, such as "nexus",
"phylip", etc, for which a specialized tree list writer is
available. If this is not implemented for the schema specified, then
a UnsupportedSchemaError is raised.
\*\*kwargs : keyword arguments, optional
Keyword arguments will be passed directly to the writer for the
specified schema. See documentation for details on keyword
arguments supported by writers of various schemas.
"""
writer = dataio.get_writer(schema, **kwargs)
writer.write_dataset(self, stream, exclude_trees, exclude_chars)
def write(self, stream, schema, **kwargs):
"""
Writes this `DataSet` object to the file-like object `stream`
in `schema`. `schema` must be a recognized and supported
phylogenetic data file schema. If writing is not implemented for
the schema specified, then a `UnsupportedSchemaError` is raised.
The following optional keyword arguments are also recognized:
- `exclude_trees` if True skips over tree data
- `exclude_chars` if True skips over character data
Additional keyword arguments may be handled by various writers
specialized to handle specific data formats.
"""
from dendropy.utility.iosys import require_format_from_kwargs
from dendropy.dataio import get_writer
kwargs["dataset"] = self
# if self.attached_taxon_set is not None:
# if "taxon_set" not in kwargs:
# kwargs["taxon_set"] = self.attached_taxon_set
# elif kwargs["taxon_set"] is not self.attached_taxon_set:
# raise TypeError("DataSet object is already attached to a TaxonSet, but different TaxonSet passed using 'taxon_set' keyword argument")
writer = get_writer(schema=schema, **kwargs)
writer.write(stream)
def _format_and_write_to_stream(self,
stream,
schema,
exclude_trees=False,
exclude_chars=False,
**kwargs):
"""
Writes out ``self`` in ``schema`` format to a destination given by
file-like object ``stream``.
Parameters
----------
stream : file or file-like object
Destination for data.
schema : string
Must be a recognized character file schema, such as "nexus",
"phylip", etc, for which a specialized tree list writer is
available. If this is not implemented for the schema specified, then
a UnsupportedSchemaError is raised.
\*\*kwargs : keyword arguments, optional
Keyword arguments will be passed directly to the writer for the
specified schema. See documentation for details on keyword
arguments supported by writers of various schemas.
"""
writer = dataio.get_writer(schema, **kwargs)
writer.write_dataset(self, stream, exclude_trees, exclude_chars)
def write(self, dest, format):
"""
Writes dataset to `dest`, a file descriptor object, in `format`.
"""
from dendropy import dataio
writer = dataio.get_writer(format)
writer.write_dataset(self, dest)