def store_chars(char_block, format, dest=None):
"Writes the CharacterBlock `char_block` to `dest` using writer."
deprecation("'dataio.store_chars()' is deprecated: use 'write()' method of a Dataset object instead", logger_obj=_LOG)
dataset = Dataset()
dataset.add_char_block(char_block=char_block)
return store_dataset(dataset=dataset,
format=format,
dest=dest)
def dataset_from_string(string, format):
"""
Returns a Dataset object parsed from the source, where:
`string` - a string containing the data to be parsed.
`format` - file format specification
"""
deprecation("'dataio.dataset_from_string()' is deprecated; use 'from_string()' method of a Dataset object instead", logger_obj=_LOG)
reader = get_reader(format)
return reader.read_dataset(source_file_handle(string=string))
def trees_from_string(string, format, encode_splits=False, rooted=RootingInterpretation.UNKNOWN_DEF_UNROOTED):
"""
Returns a *list* of TreesBlock objects parsed from the source, where:
`string` - a string containing the data to be parsed.
`format` - file format specification
"""
deprecation("'dataio.trees_from_string()' is deprecated: use 'trees_from_string()' method of a Dataset object instead", logger_obj=_LOG)
reader = get_reader(format)
return reader.read_trees(source_file_handle(string=string), encode_splits=encode_splits, rooted=rooted)
def trees_from_file(file_obj, format, encode_splits=False, rooted=RootingInterpretation.UNKNOWN_DEF_UNROOTED):
"""
Returns a *list* of TreesBlock objects parsed from the source, where:
`file_obj` - can either be a file descriptor object/handle opened
for reading or a string indicating a filepath that
can be opened for reading using open().
`format` - file format specification
"""
deprecation("'dataio.trees_from_file()' is deprecated: use 'read_trees()' method of a Dataset object instead", logger_obj=_LOG)
reader = get_reader(format)
return reader.read_trees(source_file_handle(file_obj=file_obj), encode_splits=encode_splits, rooted=rooted)
def dataset_from_file(file_obj, format):
"""
Returns a Dataset object parsed from the source, where:
`file_obj` - can either be a file descriptor object/handle opened
for reading or a string indicating a filepath that
can be opened for reading using open().
`format` - file format specification
"""
deprecation("'dataio.dataset_from_file()' is deprecated; use 'read()' method of a Dataset object instead", logger_obj=_LOG)
reader = get_reader(format)
return reader.read_dataset(source_file_handle(file_obj=file_obj))
def from_nexus(file_obj=None, string=None):
"""
Returns a Dataset object parsed from a NEXUS or NEWICK source.
`file_obj` - can either be a file descriptor object/handle opened
for reading or a string indicating a filepath that
can be opened for reading using open().
`string` - a string containing the data to be parsed.
Either `file_obj` or `string` must be given. If both are given, `file_obj` is used.
"""
deprecation("'dataio.from_nexus() is deprecated: use 'read()' method of a Dataset object instead", logger_obj=_LOG)
return nexus.read_dataset(source_file_handle(file_obj=file_obj, string=string))
def store_trees(trees_collection, format, dest=None):
"Writes the list of trees `trees` to `dest` using writer."
deprecation("'dataio.store_trees()' is deprecated: use 'write()' method of a Dataset object instead", logger_obj=_LOG)
if isinstance(trees_collection, TreesBlock):
trees_block = trees_collection
else:
trees_block = TreesBlock()
for tree in trees_collection:
trees_block.append(tree)
trees_block.normalize_taxa()
dataset = Dataset()
dataset.add_trees_block(trees_block=trees_block)
return store_dataset(dataset=dataset,
format=format,
dest=dest)
def store_dataset(dataset, format, dest=None):
"""
Writes the Dataset object `dataset` using `writer` (a DatasetWriter or
derived object) to `dest`. If `dest` is a string, then it is assumed to be
a path name, and open() is used to construct an output stream handle from it.
If `dest` is not given, then the dataset is written to a string and a string
is returned.
"""
deprecation("'dataio.store_dataset()' is deprecated: use 'write()' method of a Dataset object instead", logger_obj=_LOG)
writer = get_writer(format)
if dest is None:
dest = StringIO()
if isinstance(dest, str):
dest = open(dest, "w")
writer.write_dataset(dataset, dest)
if hasattr(dest, "getvalue"):
return dest.getvalue()