def import_keytable(self,
path,
npartitions=None,
config=TextTableConfig()):
"""Import delimited text file (text table) as key table.
The resulting key table will have no key columns, use :py:meth:`.KeyTable.key_by`
to specify keys.
:param path: files to import.
:type path: str or list of str
:param npartitions: Number of partitions.
:type npartitions: int or None
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig`
:return: Key table constructed from text table.
:rtype: :class:`.KeyTable`
"""
if not config:
config = TextTableConfig()
jkt = self._jhc.importKeyTable(jindexed_seq_args(path),
joption(npartitions), config._to_java())
return KeyTable(self, jkt)
def import_keytable(self,
path,
key_names=[],
npartitions=None,
config=TextTableConfig()):
"""Import delimited text file (text table) as KeyTable.
:param path: files to import.
:type path: str or list of str
:param key_names: The name(s) of fields to be considered keys
:type key_names: str or list of str
:param npartitions: Number of partitions.
:type npartitions: int or None
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig`
:rtype: :class:`.KeyTable`
"""
if not config:
config = TextTableConfig()
jkt = self._jhc.importKeyTable(jindexed_seq_args(path),
jindexed_seq_args(key_names),
joption(npartitions), config._to_java())
return KeyTable(self, jkt)
def import_annotations_table(self,
path,
variant_expr,
code=None,
npartitions=None,
config=TextTableConfig()):
"""Import variants and variant annotations from a delimited text file
(text table) as a sites-only VariantDataset.
:param path: The files to import.
:type path: str or list of str
:param str variant_expr: Expression to construct a variant
from a row of the text table. Must have type Variant.
:param code: Expression to build the variant annotations.
:type code: str or None
:param npartitions: Number of partitions.
:type npartitions: int or None
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig`
:rtype: :class:`.VariantDataset`
"""
jvds = self._jhc.importAnnotationsTables(jindexed_seq_args(path),
variant_expr, joption(code),
joption(npartitions),
config._to_java())
return VariantDataset(self, jvds)
def import_annotations_table(self,
path,
variant_expr,
code=None,
npartitions=None,
config=None):
"""Import variants and variant annotations from a delimited text file
(text table) as a sites-only VariantDataset.
:param path: The files to import.
:type path: str or list of str
:param str variant_expr: Expression to construct a variant
from a row of the text table. Must have type Variant.
:param code: Expression to build the variant annotations.
:type code: str or None
:param npartitions: Number of partitions.
:type npartitions: int or None
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig` or None
:rtype: :class:`.VariantDataset`
"""
pargs = ['importannotations', 'table']
if isinstance(path, str):
pargs.append(path)
else:
for p in path:
pargs.append(p)
pargs.append('--variant-expr')
pargs.append(variant_expr)
if code:
pargs.append('--code')
pargs.append(code)
if npartitions:
pargs.append('--npartition')
pargs.append(npartitions)
if not config:
config = TextTableConfig()
pargs.extend(config._as_pargs())
return self._run_command(None, pargs)
def import_keytable(self, path, key_names, npartitions=None, config=None):
"""Import delimited text file (text table) as KeyTable.
:param path: files to import.
:type path: str or list of str
:param key_names: The name(s) of fields to be considered keys
:type key_names: str or list of str
:param npartitions: Number of partitions.
:type npartitions: int or None
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig` or None
:rtype: :class:`.KeyTable`
"""
path_args = []
if isinstance(path, str):
path_args.append(path)
else:
for p in path:
path_args.append(p)
if not isinstance(key_names, str):
key_names = ','.join(key_names)
if not npartitions:
npartitions = self.sc.defaultMinPartitions
if not config:
config = TextTableConfig()
return KeyTable(
self,
self._hail.keytable.KeyTable.importTextTable(
self._jsc, jarray(self._jvm.java.lang.String, path_args),
key_names, npartitions, config._to_java()))