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.jvm.org.broadinstitute.hail.keytable.KeyTable.importTextTable(
self.jsc, jarray(self.gateway, self.jvm.java.lang.String, path_args), key_names, npartitions, config.to_java(self)))
def run_command(self, vds, pargs):
jargs = jarray(self.gateway, self.jvm.java.lang.String, pargs)
t = self.jvm.org.broadinstitute.hail.driver.ToplevelCommands.lookup(
jargs)
cmd = t._1()
cmd_args = t._2()
result = cmd.run(self._jstate(vds.jvds if vds != None else None),
cmd_args)
return VariantDataset(self, result.vds())
def run_command(self, vds, pargs):
jargs = jarray(self.gateway, self.jvm.java.lang.String, pargs)
t = self.jvm.org.broadinstitute.hail.driver.ToplevelCommands.lookup(jargs)
cmd = t._1()
cmd_args = t._2()
jstate = self._jstate(vds.jvds if vds != None else None)
try:
result = cmd.run(jstate, cmd_args)
except Py4JJavaError as e:
self._raise_py4j_exception(e)
return VariantDataset(self, result.vds())
def make_keytable(self, variant_condition, genotype_condition, key_names):
"""Make a KeyTable with one row per variant.
Per sample field names in the result are formed by concatening
the sample ID with the genotype_condition left hand side with
dot (.). If the left hand side is empty::
`` = expr
then the dot (.) is ommited.
**Example**
Consider a ``VariantDataset`` ``vds`` with 2 variants and 3 samples::
Variant FORMAT A B C
1:1:A:T GT:GQ 0/1:99 ./. 0/0:99
1:2:G:C GT:GQ 0/1:89 0/1:99 1/1:93
Then::
>>> vds = hc.import_vcf('data/sample.vcf')
>>> vds.make_keytable('v = v', 'gt = g.gt', gq = g.gq', [])
returns a ``KeyTable`` with schema::
v: Variant
A.gt: Int
B.gt: Int
C.gt: Int
A.gq: Int
B.gq: Int
C.gq: Int
in particular, the values would be::
v A.gt B.gt C.gt A.gq B.gq C.gq
1:1:A:T 1 NA 0 99 NA 99
1:2:G:C 1 1 2 89 99 93
:param variant_condition: Variant annotation expressions.
:type variant_condition: str or list of str
:param genotype_condition: Genotype annotation expressions.
:type genotype_condition: str or list of str
:param key_names: list of key columns
:type key_names: list of str
:rtype: KeyTable
"""
if isinstance(variant_condition, list):
variant_condition = ','.join(variant_condition)
if isinstance(genotype_condition, list):
genotype_condition = ','.join(genotype_condition)
jkt = (scala_package_object(self.hc.jvm.org.broadinstitute.hail.driver)
.makeKT(self.jvds, variant_condition, genotype_condition,
jarray(self.hc.gateway, self.hc.jvm.java.lang.String, key_names)))
return KeyTable(self.hc, jkt)