def annotate_samples_table(self, input, sample_expr, root=None, code=None, config=None):
"""Annotate samples with delimited text file (text table).
:param str input: Path to delimited text file.
:param str sample_expr: Expression for sample id (key).
:param str root: Sample annotation path to store text table.
:param str code: Annotation expression.
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig` or None
"""
pargs = ['annotatesamples', 'table', '-i', input, '--sample-expr', sample_expr]
if root:
pargs.append('--root')
pargs.append(root)
if code:
pargs.append('--code')
pargs.append(code)
if not config:
config = TextTableConfig()
pargs.extend(config.as_pargs())
return self.hc.run_command(self, 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.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 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 annotate_global_table(self, input, root, config=None):
"""Load delimited text file (text table) into global annotations as
Array[Struct].
:param str input: Input text file.
:param str root: Global annotation path to store text table.
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig` or None
"""
pargs = ['annotateglobal', 'table', '-i', input, '-r', root]
if not config:
config = TextTableConfig()
pargs.extend(config.as_pargs())
return self.hc.run_command(self, pargs)
def annotate_variants_table(self, path, variant_expr, root=None, code=None, config=None):
"""Annotate variant with delimited text file (text table).
:param path: Path to delimited text files.
:type path: str or list of str
:param str variant_expr: Expression for Variant (key).
:param str root: Variant annotation path to store text table.
:param str code: Annotation expression.
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig` or None
"""
pargs = ['annotatevariants', 'table', '--variant-expr', variant_expr]
if root:
pargs.append('--root')
pargs.append(root)
if code:
pargs.append('--code')
pargs.append(code)
if not config:
config = TextTableConfig()
pargs.extend(config.as_pargs())
if isinstance(path, str):
pargs.append(path)
else:
for p in path:
pargs.append(p)
return self.hc.run_command(self, pargs)
def annotate_variants_loci(self, path, locus_expr, root=None, code=None, config=None):
"""Annotate variants from an delimited text file (text table) indexed
by loci.
:param str path: Path to delimited text file.
:param str locus_expr: Expression for locus (key).
:param str root: Variant annotation path to store annotation.
:param str code: Annotation expression.
:param config: Configuration options for importing text files
:type config: :class:`.TextTableConfig` or None
"""
pargs = ['annotatevariants', 'loci', '--locus-expr', locus_expr]
if root:
pargs.append('--root')
pargs.append(root)
if code:
pargs.append('--code')
pargs.append(code)
if not config:
config = TextTableConfig()
pargs.extend(config.as_pargs())
if isinstance(path, str):
pargs.append(path)
else:
for p in path:
pargs.append(p)
return self.hc.run_command(self, pargs)
