def _convert_to_j(self, annotation):
if annotation is not None:
return scala_object(Env.hail().annotations, 'Annotation').fromSeq(
Env.jutils().arrayListToISeq(
[f.typ._convert_to_j(annotation.get(f.name)) for f in self.fields]
)
)
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return scala_object(Env.hail().annotations, 'Annotation').fromSeq(
Env.jutils().arrayListToISeq([
f.typ._convert_to_j(annotation[f.name])
for f in self.fields
]))
else:
return annotation
def __init__(self, contig, position):
if isinstance(contig, int):
contig = str(contig)
jrep = scala_object(Env.hail().variant, 'Locus').apply(contig, position)
self._init_from_java(jrep)
self._contig = contig
self._position = position
def _init_from_java(self, jtype):
jfields = Env.jutils().iterableToArrayList(jtype.fields())
self.fields = [
Field(f.name(), Type._from_java(f.typ()), dict(f.attrsJava()))
for f in jfields
]
def parse(string):
"""Parses a locus object from a CHR:POS string.
:rtype: :class:`.Locus`
"""
return Locus._from_java(scala_object(Env.hail().variant, 'Locus').parse(string))
def parse(string):
"""Parses a locus object from a CHR:POS string.
:rtype: :class:`.Locus`
"""
return Locus._from_java(scala_object(Env.hail().variant, 'Locus').parse(string))
def __init__(self, element_type):
"""
:param :class:`.Type` element_type: Hail type of set element
"""
jtype = scala_object(Env.hail().expr, 'TSet').apply(element_type._jtype)
self.element_type = element_type
super(TSet, self).__init__(jtype)
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().javaMapToMap(
{self.key_type._convert_to_j(k): self.value_type._convert_to_j(v) for k, v in annotation.iteritems()}
)
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().javaMapToMap(
{self.key_type._convert_to_j(k): self.value_type._convert_to_j(v) for k, v in annotation.iteritems()}
)
else:
return annotation
def __init__(self, element_type, required = False):
"""
:param :class:`.Type` element_type: Hail type of array element
"""
jtype = scala_object(Env.hail().expr, 'TAggregable').apply(element_type._jtype, required)
self.element_type = element_type
super(TAggregable, self).__init__(jtype)
def __init__(self, contig, position):
if isinstance(contig, int):
contig = str(contig)
jrep = scala_object(Env.hail().variant, 'Locus').apply(contig, position)
self._init_from_java(jrep)
self._contig = contig
self._position = position
def __init__(self, element_type):
"""
:param :class:`.Type` element_type: Hail type of set element
"""
jtype = scala_object(Env.hail().expr, 'TSet').apply(element_type._jtype)
self.element_type = element_type
super(TSet, self).__init__(jtype)
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().arrayListToSet(
[self.element_type._convert_to_j(elt) for elt in annotation]
)
else:
return annotation
def _convert_to_j(self, annotation):
if annotation is not None:
return Env.jutils().arrayListToISeq(
[self.element_type._convert_to_j(elt) for elt in annotation]
)
else:
return annotation
def hadoop_copy(src, dest):
"""Copy a file through the Hadoop filesystem API.
Supports distributed file systems like hdfs, gs, and s3.
**Examples**
>>> hadoop_copy('gs://hail-common/LCR.interval_list', 'file:///mnt/data/LCR.interval_list') # doctest: +SKIP
**Notes**
The provided source and destination file paths must be URIs
(uniform resource identifiers).
:param str src: Source file URI.
:param str dest: Destination file URI.
"""
Env.jutils().copyFile(src, dest, Env.hc()._jhc)
def __init__(self, contig, start, ref, alts):
if isinstance(contig, int):
contig = str(contig)
jrep = scala_object(Env.hail().variant, 'Variant').apply(contig, start, ref, alts)
self._init_from_java(jrep)
self._contig = contig
self._start = start
self._ref = ref
def __init__(self, contig, start, ref, alts):
if isinstance(contig, int):
contig = str(contig)
jrep = scala_object(Env.hail().variant, 'Variant').apply(contig, start, ref, alts)
self._init_from_java(jrep)
self._contig = contig
self._start = start
self._ref = ref
def hadoop_copy(src, dest):
"""Copy a file through the Hadoop filesystem API.
Supports distributed file systems like hdfs, gs, and s3.
**Examples**
>>> hadoop_copy('gs://hail-common/LCR.interval_list', 'file:///mnt/data/LCR.interval_list') # doctest: +SKIP
**Notes**
The provided source and destination file paths must be URIs
(uniform resource identifiers).
:param str src: Source file URI.
:param str dest: Destination file URI.
"""
Env.jutils().copyFile(src, dest, Env.hc()._jhc)
def from_fields(cls, fields, required=False):
"""Creates a new TStruct from field objects.
:param fields: The TStruct fields.
:type fields: list of :class:`.Field`
:param bool required: Flag for whether the struct can be missing.
:return: TStruct from input fields
:rtype: :class:`.TStruct`
"""
struct = TStruct.__new__(cls)
struct.fields = fields
jfields = [scala_object(Env.hail().expr, 'Field').apply(
f.name, f.typ._jtype, i, Env.jutils().javaMapToMap(f.attributes)) for i,f in enumerate(fields)]
jtype = scala_object(Env.hail().expr, 'TStruct').apply(jindexed_seq(jfields), required)
return TStruct._from_java(jtype)
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
d = dict()
for x in lst:
d[self.key_type._convert_to_py(x._1())] = self.value_type._convert_to_py(x._2())
return d
else:
return annotation
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
d = dict()
for x in lst:
d[self.key_type._convert_to_py(x._1())] = self.value_type._convert_to_py(x._2())
return d
else:
return annotation
def __init__(self, names, types):
"""
"""
if len(names) != len(types):
raise ValueError('length of names and types not equal: %d and %d' % (len(names), len(types)))
jtype = scala_object(Env.hail().expr, 'TStruct').apply(names, map(lambda t: t._jtype, types))
self.fields = [Field(names[i], types[i]) for i in xrange(len(names))]
super(TStruct, self).__init__(jtype)
def __init__(self, names, types):
"""
"""
if len(names) != len(types):
raise ValueError('length of names and types not equal: %d and %d' % (len(names), len(types)))
jtype = scala_object(Env.hail().expr, 'TStruct').apply(names, map(lambda t: t._jtype, types))
self.fields = [Field(names[i], types[i]) for i in xrange(len(names))]
super(TStruct, self).__init__(jtype)
def formatted(self):
now = datetime.datetime.now()
history = "# {}\n# version: {}\n\n".format(now.isoformat(), Env.hc().version)
history += "from hail import *\n\n"
for stmt in self.statements:
history += (stmt + "\n\n")
history += ("(" + self.expr + ")")
try:
import autopep8
return autopep8.fix_code(history)
except ImportError:
return history
def formatted(self):
now = datetime.datetime.utcnow()
history = "# {}\n# version: {}\n\n".format(now.isoformat(), Env.hc().version)
history += "from hail import *\n\n"
for stmt in self.statements:
history += (stmt + "\n\n")
history += ("(" + self.expr + ")")
try:
import autopep8
return autopep8.fix_code(history)
except ImportError:
return history
def parse(cls, string):
"""Parses a locus object from a CHR:POS string.
**Examples**
>>> l1 = Locus.parse('1:101230')
>>> l2 = Locus.parse('X:4201230')
:rtype: :class:`.Locus`
"""
return Locus._from_java(scala_object(Env.hail().variant, 'Locus').parse(string))
def parse(cls, string):
"""Parses a locus object from a CHR:POS string.
**Examples**
>>> l1 = Locus.parse('1:101230')
>>> l2 = Locus.parse('X:4201230')
:rtype: :class:`.Locus`
"""
return Locus._from_java(
scala_object(Env.hail().variant, 'Locus').parse(string))
def parse(string):
"""Parses a variant object from a string.
There are two acceptable formats: CHR:POS:REF:ALT, and
CHR:POS:REF:ALT1,ALT2,...ALTN. Below is an example of
each:
>>> v_biallelic = Variant.parse('16:20012:A:TT')
>>> v_multiallelic = Variant.parse('16:12311:T:C,TTT,A')
:rtype: :class:`.Variant`
"""
jrep = scala_object(Env.hail().variant, 'Variant').parse(string)
return Variant._from_java(jrep)
def parse(cls, string):
"""Parses a variant object from a string.
There are two acceptable formats: CHR:POS:REF:ALT, and
CHR:POS:REF:ALT1,ALT2,...ALTN. Below is an example of
each:
>>> v_biallelic = Variant.parse('16:20012:A:TT')
>>> v_multiallelic = Variant.parse('16:12311:T:C,TTT,A')
:rtype: :class:`.Variant`
"""
jrep = scala_object(Env.hail().variant, 'Variant').parse(string)
return Variant._from_java(jrep)
def __init__(self):
super(TLocus, self).__init__(scala_object(Env.hail().expr, 'TLocus'))
def __init__(self):
super(TCall, self).__init__(scala_object(Env.hail().expr, 'TCall'))
def __init__(self):
super(TGenotype, self).__init__(scala_object(Env.hail().expr, 'TGenotype'))
def __init__(self):
super(TInt, self).__init__(scala_object(Env.hail().expr, 'TInt'))
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
return set([self.element_type._convert_to_py(x) for x in lst])
else:
return annotation
def __init__(self):
super(TString, self).__init__(scala_object(Env.hail().expr, 'TString'))
def _jrep(self):
return Env.hail().stats.BetaDist.apply(float(self.a), float(self.b))
def _jrep(self):
return Env.hail().stats.UniformDist.apply(float(self.minVal), float(self.maxVal))
def types_rst(self, file_name):
Env.hail().utils.FunctionDocumentation.makeTypesDocs(file_name)
def __init__(self, key_type, value_type):
jtype = scala_object(Env.hail().expr, 'TDict').apply(key_type._jtype, value_type._jtype)
self.key_type = key_type
self.value_type = value_type
super(TDict, self).__init__(jtype)
def __init__(self, ref, alt):
jaa = scala_object(Env.hail().variant, 'AltAllele').apply(ref, alt)
self._init_from_java(jaa)
self._ref = ref
self._alt = alt
def _convert_to_py(self, annotation):
if annotation:
lst = Env.jutils().iterableToArrayList(annotation)
return set([self.element_type._convert_to_py(x) for x in lst])
else:
return annotation
def __init__(self):
super(TAltAllele,
self).__init__(scala_object(Env.hail().expr, 'TAltAllele'))
def __init__(self):
super(TInt, self).__init__(scala_object(Env.hail().expr, 'TInt'))
def _to_java(self):
"""Convert to Java TextTableConfiguration object."""
return Env.hail().utils.TextTableConfiguration.apply(
self.types, self.comment, self.delimiter, self.missing,
self.noheader, self.impute)
def _convert_to_j(self, annotation):
if annotation:
return Env.jutils().makeInt(annotation)
else:
return annotation
def _init_from_java(self, jtype):
jfields = Env.jutils().iterableToArrayList(jtype.fields())
self.fields = [Field(f.name(), Type._from_java(f.typ()), dict(f.attrsJava())) for f in jfields]
def __init__(self):
super(TDouble, self).__init__(scala_object(Env.hail().expr, 'TDouble'))
def functions_rst(self, file_name):
Env.hail().utils.FunctionDocumentation.makeFunctionsDocs(file_name)
def __init__(self):
super(TBoolean,
self).__init__(scala_object(Env.hail().expr, 'TBoolean'))
def __init__(self):
super(TAltAllele, self).__init__(scala_object(Env.hail().expr, 'TAltAllele'))
def __init__(self, key_type, value_type):
jtype = scala_object(Env.hail().expr,
'TDict').apply(key_type._jtype, value_type._jtype)
self.key_type = key_type
self.value_type = value_type
super(TDict, self).__init__(jtype)
def __init__(self):
super(TCall, self).__init__(scala_object(Env.hail().expr, 'TCall'))
def functions_rst(self, file_name):
Env.hail().utils.FunctionDocumentation.makeFunctionsDocs(file_name)
def _jrep(self):
return Env.hail().stats.TruncatedBetaDist.apply(float(self.a), float(self.b), float(self.minVal), float(self.maxVal))
def __init__(self):
super(TGenotype,
self).__init__(scala_object(Env.hail().expr, 'TGenotype'))
def __init__(self):
super(TDouble, self).__init__(scala_object(Env.hail().expr, 'TDouble'))
def __init__(self):
super(TLocus, self).__init__(scala_object(Env.hail().expr, 'TLocus'))
def __init__(self):
super(TString, self).__init__(scala_object(Env.hail().expr, 'TString'))
def _convert_to_j(self, annotation):
if annotation:
return Env.jutils().makeInt(annotation)
else:
return annotation
def __init__(self):
super(TBoolean, self).__init__(scala_object(Env.hail().expr, 'TBoolean'))