import json
import re
from hail.typecheck import *
from hail.utils import wrap_to_list
from hail.utils.java import jiterable_to_list, Env, joption
from hail.typecheck import oneof, transformed
import hail as hl
rg_type = lazy()
reference_genome_type = oneof(
transformed((str, lambda x: hl.get_reference(x))), rg_type)
class ReferenceGenome(object):
"""An object that represents a `reference genome <https://en.wikipedia.org/wiki/Reference_genome>`__.
Examples
--------
>>> contigs = ["1", "X", "Y", "MT"]
>>> lengths = {"1": 249250621, "X": 155270560, "Y": 59373566, "MT": 16569}
>>> par = [("X", 60001, 2699521)]
>>> my_ref = hl.ReferenceGenome("my_ref", contigs, lengths, "X", "Y", "MT", par)
Notes
-----
Hail comes with predefined reference genomes (case sensitive!):
- GRCh37
- GRCh38
- GRCm38
raise NotImplementedError
@abc.abstractmethod
def clear(self):
raise NotImplementedError
def _get_context(self):
return _empty_context
def get_context(self):
if self._context is None:
self._context = self._get_context()
return self._context
hail_type = oneof(HailType, transformed((str, dtype)))
class _tvoid(HailType):
def __init__(self):
super(_tvoid, self).__init__()
def __str__(self):
return "void"
def _eq(self, other):
return isinstance(other, _tvoid)
def _parsable_string(self):
return "Void"
import json
import re
from hail.typecheck import *
from hail.utils import wrap_to_list
from hail.utils.java import jiterable_to_list, Env, joption
from hail.typecheck import oneof, transformed
import hail as hl
rg_type = lazy()
reference_genome_type = oneof(transformed((str, lambda x: hl.get_reference(x))), rg_type)
class ReferenceGenome(object):
"""An object that represents a `reference genome <https://en.wikipedia.org/wiki/Reference_genome>`__.
Examples
--------
>>> contigs = ["1", "X", "Y", "MT"]
>>> lengths = {"1": 249250621, "X": 155270560, "Y": 59373566, "MT": 16569}
>>> par = [("X", 60001, 2699521)]
>>> my_ref = hl.ReferenceGenome("my_ref", contigs, lengths, "X", "Y", "MT", par)
Notes
-----
Hail comes with predefined reference genomes (case sensitive!):
- GRCh37
- GRCh38
- GRCm38
y_contigs, mt_contigs, par))
def _init_from_java(self, jrep):
self._jrep = jrep
@classmethod
def _from_java(cls, jrep):
gr = ReferenceGenome.__new__(cls)
gr._init_from_java(jrep)
gr._name = None
gr._contigs = None
gr._lengths = None
gr._x_contigs = None
gr._y_contigs = None
gr._mt_contigs = None
gr._par = None
gr._par_tuple = None
super(ReferenceGenome, gr).__init__()
ReferenceGenome._references[gr.name] = gr
return gr
def _check_locus(self, l_jrep):
self._jrep.checkLocus(l_jrep)
def _check_interval(self, interval_jrep):
self._jrep.checkInterval(interval_jrep)
reference_genome_type = oneof(
transformed((str, lambda x: hl.get_reference(x))), ReferenceGenome)
import json
import re
from hail.typecheck import *
from hail.utils import wrap_to_list
from hail.utils.java import jiterable_to_list, Env, joption
from hail.typecheck import oneof, transformed
import hail as hl
rg_type = lazy()
reference_genome_type = oneof(transformed((str, lambda x: hl.get_reference(x))), rg_type)
class ReferenceGenome(object):
"""An object that represents a `reference genome <https://en.wikipedia.org/wiki/Reference_genome>`__.
Examples
--------
>>> contigs = ["1", "X", "Y", "MT"]
>>> lengths = {"1": 249250621, "X": 155270560, "Y": 59373566, "MT": 16569}
>>> par = [("X", 60001, 2699521)]
>>> my_ref = hl.ReferenceGenome("my_ref", contigs, lengths, "X", "Y", "MT", par)
Notes
-----
Hail comes with predefined reference genomes (case sensitive!):
- GRCh37
- GRCh38
- GRCm38
