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 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, path):
self._jfile = Env.jutils().writeFile(path, Env.hc()._jhc)
super(HadoopWriter, self).__init__()
def __init__(self, path):
self._jfile = Env.jutils().readFile(path, Env.hc()._jhc)
super(HadoopReader, self).__init__()
def __init__(self, reference_genome=None, required = False):
self._rg = reference_genome if reference_genome else Env.hc().default_reference
jtype = scala_object(Env.hail().expr, 'TInterval').apply(self._rg._jrep, required)
super(TInterval, self).__init__(jtype)
