import numpy as np
import pandas as pd
# http://mikegrouchy.com/blog/2012/05/be-pythonic-__init__py.html
from lineage.ensembl import EnsemblRestClient
from lineage.individual import Individual
from lineage.resources import Resources
from lineage.snps import SNPs
from lineage.utils import Parallelizer, create_dir, save_df_as_csv
from lineage.visualization import plot_chromosomes
# set version string with Versioneer
from lineage._version import get_versions
__version__ = get_versions()["version"]
del get_versions
class Lineage:
""" Object used to interact with the `lineage` framework. """
def __init__(
self,
output_dir="output",
resources_dir="resources",
parallelize=True,
processes=os.cpu_count(),
):
""" Initialize a ``Lineage`` object.
Parameters
"""
import os
import numpy as np
import pandas as pd
# http://mikegrouchy.com/blog/2012/05/be-pythonic-__init__py.html
from lineage.ensembl import EnsemblRestClient
from lineage.individual import Individual
from lineage.resources import Resources
from lineage.visualization import plot_chromosomes
# set version string with Versioneer
from lineage._version import get_versions
__version__ = get_versions()['version']
del get_versions
class Lineage(object):
""" Object used to interact with the `lineage` framework. """
def __init__(self, output_dir='output', resources_dir='resources'):
""" Initialize a ``Lineage`` object.
Parameters
----------
output_dir : str
name / path of output directory
resources_dir
name / path of resources directory