def healthy_lines():
initialize_promoters = classes.Promoters(
promoter_file_name,
three_donors_cell_list,
celltype_exclude=primary_exclude_list,
not_include=primary_not_include_codes,
partial_exclude=primary_cells_supersets,
sample_types="primary cells",
second_parser=None)
""" get the percentage of VEnCodes taken for 1 donor that work for all donors: """
initialize_promoters.ven_diagram_interception(2000,
5,
3,
combinations_number=4,
threshold=90)
""" get the percentage of VEnCodes taken for 1, 2, 3, etc donors that work for all and com """
def cancer_lines():
for line in lines_3donors:
primary_cell_list.append(line)
initialize = classes.Promoters(
promoter_file_name,
primary_cell_list,
celltype_exclude=primary_exclude_list,
not_include=primary_not_include_codes,
partial_exclude=primary_cells_supersets,
sample_types=["primary cells", "cell lines"],
second_parser="primary cells")
initialize.ven_diagram_interception(2000,
5,
3,
combinations_number=4,
threshold=90,
custom_celltypes=[line])
primary_cell_list.remove(line)
break
"""
init = classes.Promoters(promoter_file_name, complete_primary_cell_list,
celltype_exclude=complete_primary_exclude_list,
not_include=complete_primary_non_include_list,
partial_exclude=complete_primary_jit_exclude_list,
sample_types="primary cells", second_parser=None,
conservative=True, log_level="info", nrows=None)
"""
# Enhancers:
init = classes.Promoters(enhancer_file_name,
primary_cell_list,
celltype_exclude=primary_exclude_list,
not_include=primary_not_include_codes,
partial_exclude=primary_cells_supersets,
sample_types="primary cells",
second_parser=None,
conservative=True,
log_level="info",
enhancers=enhancer_names_db,
skiprows=None,
nrows=None)
data_copy = init.data.copy()
init.data = init.merge_donors_into_celltypes()
for celltype in tqdm(primary_cell_list):
# file name:
filename = "{}_tpm_enhancers".format(celltype)
results_directory = dhs.check_if_and_makefile(os.path.join(
"Files", "Dbs", filename),
path_type="parent3")
# Data
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import classes
from VEnCode.common_variables import file_name, primary_exclude_list, \
primary_not_include_codes, primary_cells_supersets
if __name__ == "__main__":
initialize_promoters = classes.Promoters(file_name,
"acute myeloid leukemia",
celltype_exclude=primary_exclude_list,
not_include=primary_not_include_codes,
partial_exclude=primary_cells_supersets,
sample_types=["primary cells", "cell lines"],
second_parser="primary cells")
# get vencodes:
initialize_promoters.get_vencodes(n=1, write_file=True)
"""
import os
import sys
sys.path.append(os.path.abspath(os.path.join('..', '')))
import classes
from VEnCode.common_variables import promoter_file_name, primary_cell_list, \
primary_exclude_list, \
primary_not_include_codes, primary_cells_supersets
# Promoters
initialize_promoters = classes.Promoters(promoter_file_name, primary_cell_list,
celltype_exclude=primary_exclude_list,
not_include=primary_not_include_codes,
partial_exclude=primary_cells_supersets,
sample_types="primary cells", second_parser=None,
conservative=True, log_level="info")
results = initialize_promoters.find_vencodes_each_celltype(stop=5, combinations_number=range(4, 8),
method="sampling",
n_samples=10000, threshold_inactivity=0,
threshold_activity=1)
"""
# Enhancers
initialize_enhancers = classes.Promoters(enhancer_file_name,
complete_primary_cell_list,
celltype_exclude=complete_primary_exclude_list,
not_include=complete_primary_non_include_list,
"""
Sets the variables and other
"""
def __init__(self):
self.cell_list = primary_cell_list
self.vens_to_take = 20
self.combinations_number = 4
self.threshold = 90
if __name__ == "__main__":
Setup = Setup()
initialize_promoters = classes.Promoters(promoter_file_name, Setup.cell_list,
celltype_exclude=primary_exclude_list,
not_include=primary_not_include_codes,
partial_exclude=primary_cells_supersets,
sample_types="primary cells", second_parser=None,
conservative=True, skip_raw_data=True)
""" All cell types
# use: cell_list = complete_primary_cell_list
initialize_promoters.codes_to_csv("codes_all_cells.csv", "list", "/Figure 2/Test codes/")
initialize_promoters.celltypes_to_csv("celltypes_all.csv", "list", "/Figure 2/Test codes/")
"""
""" 3 Donors
# use: cell_list = three_donors_cell_list
initialize_promoters.codes_to_csv("codes_3_donors.csv", "list", "/Figure 2/Test codes/")
initialize_promoters.celltypes_to_csv("celltypes_3_donors.csv", "list", "/Figure 2/Test codes/")
"""
""" 4 Donors