import os
import sys
is_exp_script = True
script_dir = os.path.split(os.path.realpath(__file__))[0]
#sys.path.append("../../../src")
import util.myconfig as myconfig
import util.utility as util
data_type = "fc"
if is_exp_script:
root_path = os.path.join(script_dir, "../../../")
configs = myconfig.config(root_path,
log_dir=script_dir,
data_type=data_type)
else:
root_path = os.path.join(script_dir, "../../")
configs = myconfig.config(root_path, data_type=data_type)
import models.state_space_model.ssm as ssm
import numpy as np
import subprocess
from pomegranate import *
def main(argvs):
process_id = int(argvs[1])
train_dir = argvs[2]
chromosome = argvs[3]
start_index = int(argvs[4])
end_index = int(argvs[5])
print(process_id, train_dir, chromosome, start_index, end_index)
# set up parameter file
import os
import sys
is_exp_script = True
script_dir = os.path.split(os.path.realpath(__file__))[0]
import util.myconfig as myconfig
import util.utility as util
if is_exp_script:
root_path = os.path.join(script_dir, "../../../")
configs = myconfig.config(root_path, log_dir = script_dir)
else:
root_path = os.path.join(script_dir, "../../")
configs = myconfig.config(root_path)
import models.state_space_model.ssm as ssm
import numpy as np
import subprocess
from pomegranate import *
def main(argvs):
process_id = int(argvs[1])
train_dir = argvs[2]
chromosome = argvs[3]
start_index = int(argvs[4])
end_index = int(argvs[5])
print(process_id, train_dir, chromosome, start_index, end_index)
# set up parameter file
with open(os.path.join(train_dir, "log.txt"), 'r') as param_f:
E = int(param_f.readline().strip('\n').split()[-1])
K = int(param_f.readline().strip('\n').split()[-1])
assay_list = param_f.readline().strip('\n').split()[1:]
# only need is resolution size here
"""
import os
import sys
import math
import numpy as np
import pandas as pd
import tensorflow as tf
from functools import partial
script_dir = os.path.split(os.path.realpath(__file__))[0]
sys.path.insert(0, os.path.join(script_dir, "../"))
import util.utility as util
import util.myconfig as myconfig
root_path = os.path.join(script_dir, "../../")
configs = myconfig.config(root_path)
bl_rm_data_path = configs.blacklist_rm_data_path
experiment_serial = "15-04-19-nhl1lhl5/" # nhl: number of hidden layer, lhl: length of hidden layer
experiment_folder = configs.experiment_path + experiment_serial
annotation_folder = experiment_folder + "annotation_result/"
model_file = os.path.join(experiment_folder, "my_model_all_layers.ckpt")
model_metadata_file = os.path.join(experiment_folder,
"my_model_all_layers.ckpt.meta")
assay_record = []
#assay_control = 2
#valid_size = 200 # size of validation vector
#window_size = 100 # size of slide window, determine within how much upstream(with resolution)
resolution_size = 200
