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