run.py

import os
import sys
import tensorflow as tf
import pandas as pd

GUIDE_LEN = 23
NUCLEOTIDE_TOKENS = dict(zip(['A', 'C', 'G', 'T'], [0, 1, 2, 3]))

# load model
if os.path.exists('model'):
    tiger = tf.keras.models.load_model('model')
else:
    print('no saved model!')
    exit()


def process_data(x):
    x = [item.upper() for item in x]
    number_of_input = len(x) - GUIDE_LEN + 1
    input_gens = []
    for i in range(number_of_input):
        input_gens.append("".join(x[i:i + GUIDE_LEN]))
    merged_token = []
    token_x = [NUCLEOTIDE_TOKENS[item] for item in x]
    for i in range(number_of_input):
        merged_token.extend(token_x[i:i + GUIDE_LEN])
    one_hot_x = tf.one_hot(merged_token, depth=4)
    model_input_x = tf.reshape(one_hot_x, [-1, GUIDE_LEN * 4])
    return input_gens, model_input_x


def gen_report_table(input_gens, res):
    res = res.numpy().flatten().tolist()
    # print("ftaltten res: ", res)
    data = {"Gene": input_gens, "res": res}
    tbl = pd.DataFrame.from_dict(data)
    return tbl


def run(x):
    input_gens, model_input_x = process_data(x)
    # print("input gene: ", input_gens)
    # print("model_input: ", model_input_x)
    res = tiger.model.predict_step(model_input_x)
    # print("res: ", res)
    return gen_report_table(input_gens, res)


if __name__ == "__main__":
    if len(sys.argv) == 1:
        print("you need to specify 23 character gen information")
        exit()
    x = sys.argv[1]
    if len(x) != 23:
        print("you need to specify 23 character gen information. You typed %s chars" % len(x))
        exit()
    elif all([True if item in "ACGT" else False for item in x]):
        print("run succesfully: ", run(x))
    else:
        print("your gen sequence need 23 character only from ACGT")
        exit()