deepnovo_main.py

# Copyright 2017 Hieu Tran. All Rights Reserved.
#
# DeepNovo is publicly available for non-commercial uses.
# ==============================================================================

"""TODO(nh2tran): docstring."""

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

import tensorflow as tf

import deepnovo_config
import deepnovo_model
import deepnovo_worker_db
import deepnovo_worker_denovo
import deepnovo_worker_io
import deepnovo_worker_test
import deepnovo_main_modules


def main(_):
  """TODO(nh2tran): docstring."""

  print("main()")

  if deepnovo_config.FLAGS.knapsack_build:
    deepnovo_main_modules.knapsack_build()
  elif deepnovo_config.FLAGS.train:
    deepnovo_main_modules.train()
  elif deepnovo_config.FLAGS.test_true_feeding:
    deepnovo_main_modules.test_true_feeding()
  elif deepnovo_config.FLAGS.decode:
    deepnovo_main_modules.decode()
  elif deepnovo_config.FLAGS.search_denovo:
    model = deepnovo_model.ModelInference()
    model.build_model()
    worker_io = deepnovo_worker_io.WorkerIO(
        input_file=deepnovo_config.denovo_input_file,
        output_file=deepnovo_config.denovo_output_file)
    worker_denovo = deepnovo_worker_denovo.WorkerDenovo()
    worker_denovo.search_denovo(model, worker_io)
  elif deepnovo_config.FLAGS.search_db:
    model = deepnovo_model.ModelInference()
    model.build_model()
    worker_io = deepnovo_worker_io.WorkerIO(
        input_file=deepnovo_config.db_input_file,
        output_file=deepnovo_config.db_output_file)
    worker_db = deepnovo_worker_db.WorkerDB()
    worker_db.build_db()
    worker_db.search_db(model, worker_io)
  elif deepnovo_config.FLAGS.search_hybrid:
    model = deepnovo_model.ModelInference()
    model.build_model()
    # denovo search
    worker_io = deepnovo_worker_io.WorkerIO(
        input_file=deepnovo_config.hybrid_input_file,
        output_file=deepnovo_config.hybrid_denovo_file)
    worker_denovo = deepnovo_worker_denovo.WorkerDenovo()
    predicted_denovo_list = worker_denovo.search_denovo(model, worker_io)
    # db search with predicted_denovo_list
    worker_io = deepnovo_worker_io.WorkerIO(
        input_file=deepnovo_config.hybrid_input_file,
        output_file=deepnovo_config.hybrid_output_file)
    worker_db = deepnovo_worker_db.WorkerDB()
    worker_db.build_db()
    worker_db.search_db(model, worker_io, predicted_denovo_list)
  elif deepnovo_config.FLAGS.test:
    # test 1%FDR
    #~ worker_db = deepnovo_worker_db.WorkerDB()
    #~ worker_db.build_db()
    #~ worker_test = deepnovo_worker_test.WorkerTest()
    #~ worker_test.test_accuracy(worker_db.peptide_list)
    worker_test = deepnovo_worker_test.WorkerTest()
    worker_test.test_accuracy()
  else:
    print("ERROR: wrong option!")
    sys.exit()


if __name__ == "__main__":
  tf.app.run()