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deepnovo_config.py
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deepnovo_config.py
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# 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 numpy as np
import tensorflow as tf
# ==============================================================================
# FLAGS (options) for this app
# ==============================================================================
tf.app.flags.DEFINE_string("train_dir", # flag_name
"train", # default_value
"Training directory.") # docstring
tf.app.flags.DEFINE_integer("direction",
2,
"Set to 0/1/2 for Forward/Backward/Bi-directional.")
tf.app.flags.DEFINE_boolean("use_intensity",
True,
"Set to True to use intensity-model.")
tf.app.flags.DEFINE_boolean("shared",
False,
"Set to True to use shared weights.")
tf.app.flags.DEFINE_boolean("use_lstm",
True,
"Set to True to use lstm-model.")
tf.app.flags.DEFINE_boolean("knapsack_build",
False,
"Set to True to build knapsack matrix.")
tf.app.flags.DEFINE_boolean("train",
False,
"Set to True for training.")
tf.app.flags.DEFINE_boolean("test_true_feeding",
False,
"Set to True for testing.")
tf.app.flags.DEFINE_boolean("decode",
False,
"Set to True for decoding.")
tf.app.flags.DEFINE_boolean("beam_search",
False,
"Set to True for beam search.")
tf.app.flags.DEFINE_integer("beam_size",
5,
"Number of optimal paths to search during decoding.")
tf.app.flags.DEFINE_boolean("search_db",
False,
"Set to True to do a database search.")
tf.app.flags.DEFINE_boolean("search_denovo",
False,
"Set to True to do a denovo search.")
tf.app.flags.DEFINE_boolean("search_hybrid",
False,
"Set to True to do a hybrid, db+denovo, search.")
tf.app.flags.DEFINE_boolean("test",
False,
"Set to True to test the prediction accuracy.")
tf.app.flags.DEFINE_boolean("header_seq",
True,
"Set to False if peptide sequence is not provided.")
tf.app.flags.DEFINE_boolean("decoy",
False,
"Set to True to search decoy database.")
FLAGS = tf.app.flags.FLAGS
# ==============================================================================
# GLOBAL VARIABLES for VOCABULARY
# ==============================================================================
# Special vocabulary symbols - we always put them at the start.
_PAD = "_PAD"
_GO = "_GO"
_EOS = "_EOS"
_START_VOCAB = [_PAD, _GO, _EOS]
PAD_ID = 0
GO_ID = 1
EOS_ID = 2
vocab_reverse = ['A',
'R',
'N',
'Nmod',
'D',
#~ 'C',
'Cmod',
'E',
'Q',
'Qmod',
'G',
'H',
'I',
'L',
'K',
'M',
'Mmod',
'F',
'P',
'S',
'T',
'W',
'Y',
'V',
]
vocab_reverse = _START_VOCAB + vocab_reverse
print("vocab_reverse ", vocab_reverse)
vocab = dict([(x, y) for (y, x) in enumerate(vocab_reverse)])
print("vocab ", vocab)
vocab_size = len(vocab_reverse)
print("vocab_size ", vocab_size)
# ==============================================================================
# GLOBAL VARIABLES for THEORETICAL MASS
# ==============================================================================
mass_H = 1.0078
mass_H2O = 18.0106
mass_NH3 = 17.0265
mass_N_terminus = 1.0078
mass_C_terminus = 17.0027
mass_CO = 27.9949
mass_AA = {'_PAD': 0.0,
'_GO': mass_N_terminus-mass_H,
'_EOS': mass_C_terminus+mass_H,
'A': 71.03711, # 0
'R': 156.10111, # 1
'N': 114.04293, # 2
'Nmod': 115.02695,
'D': 115.02694, # 3
#~ 'C': 103.00919, # 4
'Cmod': 160.03065, # C(+57.02)
#~ 'Cmod': 161.01919, # C(+58.01) # orbi
'E': 129.04259, # 5
'Q': 128.05858, # 6
'Qmod': 129.0426,
'G': 57.02146, # 7
'H': 137.05891, # 8
'I': 113.08406, # 9
'L': 113.08406, # 10
'K': 128.09496, # 11
'M': 131.04049, # 12
'Mmod': 147.0354,
'F': 147.06841, # 13
'P': 97.05276, # 14
'S': 87.03203, # 15
'T': 101.04768, # 16
'W': 186.07931, # 17
'Y': 163.06333, # 18
'V': 99.06841, # 19
}
mass_ID = [mass_AA[vocab_reverse[x]] for x in range(vocab_size)]
mass_ID_np = np.array(mass_ID, dtype=np.float32)
mass_AA_min = mass_AA["G"] # 57.02146
# ==============================================================================
# GLOBAL VARIABLES for PRECISION, RESOLUTION, temp-Limits of MASS & LEN
# ==============================================================================
# if change, need to re-compile cython_speedup
SPECTRUM_RESOLUTION = 10 # bins for 1.0 Da = precision 0.1 Da
#~ SPECTRUM_RESOLUTION = 20 # bins for 1.0 Da = precision 0.05 Da
#~ SPECTRUM_RESOLUTION = 40 # bins for 1.0 Da = precision 0.025 Da
#~ SPECTRUM_RESOLUTION = 50 # bins for 1.0 Da = precision 0.02 Da
#~ SPECTRUM_RESOLUTION = 80 # bins for 1.0 Da = precision 0.0125 Da
print("SPECTRUM_RESOLUTION ", SPECTRUM_RESOLUTION)
# if change, need to re-compile cython_speedup
WINDOW_SIZE = 10 # 10 bins
print("WINDOW_SIZE ", WINDOW_SIZE)
MZ_MAX = 3000.0
MZ_SIZE = int(MZ_MAX * SPECTRUM_RESOLUTION) # 30k
KNAPSACK_AA_RESOLUTION = 10000 # 0.0001 Da
mass_AA_min_round = int(round(mass_AA_min * KNAPSACK_AA_RESOLUTION)) # 57.02146
KNAPSACK_MASS_PRECISION_TOLERANCE = 100 # 0.01 Da
num_position = 0
PRECURSOR_MASS_PRECISION_TOLERANCE = 0.01
# ONLY for accuracy evaluation
#~ PRECURSOR_MASS_PRECISION_INPUT_FILTER = 0.01
PRECURSOR_MASS_PRECISION_INPUT_FILTER = 1000
AA_MATCH_PRECISION = 0.1
# skip (x > MZ_MAX,MAX_LEN)
MAX_LEN = 50 if FLAGS.decode else 30
print("MAX_LEN ", MAX_LEN)
# We use a number of buckets and pad to the closest one for efficiency.
_buckets = [12, 22, 32]
#~ _buckets = [12,22,32,42,52] # for decode
print("_buckets ", _buckets)
# ==============================================================================
# HYPER-PARAMETERS of the NEURAL NETWORKS
# ==============================================================================
num_ion = 8 # 2
print("num_ion ", num_ion)
l2_loss_weight = 0.0 # 0.0
print("l2_loss_weight ", l2_loss_weight)
#~ encoding_cnn_size = 4 * (RESOLUTION//10) # 4 # proportion to RESOLUTION
#~ encoding_cnn_filter = 4
#~ print("encoding_cnn_size ", encoding_cnn_size)
#~ print("encoding_cnn_filter ", encoding_cnn_filter)
embedding_size = 512
print("embedding_size ", embedding_size)
num_layers = 1
num_units = 512
print("num_layers ", num_layers)
print("num_units ", num_units)
keep_conv = 0.75
keep_dense = 0.5
print("keep_conv ", keep_conv)
print("keep_dense ", keep_dense)
batch_size = 128
print("batch_size ", batch_size)
epoch_stop = 20 # 50
print("epoch_stop ", epoch_stop)
train_stack_size = 4500
valid_stack_size = 15000 # 10%
test_stack_size = 4000
buffer_size = 4000
print("train_stack_size ", train_stack_size)
print("valid_stack_size ", valid_stack_size)
print("test_stack_size ", test_stack_size)
print("buffer_size ", buffer_size)
steps_per_checkpoint = 100 # 20 # 100 # 2 # 4 # 200
random_test_batches = 10
print("steps_per_checkpoint ", steps_per_checkpoint)
print("random_test_batches ", random_test_batches)
max_gradient_norm = 5.0
print("max_gradient_norm ", max_gradient_norm)
# ==============================================================================
# DATASETS
# ==============================================================================
# ==============================================================================
# YEAST-LOW-EXCLUDE_HEINEMANN_2015-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-EXCLUDE_COON_2013-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-TAKEDA_2015-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.takeda_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.takeda_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.takeda_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.takeda_2015/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-PEREDO_2015-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.peredo_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.peredo_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.peredo_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.peredo_2015/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-HEINEMANN_2015-PEAKS-DB-REPEAT
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.train.repeat"
#~ input_file_valid = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.valid.repeat"
#~ input_file_test = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.test.repeat"
#~ decode_test_file = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.test.repeat"
# YEAST-LOW-HEINEMANN_2015-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-MANN_2015-PEAKS-DB-REPEAT
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.mann_2015/peaks.db.mgf.train.repeat"
#~ input_file_valid = "data.training/yeast.low.mann_2015/peaks.db.mgf.valid.repeat"
#~ input_file_test = "data.training/yeast.low.mann_2015/peaks.db.mgf.test.repeat"
#~ decode_test_file = "data.training/yeast.low.mann_2015/peaks.db.mgf.test.repeat"
# YEAST-LOW-MANN_2015-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.mann_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.mann_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.mann_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.mann_2015/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-GRANT_2015-PEAKS-DB-REPEAT
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.grant_2015/peaks.db.mgf.train.repeat"
#~ input_file_valid = "data.training/yeast.low.grant_2015/peaks.db.mgf.valid.repeat"
#~ input_file_test = "data.training/yeast.low.grant_2015/peaks.db.mgf.test.repeat"
#~ decode_test_file = "data.training/yeast.low.grant_2015/peaks.db.mgf.test.repeat"
# YEAST-LOW-GRANT_2015-PEAKS-DB-DUP
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.grant_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.grant_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.grant_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.grant_2015/peaks.db.mgf.test.dup"
# ==============================================================================
# ==============================================================================
# YEAST-LOW-COON_2013-PEAKS-DB-REPEAT
#~ data_format = "mgf"
#~ input_file_train = "data.training/yeast.low.coon_2013/peaks.db.mgf.train.repeat"
#~ input_file_valid = "data.training/yeast.low.coon_2013/peaks.db.mgf.valid.repeat"
#~ input_file_test = "data.training/yeast.low.coon_2013/peaks.db.mgf.test.repeat"
#~ decode_test_file = "data.training/yeast.low.coon_2013/peaks.db.mgf.test.repeat"
# YEAST-LOW-COON_2013-PEAKS-DB-DUP
data_format = "mgf"
cleavage_rule = "trypsin"
num_missed_cleavage = 2
fixed_mod_list = ['C']
var_mod_list = ['N', 'Q', 'M']
precursor_mass_tolerance = 0.01 # Da
precursor_mass_ppm = 10.0/1000000 # ppm (20 better) # instead of absolute 0.01 Da
knapsack_file = "knapsack.npy"
# training/testing/decoding files
#~ input_file_train = "data.training/yeast.low.coon_2013/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.coon_2013/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.coon_2013/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.coon_2013/peaks.db.mgf.test.dup"
#~ input_file_train = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.exclude_coon_2013/peaks.db.mgf.test.dup"
#~ input_file_train = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.train.dup"
#~ input_file_valid = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.valid.dup"
#~ input_file_test = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.test.dup"
#~ decode_test_file = "data.training/yeast.low.exclude_heinemann_2015/peaks.db.mgf.test.dup"
input_file_train = "data.training/dia.xchen.nov27/fraction_1.mgf.split.train.dup"
input_file_valid = "data.training/dia.xchen.nov27/fraction_1.mgf.split.valid.dup"
input_file_test = "data.training/dia.xchen.nov27/fraction_1.mgf.split.test.dup"
decode_test_file = "data.training/dia.xchen.nov27/fraction_1.mgf.split.test.dup"
decode_output_file = decode_test_file + ".deepnovo_decode"
# denovo files
denovo_input_file = "data.training/dia.xchen.nov27/fraction_1.mgf.split.test.dup"
denovo_output_file = denovo_input_file + ".deepnovo_denovo"
# db files
db_fasta_file = "data/uniprot_sprot.human.fasta"
db_input_file = "data.training/dia.xchen.nov27/fraction_1.mgf.split.test.dup"
db_output_file = db_input_file + ".deepnovo_db"
if FLAGS.decoy:
db_output_file += ".decoy"
# hybrid files
hybrid_input_file = "data.training/yeast.low.heinemann_2015/peaks.db.mgf.test.dup"
hybrid_denovo_file = hybrid_input_file + ".deepnovo_hybrid_denovo"
hybrid_output_file = hybrid_input_file + ".deepnovo_hybrid"
if FLAGS.decoy:
hybrid_output_file += ".decoy"
# test accuracy
predicted_format = "deepnovo"
target_file = "data.training/dia.xchen.nov27/fraction_1.mgf.split.test.dup.target"
predicted_file = denovo_output_file
accuracy_file = predicted_file + ".accuracy"
# ==============================================================================