def write_fastq(forward_path, reverse_path, fastq_reads):
"""Write forward and reverse reads into a pair of FASTQ files.
Args:
forward_path: path to which to save forward reads.
reverse_path: path to which to save reverse reads.
fastq_reads: iterable of Read objects.
"""
with gfile.Open(forward_path, "w") as forward:
with gfile.Open(reverse_path, "w") as reverse:
for read in fastq_reads:
comp_sequence = dna.reverse_complement(read.sequence)
forward.write("@%s\n%s\n+\n%s\n" %
(read.title, read.sequence, read.quality))
reverse.write("@%s\n%s\n+\n%s\n" %
(read.title, comp_sequence, read.quality[::-1]))
def history_of_iter_dir(iter_dir, can_write_cache=False):
execution_data_iter_dir = os.path.join(
iter_dir.replace('results', 'execution_data'), 'eval')
if not gfile.IsDirectory(execution_data_iter_dir):
return None
test_acc = None
test_iter = None
for events_file in gfile.ListDirectory(execution_data_iter_dir):
if not events_file.startswith('events.out'):
continue
for e in tf.train.summary_iterator(
os.path.join(execution_data_iter_dir, events_file)):
for v in e.summary.value:
if v.tag == 'accuracy' or v.tag == 'top_1_accuracy':
if test_iter is None or e.step > test_iter:
test_iter = e.step
test_acc = v.simple_value
try:
with gfile.Open(os.path.join(iter_dir, 'density_ratio')) as f:
density_ratio = float(f.read())
except Exception as e:
density_ratio = 1.0
res = IterDatum(
iter=os.path.basename(iter_dir),
density_ratio=density_ratio,
test_acc=test_acc,
)
if can_write_cache and test_acc is not None:
write_iter(iter_dir, density_ratio, test_acc)
with gfile.Open(plot_cache, 'w') as f:
f.write('')
f.flush()
with gfile.Open(plot_cache, 'wb') as f:
pickle.dump(res, f)
return res
def update_best_model(path, cur_epoch):
"""Update the records of the model with the lowest validation error.
Args:
path: the path to the checkpoint of the current model.
cur_epoch: a integer of the current epoch
"""
cur_checkpoint = path
cur_checkpoint_meta = six.ensure_str(cur_checkpoint) + '.meta'
gfile.Copy(cur_train_report, best_train_report, overwrite=True)
gfile.Copy(cur_valid_report, best_valid_report, overwrite=True)
gfile.Copy(cur_checkpoint, best_checkpoint, overwrite=True)
gfile.Copy(cur_checkpoint_meta, best_checkpoint_meta, overwrite=True)
with gfile.Open(best_epoch_file, 'w') as f:
f.write(str(cur_epoch)+'\n')
def trial_datum_of_trial(experiment_dir, trial):
plot_cache = os.path.join(experiment_dir, trial, 'plot_cache.pkl')
if gfile.Exists(plot_cache):
with gfile.Open(plot_cache, 'rb') as f:
return pickle.loads(f.read())
iter_dirs = sorted(
iter_dirs_of_trial_dir(os.path.join(experiment_dir, trial)),
key=lambda x: int(iter_re.match(os.path.basename(x)).group('iter')))
pool = mp.Pool(5)
res = TrialDatum(
trial=trial,
iter_data=list(
filter(
lambda x: x is not None,
pool.map(
iter_datum_of_iter_dir,
map(lambda x: (x[1], x[0] < len(iter_dirs) - 1),
enumerate(iter_dirs))))),
)
pool.close()
return res
def iter_datum_of_iter_dir(iter_dir_and_can_write_cache,
verbose=True,
ignore_cache=False):
iter_dir, can_write_cache = iter_dir_and_can_write_cache
if not ignore_cache:
res = read_iter(iter_dir)
if res:
return IterDatum(
iter=os.path.basename(res[0]),
density_ratio=res[1],
test_acc=res[2],
)
plot_cache = os.path.join(iter_dir, 'plot_cache.pkl')
if gfile.Exists(plot_cache):
if verbose:
print('PLOT CACHE EXISTS: {}'.format(plot_cache))
with gfile.Open(plot_cache, 'rb') as f:
try:
it = pickle.loads(f.read())
write_iter(iter_dir, it.density_ratio, it.test_acc)
return it
except:
gfile.Remove(plot_cache)
execution_data_iter_dir = os.path.join(
iter_dir.replace('results', 'execution_data'), 'eval')
if not gfile.IsDirectory(execution_data_iter_dir):
return None
test_acc = None
test_iter = None
for events_file in gfile.ListDirectory(execution_data_iter_dir):
if not events_file.startswith('events.out'):
continue
for e in tf.train.summary_iterator(
os.path.join(execution_data_iter_dir, events_file)):
for v in e.summary.value:
if v.tag == 'accuracy' or v.tag == 'top_1_accuracy':
if test_iter is None or e.step > test_iter:
test_iter = e.step
test_acc = v.simple_value
if verbose:
print(test_acc)
try:
with gfile.Open(os.path.join(iter_dir, 'density_ratio')) as f:
density_ratio = float(f.read())
except Exception as e:
density_ratio = 1.0
res = IterDatum(
iter=os.path.basename(iter_dir),
density_ratio=density_ratio,
test_acc=test_acc,
)
if can_write_cache and test_acc is not None:
write_iter(iter_dir, density_ratio, test_acc)
# with gfile.Open(plot_cache, 'w') as f:
# f.write('')
# f.flush()
# with gfile.Open(plot_cache, 'wb') as f:
# pickle.dump(res, f)
return res
def run_training(hps,
experiment_proto,
train_dir,
train_input_paths,
val_input_paths,
tuner=None,
master='',
metrics_targets=None,
metrics_measures=None):
"""Main training function.
Trains the model given a directory to write to and a logfile to write to.
Args:
hps: tf.HParams with training parameters.
experiment_proto: selection_pb2.Experiment proto for training.
train_dir: str path to train directory.
train_input_paths: List[str] giving paths to input sstables for training.
val_input_paths: List[str] giving paths to input sstable(s) for validation.
tuner: optional hp_tuner.HPTuner.
master: optional string to pass to a tf.Supervisor.
metrics_targets: String list of network targets to report metrics for.
metrics_measures: Measurements about the performance of the network to
report, e.g. 'auc/top_1p'.
Returns:
None.
Raises:
Error: if the hyperparamter combination in hps is infeasible and there is
no tuner. (If the hyperparameter combination is infeasible and there is
a tuner then the params are reported back to the tuner as infeasible.)
"""
hps_infeasible, infeasible_reason = hps_is_infeasible(
hps, experiment_proto.sequence_length)
if hps_infeasible:
if tuner:
tuner.report_done(True, infeasible_reason)
logger.info('report_done(infeasible=%r)', hps_infeasible)
return
else:
raise Error('Hyperparams are infeasible: %s', infeasible_reason)
logger.info('Starting training.')
if tuner:
logger.info('Using tuner: loaded HParams from Vizier')
else:
logger.info('No tuner: using default HParams')
logger.info('experiment_proto: %s', experiment_proto)
logger.info('train_dir: %s', train_dir)
logger.info('train_input_paths[0]: %s', train_input_paths[0])
logger.info('val_input_paths[0]: %s', val_input_paths[0])
logger.info('%r', list(hps.values()))
generationinfo.to_file(os.path.join(train_dir, 'geninfo.pbtxt'))
with gfile.Open(os.path.join(train_dir, config.hparams_name), 'w') as f:
f.write(str(hps.to_proto()))
eval_size = hps.eval_size or None
def make_subdir(subdirectory_mame):
path = os.path.join(train_dir, subdirectory_mame)
gfile.MakeDirs(path)
return path
logger.info('Computing preprocessing statistics')
# TODO(shoyer): move this over into preprocessing instead?
experiment_proto = dataset_stats.compute_experiment_statistics(
experiment_proto,
train_input_paths,
os.path.join(
hps.input_dir,
six.ensure_str(
config.wetlab_experiment_train_pbtxt_path[hps.val_fold]) +
'.wstats'),
preprocess_mode=hps.preprocess_mode,
max_size=eval_size,
logdir=make_subdir('compute-statistics'),
save_stats=hps.save_stats)
logging.info('Saving experiment proto with statistics')
with gfile.Open(
os.path.join(train_dir, config.wetlab_experiment_train_name), 'w') as f:
f.write(str(experiment_proto))
logger.debug(str(hps.to_proto()))
logger.debug(hps.run_name)
tr_entries = len(sstable.MergedSSTable(train_input_paths))
logger.info('Training sstable size: %d', tr_entries)
val_entries = len(sstable.MergedSSTable(val_input_paths))
logger.info('Validation sstable size: %d', val_entries)
epoch_size = hps.epoch_size or int(tr_entries * (1 + hps.ratio_random_dna))
num_batches_per_epoch = int(float(epoch_size) / hps.mbsz)
eval_ff.config_pandas_display(FLAGS.interactive_display)
tr_evaluator = eval_ff.Evaluator(
hps,
experiment_proto,
train_input_paths,
make_subdir(config.experiment_training_dir),
verbose=FLAGS.verbose_eval)
val_evaluator = eval_ff.Evaluator(
hps,
experiment_proto,
val_input_paths,
make_subdir(config.experiment_validation_dir),
verbose=FLAGS.verbose_eval)
with tf.Graph().as_default():
# we need to use the registered key 'hparams'
tf.add_to_collection('hparams', hps)
# TODO(shoyer): collect these into a Model class:
dummy_inputs = data.dummy_inputs(
experiment_proto,
input_features=hps.input_features,
kmer_k_max=hps.kmer_k_max,
additional_output=six.ensure_str(hps.additional_output).split(','))
output_layer = output_layers.create_output_layer(experiment_proto, hps)
net = ff.FeedForward(dummy_inputs, output_layer.logit_axis, hps)
trainer = FeedForwardTrainer(hps, net, output_layer, experiment_proto,
train_input_paths)
summary_writer = tf.SummaryWriter(make_subdir('training'), flush_secs=30)
# TODO(shoyer): file a bug to figure out why write_version=2 (now the
# default) doesn't work.
saver = tf.Saver(write_version=1)
# We are always the chief since we do not do distributed training.
# Every replica with a different task id is completely independent and all
# must be their own chief.
sv = tf.Supervisor(
logdir=train_dir,
is_chief=True,
summary_writer=summary_writer,
save_summaries_secs=10,
save_model_secs=180,
saver=saver)
logger.info('Preparing session')
train_report_dir = os.path.join(train_dir, config.experiment_training_dir)
cur_train_report = os.path.join(train_report_dir,
config.experiment_report_name)
best_train_report = os.path.join(train_report_dir,
config.experiment_best_report_name)
valid_report_dir = os.path.join(train_dir, config.experiment_validation_dir)
cur_valid_report = os.path.join(valid_report_dir,
config.experiment_report_name)
best_valid_report = os.path.join(valid_report_dir,
config.experiment_best_report_name)
best_checkpoint = os.path.join(train_dir, 'model.ckpt-lowest_val_loss')
best_checkpoint_meta = best_checkpoint + '.meta'
best_epoch_file = os.path.join(train_dir, 'best_epoch.txt')
with sv.managed_session(master) as sess:
logger.info('Starting queue runners')
sv.start_queue_runners(sess)
def save_and_evaluate():
"""Save and evaluate the current model.
Returns:
path: the path string to the checkpoint.
summary_df: pandas.DataFrame storing the evaluation result on the
validation dataset with rows for each output name and columns for
each metric value
"""
logger.info('Saving model checkpoint')
path = sv.saver.save(
sess,
sv.save_path,
global_step=sv.global_step,
write_meta_graph=True)
tr_evaluator.run(path, eval_size)
summary_df, _ = val_evaluator.run_and_report(
tuner,
path,
eval_size,
metrics_targets=metrics_targets,
metrics_measures=metrics_measures)
return path, summary_df
def update_best_model(path, cur_epoch):
"""Update the records of the model with the lowest validation error.
Args:
path: the path to the checkpoint of the current model.
cur_epoch: a integer of the current epoch
"""
cur_checkpoint = path
cur_checkpoint_meta = six.ensure_str(cur_checkpoint) + '.meta'
gfile.Copy(cur_train_report, best_train_report, overwrite=True)
gfile.Copy(cur_valid_report, best_valid_report, overwrite=True)
gfile.Copy(cur_checkpoint, best_checkpoint, overwrite=True)
gfile.Copy(cur_checkpoint_meta, best_checkpoint_meta, overwrite=True)
with gfile.Open(best_epoch_file, 'w') as f:
f.write(str(cur_epoch)+'\n')
def compare_with_best_model(checkpoint_path, summary_df, cur_epoch):
logger.info('Comparing current val loss with the best model')
if not gfile.Exists(best_train_report):
logger.info('No best model saved. Adding current model...')
update_best_model(checkpoint_path, cur_epoch)
else:
with gfile.GFile(best_valid_report) as f:
with xarray.open_dataset(f) as best_ds:
best_ds.load()
cur_loss = summary_df['loss'].loc['mean']
best_loss = best_ds['loss'].mean('output')
logger.info('Current val loss:%f', cur_loss)
logger.info('The best val loss:%f', best_loss)
if cur_loss < best_loss:
logger.info(
'Current model has lower loss. Updating the best model.')
update_best_model(checkpoint_path, cur_epoch)
else:
logger.info('The best model has lower loss.')
logger.info('Running eval before starting training')
save_and_evaluate()
try:
for cur_epoch in trainer.train(sess, hps.epochs, num_batches_per_epoch):
checkpoint_path, val_summary_df = save_and_evaluate()
if (cur_epoch+1) % hps.epoch_interval_to_save_best == 0:
compare_with_best_model(checkpoint_path, val_summary_df, cur_epoch)
if tuner and tuner.should_trial_stop():
break
except eval_ff.TrainingDivergedException as error:
logger.error('Training diverged: %s', str(error))
infeasible = True
else:
infeasible = False
logger.info('Saving final checkpoint')
sv.saver.save(sess, sv.save_path, global_step=sv.global_step)
if tuner:
# should be at the very end of execution, to avoid possible race conditions
tuner.report_done(infeasible=infeasible)
logger.info('report_done(infeasible=%r)', infeasible)
logger.info('Done.')