def summarize(self, write_example=True):
with self.g.as_default():
is_training(False, session=self.sess)
iter_step = self.get_global_step()
fetches = [
self.loss, self.grad_summ, self.activation_summ, self.edit_distance
]
if write_example:
fetches.append(self.pred)
vals = self._rnn_roll(fetches)
edit_distance = np.mean(vals[3]).item()
summaries = [x[0] for x in vals[1:3]]
for summary in summaries:
self.train_writer.add_summary(summary, global_step=iter_step)
self.train_writer.add_summary(tf.Summary(value=[
tf.Summary.Value(tag="train/edit_distance",
simple_value=edit_distance)
]),
global_step=iter_step)
if write_example:
out_net = list(map(lambda x: decode_sparse(x)[0], vals[-1]))
target = self.decode_target(0, pad=self.block_size_y)
for a, b in zip(out_net, target):
print("OUTPUT:", a)
print("TARGET:", b)
print('----')
def train_minibatch(self, log_every=100, trace_every=10000):
"""
Trains minibatch and performs all required operations
Args:
log_every: how many time steps to log train_writer and stdout
trace_every: how many time steps to perform full trace execution (slow). It always performs it at global step 25.
"""
with self.g.as_default():
is_training(True, session=self.sess)
tt = perf_counter()
iter_step, _ = self.sess.run([self.global_step, self.load_train])
self.sess.run([self.inc_gs])
self.dequeue_time = 0.8 * self.dequeue_time + 0.2 * (perf_counter() -
tt)
if trace_every > 0:
if (iter_step > 0
and iter_step % trace_every == 0) or iter_step == 25:
self.trace_level = tf.RunOptions.FULL_TRACE
self.bbt = 0.8 * (self.bbt) + 0.2 * (perf_counter() - self.bbt_clock)
tt = perf_counter()
fetches = [self.train_op, self.loss, self.reg]
vals = self._rnn_roll(add_fetch=fetches, timeline_suffix="ctc_loss")
self.batch_time = 0.8 * self.batch_time + 0.2 * (perf_counter() - tt)
self.bbt_clock = perf_counter()
loss = np.sum(vals[1]).item()
reg_loss = np.sum(vals[2]).item()
self.train_writer.add_summary(tf.Summary(value=[
tf.Summary.Value(tag="train/loss", simple_value=loss),
tf.Summary.Value(tag="train/reg_loss", simple_value=reg_loss),
tf.Summary.Value(tag="input/batch_time",
simple_value=self.batch_time),
tf.Summary.Value(tag="input/dequeue_time",
simple_value=self.dequeue_time),
tf.Summary.Value(tag="input/between_batch_time",
simple_value=self.bbt),
]),
global_step=iter_step)
if iter_step % log_every == 0:
train_summ, y_len = self.sess.run([self.train_summ, self.Y_len])
self.train_writer.add_summary(train_summ, global_step=iter_step)
self.logger.info(
"%4d loss %6.3f reg_loss %6.3f bt %.3f, bbt %.3f, avg_y_len %.3f dequeue %.3fs",
iter_step, loss, reg_loss, self.batch_time, self.bbt,
np.mean(y_len), self.dequeue_time)
self.trace_level = tf.RunOptions.NO_TRACE
return loss
def run_validation(self, num_batches=5):
"""
Runs validation.
Args:
num_batches: Number of batches to run validation.
Returns:
A tuple (average loss, average edit distance) on validation set
"""
with self.g.as_default():
is_training(False, session=self.sess)
losses = []
reg_losses = []
edit_distances = []
for _ in range(num_batches):
_, iter_step, summ = self.sess.run(
[self.load_test, self.global_step, self.test_queue_size])
self.test_writer.add_summary(summ, global_step=iter_step)
loss, reg_loss, edit_distance = self._rnn_roll(
add_fetch=[self.loss, self.reg, self.edit_distance],
timeline_suffix="ctc_val_loss")
losses.append(np.sum(loss))
reg_losses.append(np.sum(reg_loss))
edit_distances.append(edit_distance)
avg_loss = np.mean(losses).item()
avg_reg_loss = np.mean(reg_losses).item()
avg_edit_distance = np.mean(edit_distances).item()
self.test_writer.add_summary(tf.Summary(value=[
tf.Summary.Value(tag="train/loss", simple_value=avg_loss),
tf.Summary.Value(tag="train/reg_loss", simple_value=avg_reg_loss),
tf.Summary.Value(tag="train/edit_distance",
simple_value=avg_edit_distance),
]),
global_step=iter_step)
self.logger.info(
"%4d validation loss %6.3f edit_distance %.3f in %.3fs" %
(iter_step, avg_loss, avg_edit_distance,
perf_counter() - self.bbt_clock))
self.bbt_clock = perf_counter()
return avg_loss, avg_edit_distance
def run_validation_full(self,
frac,
verbose=False,
fasta_out_dir=None,
ref=None):
"""
Runs full validation on test set with whole sequence_length
Args:
frac: fraction of test set to evaluate, or number of test cases if int
"""
test_root = os.path.join(input_readers.root_dir_default, 'test')
items = np.array(glob(os.path.join(test_root, '*.fa')))
np.random.shuffle(items)
if isinstance(frac, (int)):
items = items[:frac]
else:
items = items[:int(len(items) * frac)]
self.logger.info("Running validation on %d examples", len(items))
nedit = np.zeros(items.shape, dtype=np.float32)
acc = np.zeros(items.shape, dtype=np.float32)
n = len(acc)
total_time = 1e-6
total_bases_read = 0
cigar_stat = defaultdict(int)
with self.g.as_default():
is_training(False, session=self.sess)
pbar = tqdm(items)
for i, fast5_path in enumerate(pbar):
t = perf_counter()
nedit[i], acc[
i], read_len, cigar_read_stat = self.get_aligement(
fast5_path,
input_readers.find_ref(fast5_path),
verbose=verbose,
fasta_out_dir=fasta_out_dir,
ref=ref)
total_time += perf_counter() - t
total_bases_read += read_len
for k in ['=', 'X', 'I', 'D']:
cigar_stat[k] += cigar_read_stat[k]
mu_edit, mu_acc = np.mean(nedit[:i + 1]), np.mean(acc[:i + 1])
std_edit, std_acc = np.std(nedit[:i + 1]), np.std(acc[:i + 1])
se_edit, se_acc = std_edit / np.sqrt(i +
1), std_acc / np.sqrt(i +
1)
pbar.set_postfix(
stat=
"avg edit %.4f s %.4f CI <%.4f, %.4f> avg_acc %.4f s %.4f CI <%.4f, %.4f> %.2f bps"
% (mu_edit, std_edit, mu_edit - 2 * se_edit, mu_edit +
2 * se_edit, mu_acc, std_acc, mu_acc - 2 * se_acc,
mu_acc + 2 * se_acc, total_bases_read / total_time))
mu_edit, mu_acc = np.mean(nedit), np.mean(acc)
std_edit, std_acc = np.std(nedit), np.std(acc)
se_edit, se_acc = std_edit / np.sqrt(
len(nedit) + 1), std_acc / np.sqrt(len(nedit) + 1)
self.logger.info(
"step: %d [samples %d] avg edit %.4f s %.4f CI <%.4f, %.4f> avg_acc %.4f s %.4f CI <%.4f, %.4f> %.3f bps",
self.get_global_step(), n, mu_edit, std_edit,
mu_edit - 2 * se_edit, mu_edit + 2 * se_edit, mu_acc, std_acc,
mu_acc - 2 * se_acc, mu_acc + 2 * se_acc,
total_bases_read / total_time)
total_cigar_elements = np.sum(list(cigar_stat.values()))
for k in ['=', 'X', 'I', 'D']:
self.logger.info("Step %d; %s %.2f%%", self.get_global_step(), k,
100 * cigar_stat[k] / total_cigar_elements)
self.logger.info("Speed = %.3f bases per second",
total_bases_read / total_time)
return {
'edit': {
'mu': mu_edit.item(),
'std': std_edit.item(),
'se': se_edit.item()
},
'accuracy': {
'mu': mu_acc.item(),
'std': std_acc.item(),
'se': se_acc.item()
}
}
def basecall_singal(self,
fast5_path,
signal,
start_pad,
write_logits=None,
block_size=100000,
pad=512,
debug=False):
with self.g.as_default():
is_training(False, session=self.sess)
t = perf_counter()
original_len = signal.shape[1]
original_signal = signal
# print(signal.shape, original_len/block_size)
signal = np.pad(signal, ((0, 0), (pad, pad), (0, 0)), 'constant')
# print(signal.shape)
chunks = [
signal[:, i - pad:i + block_size + pad, :]
for i in range(pad, signal.shape[1] - 2 * pad, block_size)
]
# print(len(chunks), (signal.shape[1] - 2*pad)/block_size)
# print("and now goes the chunks")
np.testing.assert_equal(
np.sum([chunk.shape[1] - 2 * pad for chunk in chunks]),
original_len)
if debug:
np.testing.assert_equal(
np.concatenate([c[:, pad:-pad, :] for c in chunks], axis=1),
original_signal)
logits_all = []
for chunk in chunks:
logits = self.sess.run(self.logits,
feed_dict={
self.X_batch:
chunk,
self.X_batch_len:
np.array(chunk.shape[1]).reshape([
1,
]),
self.block_idx:
0,
self.batch_size_var:
1,
self.block_size_x_tensor:
chunk.shape[1]
})
cut = pad // self.shrink_factor
logits = logits[cut:-cut]
logits_all.append(logits)
logits = np.concatenate(logits_all)
assert logits.shape[0] in [
original_len // self.shrink_factor,
original_len // self.shrink_factor + 1,
]
basecalled = self.sess.run(
self.dense_pred,
feed_dict={
self.logits:
logits,
self.X_batch_len:
np.array([self.shrink_factor * logits.shape[0]]).reshape([
1,
])
}).ravel()
if write_logits:
with h5py.File(fast5_path, 'a') as h5:
h5_path = 'Analyses/MinCall/Logits'
logits = np.squeeze(logits, (1, ))
try:
h5.create_dataset(h5_path, data=logits)
except RuntimeError:
del h5[h5_path]
h5.create_dataset(h5_path, data=logits)
h5[h5_path].attrs['start_pad'] = start_pad
h5[h5_path].attrs['model_logdir'] = self.log_dir
h5[h5_path].attrs['run_id'] = self.run_id
h5[h5_path].attrs['in_data_classname'] = type(
self.in_data).__name__
h5[h5_path].attrs['shrink_factor'] = self.shrink_factor
fname = os.path.join(self.log_dir, 'model_hyperparams.json')
with open(fname, 'r') as f:
hyper = json.load(f)
for k, v in hyper.items():
h5[h5_path].attrs[k] = v
self.logger.debug("Basecalled %s in %.3f", fast5_path,
perf_counter() - t)
basecalled = "".join(util.decode(basecalled))
return basecalled
