hps = hps.parse(FLAGS.hpconfig)
_copy_flags_to_hparams(hps)
run_training_with_default_inputs(hps, train_dir, tuner, FLAGS.master,
FLAGS.validation_fold_template)
def main(unused_argv):
if (FLAGS.input_dir is None) == (FLAGS.dataset is None):
raise ValueError('exactly one of --input_dir or --dataset required')
invalid_input_features = set(FLAGS.input_features) - _VALID_INPUT_FEATURES
if invalid_input_features:
raise ValueError('invalid input_features: %r' % invalid_input_features)
# use r=3 subdirectory to fix empty events files (see b/28535367)
root_dir = os.path.join(FLAGS.save_base, FLAGS.run_name, 'r=3')
gfile.MakeDirs(root_dir)
if FLAGS.autotune:
_train_with_autotune(root_dir)
else:
_train_without_autotune(root_dir)
if __name__ == '__main__':
flags.mark_flag_as_required('save_base')
flags.mark_flag_as_required('run_name')
flags.mark_flag_as_required('num_fc_layers')
app.run()
None,
count_table,
0,
expected_sequence_length=FLAGS.sequence_length,
base_qual_threshold=FLAGS.base_qual_threshold,
bad_base_threshold=FLAGS.bad_base_threshold,
avg_qual_threshold=FLAGS.avg_qual_threshold,
num_reads=FLAGS.num_reads)
# write out the statistics
stats.fastq_read1_name = FLAGS.fastq1
stats.fastq_read2_name = FLAGS.fastq2
with gfile.FastGFile(FLAGS.output_name + ".statistics.pbtxt", "w") as out:
out.write(str(stats))
# write to an SSTable of measurement protos
with sstable.SortingBuilder(FLAGS.output_name) as builder:
for sequence, counts in count_table.iteritems():
key = sequence
proto = measurement_pb2.Measurement()
proto.counts[FLAGS.measurement_id] = counts[0]
builder.Add(key, proto.SerializeToString())
if __name__ == "__main__":
# mark required flags here so unit test doesn't need the sys.argv.extend hack
flags.mark_flag_as_required("fastq1")
flags.mark_flag_as_required("measurement_id")
app.run()