def test_draw_deepvariant_pileup_with_example_input(self, composite_type):
_, example = _mock_example_with_image((100, 10, 7))
# Testing that it runs without error
vis.draw_deepvariant_pileup(example=example,
composite_type=composite_type)
def test_draw_deepvariant_pileup_with_channels_input(self, composite_type):
channels = [_image_array((100, 221)) for _ in range(6)]
# Testing that it runs without error
vis.draw_deepvariant_pileup(channels=channels,
composite_type=composite_type)
def run():
"""Create pileup images from examples, filtered in various ways."""
with errors.clean_commandline_error_exit():
if FLAGS.column_labels:
column_labels = FLAGS.column_labels.split(',')
else:
column_labels = None
filter_to_vcf = FLAGS.vcf is not None
if filter_to_vcf:
ids_from_vcf = parse_vcf(FLAGS.vcf)
logging.info(
'Found %d loci in VCF. '
'Only examples matching these loci will be output.',
len(ids_from_vcf))
filter_to_region = FLAGS.regions is not None
if filter_to_region:
passes_region_filter = create_region_filter(
region_flag_string=FLAGS.regions, verbose=FLAGS.verbose)
# Use nucleus.io.tfrecord to read all shards.
dataset = tfrecord.read_tfrecords(FLAGS.examples)
# Check flag here to avoid expensive string matching on every iteration.
make_rgb = FLAGS.image_type in ['both', 'RGB']
make_channels = FLAGS.image_type in ['both', 'channels']
num_scanned = 0
num_output = 0
for example in dataset:
num_scanned += 1
# Only when scanning many examples, print a dot for each one to
# indicate that the script is making progress and not stalled.
if num_scanned % UPDATE_EVERY_N_EXAMPLES == 0:
if num_scanned == UPDATE_EVERY_N_EXAMPLES:
print('Reporting progress below. Writing one dot every time {} '
'examples have been scanned:'.format(UPDATE_EVERY_N_EXAMPLES))
# Print another dot on the same line, using print since logging does
# not support printing without a newline.
print('.', end='', flush=True)
# Extract variant from example.
variant = vis.variant_from_example(example)
locus_id = vis.locus_id_from_variant(variant)
indices = vis.alt_allele_indices_from_example(example)
# Optionally filter to variants in the VCF.
if filter_to_vcf:
# Check if the locus is in the VCF.
if locus_id not in ids_from_vcf:
# Skip this example since it doesn't match the VCF.
continue
if filter_to_region and not passes_region_filter(variant):
continue
# Use locus ID in the filename, replacing long alleles with INS/DEL sizes.
locus_with_alt_id = get_short_id(variant, indices)
# Examples of long alleles replaced with their sizes:
# 20:62456134_INS103bp.png
# 20:62481177_DEL51bp.png
# Examples of short alleles where the full string is included:
# 1:55424995_TC->T.png
# 1:55424996_CT->CTT.png
# 1:55424996_CT->C.png
# 1:55424996_CT->TTT.png
# 1:55424996_CT->C|CTT.png
if FLAGS.verbose:
logging.info('\nOutputting image for: %s', locus_with_alt_id)
full_id = get_full_id(variant, indices)
if locus_with_alt_id != full_id:
logging.info(
'ID above was shortened due to long ref/alt strings. '
'Original: %s', full_id)
# If the example has a truth label, optionally include it.
optional_truth_label = ''
if FLAGS.truth_labels:
truth_label = get_label(example)
if truth_label is not None:
optional_truth_label = '_label{}'.format(truth_label)
# Extract and format example into channels.
channels = vis.channels_from_example(example)
if column_labels is not None and len(column_labels) != len(channels):
raise ValueError(
'--column_labels must have {} names separated by commas, since '
'there are {} channels in the examples. '
'However, {} column labels were found: {}'.format(
len(channels), len(channels), len(column_labels),
','.join(['"{}"'.format(x) for x in column_labels])))
output_prefix = '{}_'.format(
FLAGS.output) if FLAGS.output is not None else ''
# Create image with a grey-scale row of channels and save to file.
if make_channels:
channels_output = '{}channels_{}{}.png'.format(output_prefix,
locus_with_alt_id,
optional_truth_label)
vis.draw_deepvariant_pileup(
channels=channels,
path=channels_output,
scale=1,
show=False,
annotated=FLAGS.annotation,
labels=column_labels)
# Create RGB image and save to file.
if make_rgb:
rgb_output = '{}rgb_{}{}.png'.format(output_prefix, locus_with_alt_id,
optional_truth_label)
vis.draw_deepvariant_pileup(
channels=channels,
composite_type='RGB',
path=rgb_output,
scale=1,
show=False,
annotated=FLAGS.annotation,
labels=column_labels)
# Check if --num_records quota has been hit yet.
num_output += 1
if FLAGS.num_records != -1 and num_output >= FLAGS.num_records:
break
logging.info('Scanned %d examples and output %d images.', num_scanned,
num_output)
if num_scanned == 0 and FLAGS.examples.startswith('gs://'):
if sharded_file_utils.is_sharded_file_spec(FLAGS.examples):
paths = sharded_file_utils.generate_sharded_filenames(FLAGS.examples)
special_gcs_message = ('WARNING: --examples sharded files are either '
'all empty or do not exist. Please check that '
'the paths are correct:\n')
for p in paths[0:3]:
special_gcs_message += 'gsutil ls {}\n'.format(p)
logging.warning(special_gcs_message)
else:
logging.warning(
'WARNING: --examples file is either empty or does not exist. '
'Please check that the path is correct: \n'
'gsutil ls %s', FLAGS.examples)