Format Python files.

PiperOrigin-RevId: 518020013

deeptrio/dt_constants.py

@@ -50,7 +50,9 @@
 
 # The dimensions of a pileup image tensor as height x width x rank.
 PILEUP_DEFAULT_DIMS = [
-    PILEUP_DEFAULT_HEIGHT, PILEUP_DEFAULT_WIDTH, PILEUP_NUM_CHANNELS
+    PILEUP_DEFAULT_HEIGHT,
+    PILEUP_DEFAULT_WIDTH,
+    PILEUP_NUM_CHANNELS,
 ]
 
 # Number of classes represented in the data set. The three classes are

deeptrio/make_examples.py

@@ -54,77 +54,129 @@
 
 # Flags related to samples in DeepTrio:
 SAMPLE_NAME_TO_TRAIN_ = flags.DEFINE_string(
-    'sample_name_to_train', None,
-    'Optional - if not set, default to the value in '
-    '--sample_name, i.e. the child. The default is set to be backward '
-    'compatible. If set, it has to match one of --sample_name, '
-    '--sample_name_parent1, or --sample_name_parent2. '
-    'Only used for training. When run in calling mode, this is unused because '
-    'examples are generated for all 3 samples together.')
+    'sample_name_to_train',
+    None,
+    (
+        'Optional - if not set, default to the value in --sample_name, i.e. the'
+        ' child. The default is set to be backward compatible. If set, it has'
+        ' to match one of --sample_name, --sample_name_parent1, or'
+        ' --sample_name_parent2. Only used for training. When run in calling'
+        ' mode, this is unused because examples are generated for all 3 samples'
+        ' together.'
+    ),
+)
 READS_ = flags.DEFINE_string(
-    'reads', None,
-    'Required. Aligned, sorted, indexed BAM file containing reads from the '
-    'child of the trio. '
-    'Should be aligned to a reference genome compatible with --ref. '
-    'Can provide multiple BAMs (comma-separated).')
+    'reads',
+    None,
+    (
+        'Required. Aligned, sorted, indexed BAM file containing reads from the '
+        'child of the trio. '
+        'Should be aligned to a reference genome compatible with --ref. '
+        'Can provide multiple BAMs (comma-separated).'
+    ),
+)
 READS_PARENT1_ = flags.DEFINE_string(
-    'reads_parent1', None,
-    'Required. Aligned, sorted, indexed BAM file containing reads from parent '
-    '1 of the trio. Should be aligned to a reference genome compatible with '
-    '--ref. Can provide multiple BAMs (comma-separated).')
+    'reads_parent1',
+    None,
+    (
+        'Required. Aligned, sorted, indexed BAM file containing reads from'
+        ' parent 1 of the trio. Should be aligned to a reference genome'
+        ' compatible with --ref. Can provide multiple BAMs (comma-separated).'
+    ),
+)
 READS_PARENT2_ = flags.DEFINE_string(
-    'reads_parent2', None,
-    'Aligned, sorted, indexed BAM file containing reads from parent 2 of the '
-    'trio. Should be aligned to a reference genome compatible with --ref. '
-    'Can provide multiple BAMs (comma-separated).')
+    'reads_parent2',
+    None,
+    (
+        'Aligned, sorted, indexed BAM file containing reads from parent 2 of'
+        ' the trio. Should be aligned to a reference genome compatible with'
+        ' --ref. Can provide multiple BAMs (comma-separated).'
+    ),
+)
 DOWNSAMPLE_FRACTION_CHILD_ = flags.DEFINE_float(
-    'downsample_fraction_child', NO_DOWNSAMPLING,
-    'If not ' + str(NO_DOWNSAMPLING) + ' must be a value between 0.0 and 1.0. '
+    'downsample_fraction_child',
+    NO_DOWNSAMPLING,
+    'If not '
+    + str(NO_DOWNSAMPLING)
+    + ' must be a value between 0.0 and 1.0. '
     'Reads will be kept (randomly) with a probability of downsample_fraction '
     'from the input child BAM. This argument makes it easy to create examples '
-    'as though the input BAM had less coverage.')
+    'as though the input BAM had less coverage.',
+)
 DOWNSAMPLE_FRACTION_PARENTS_ = flags.DEFINE_float(
-    'downsample_fraction_parents', NO_DOWNSAMPLING,
-    'If not ' + str(NO_DOWNSAMPLING) + ' must be a value between 0.0 and 1.0. '
+    'downsample_fraction_parents',
+    NO_DOWNSAMPLING,
+    'If not '
+    + str(NO_DOWNSAMPLING)
+    + ' must be a value between 0.0 and 1.0. '
     'Reads will be kept (randomly) with a probability of downsample_fraction '
     'from the input parent BAMs. This argument makes it easy to create examples'
-    ' as though the input BAMs had less coverage.')
+    ' as though the input BAMs had less coverage.',
+)
 SAMPLE_NAME_ = flags.DEFINE_string(
-    'sample_name', '',
-    'Child sample name to use for our sample_name in the output '
-    'Variant/DeepVariantCall protos. If not specified, will be inferred from '
-    'the header information from --reads.')
+    'sample_name',
+    '',
+    (
+        'Child sample name to use for our sample_name in the output'
+        ' Variant/DeepVariantCall protos. If not specified, will be inferred'
+        ' from the header information from --reads.'
+    ),
+)
 SAMPLE_NAME_PARENT1_ = flags.DEFINE_string(
-    'sample_name_parent1', '',
-    'Parent1 Sample name to use for our sample_name in the output '
-    'Variant/DeepVariantCall protos. If not specified, will be inferred from '
-    'the header information from --reads_parent1.')
+    'sample_name_parent1',
+    '',
+    (
+        'Parent1 Sample name to use for our sample_name in the output'
+        ' Variant/DeepVariantCall protos. If not specified, will be inferred'
+        ' from the header information from --reads_parent1.'
+    ),
+)
 SAMPLE_NAME_PARENT2_ = flags.DEFINE_string(
-    'sample_name_parent2', '',
-    'Parent2 Sample name to use for our sample_name in the output '
-    'Variant/DeepVariantCall protos. If not specified, will be inferred from '
-    'the header information from --reads_parent2.')
+    'sample_name_parent2',
+    '',
+    (
+        'Parent2 Sample name to use for our sample_name in the output'
+        ' Variant/DeepVariantCall protos. If not specified, will be inferred'
+        ' from the header information from --reads_parent2.'
+    ),
+)
 PILEUP_IMAGE_HEIGHT_PARENT_ = flags.DEFINE_integer(
-    'pileup_image_height_parent', 0,
-    'Height for the parent pileup image. If 0, uses the default height')
+    'pileup_image_height_parent',
+    0,
+    'Height for the parent pileup image. If 0, uses the default height',
+)
 PILEUP_IMAGE_HEIGHT_CHILD_ = flags.DEFINE_integer(
-    'pileup_image_height_child', 0,
-    'Height for the child pileup image. If 0, uses the default height')
+    'pileup_image_height_child',
+    0,
+    'Height for the child pileup image. If 0, uses the default height',
+)
 PROPOSED_VARIANTS_CHILD_ = flags.DEFINE_string(
-    'proposed_variants_child', None,
-    '(Only used when --variant_caller=vcf_candidate_importer.) '
-    'Tabix-indexed VCF file containing the proposed positions and alts for '
-    '`vcf_candidate_importer` for the child. The GTs will be ignored.')
+    'proposed_variants_child',
+    None,
+    (
+        '(Only used when --variant_caller=vcf_candidate_importer.) '
+        'Tabix-indexed VCF file containing the proposed positions and alts for '
+        '`vcf_candidate_importer` for the child. The GTs will be ignored.'
+    ),
+)
 PROPOSED_VARIANTS_PARENT1_ = flags.DEFINE_string(
-    'proposed_variants_parent1', None,
-    '(Only used when --variant_caller=vcf_candidate_importer.) '
-    'Tabix-indexed VCF file containing the proposed positions and alts for '
-    '`vcf_candidate_importer` for the parent 1. The GTs will be ignored.')
+    'proposed_variants_parent1',
+    None,
+    (
+        '(Only used when --variant_caller=vcf_candidate_importer.) '
+        'Tabix-indexed VCF file containing the proposed positions and alts for '
+        '`vcf_candidate_importer` for the parent 1. The GTs will be ignored.'
+    ),
+)
 PROPOSED_VARIANTS_PARENT2_ = flags.DEFINE_string(
-    'proposed_variants_parent2', None,
-    '(Only used when --variant_caller=vcf_candidate_importer.) '
-    'Tabix-indexed VCF file containing the proposed positions and alts for '
-    '`vcf_candidate_importer` for the parent 2. The GTs will be ignored.')
+    'proposed_variants_parent2',
+    None,
+    (
+        '(Only used when --variant_caller=vcf_candidate_importer.) '
+        'Tabix-indexed VCF file containing the proposed positions and alts for '
+        '`vcf_candidate_importer` for the parent 2. The GTs will be ignored.'
+    ),
+)
 # We are using this flag for determining intervals for both child and parent
 # models. In the future, we can consider extending into 3 samples.
 CANDIDATE_POSITIONS_ = flags.DEFINE_string(
@@ -145,38 +197,47 @@ def trio_samples_from_flags(add_flags=True, flags_obj=None):
   """Collects sample-related options into a list of samples."""
   # Sample-specific options.
   child_sample_name = make_examples_core.assign_sample_name(
-      sample_name_flag=SAMPLE_NAME_.value, reads_filenames=READS_.value)
+      sample_name_flag=SAMPLE_NAME_.value, reads_filenames=READS_.value
+  )
 
   parent1_sample_name = make_examples_core.assign_sample_name(
       sample_name_flag=SAMPLE_NAME_PARENT1_.value,
-      reads_filenames=READS_PARENT1_.value)
+      reads_filenames=READS_PARENT1_.value,
+  )
 
   parent2_sample_name = make_examples_core.assign_sample_name(
       sample_name_flag=SAMPLE_NAME_PARENT2_.value,
-      reads_filenames=READS_PARENT2_.value)
+      reads_filenames=READS_PARENT2_.value,
+  )
 
   parent1_options = deepvariant_pb2.SampleOptions(
       role='parent1',
       name=parent1_sample_name,
       variant_caller_options=make_examples_core.make_vc_options(
-          sample_name=parent1_sample_name, flags_obj=flags_obj),
+          sample_name=parent1_sample_name, flags_obj=flags_obj
+      ),
       order=[0, 1, 2],
-      pileup_height=dt_constants.PILEUP_DEFAULT_HEIGHT_PARENT)
+      pileup_height=dt_constants.PILEUP_DEFAULT_HEIGHT_PARENT,
+  )
   child_options = deepvariant_pb2.SampleOptions(
       role='child',
       name=child_sample_name,
       variant_caller_options=make_examples_core.make_vc_options(
-          sample_name=child_sample_name, flags_obj=flags_obj),
+          sample_name=child_sample_name, flags_obj=flags_obj
+      ),
       order=[0, 1, 2],
-      pileup_height=dt_constants.PILEUP_DEFAULT_HEIGHT_CHILD)
+      pileup_height=dt_constants.PILEUP_DEFAULT_HEIGHT_CHILD,
+  )
   parent2_options = deepvariant_pb2.SampleOptions(
       role='parent2',
       name=parent2_sample_name,
       variant_caller_options=make_examples_core.make_vc_options(
-          sample_name=parent2_sample_name, flags_obj=flags_obj),
+          sample_name=parent2_sample_name, flags_obj=flags_obj
+      ),
       # Swap the two parents when calling on parent2.
       order=[2, 1, 0],
-      pileup_height=dt_constants.PILEUP_DEFAULT_HEIGHT_PARENT)
+      pileup_height=dt_constants.PILEUP_DEFAULT_HEIGHT_PARENT,
+  )
 
   # If --sample_name_to_train is not set, train on the child.
   # This is for backward compatibility.
@@ -196,9 +257,13 @@ def trio_samples_from_flags(add_flags=True, flags_obj=None):
     if PROPOSED_VARIANTS_CHILD_.value:
       child_options.proposed_variants_filename = PROPOSED_VARIANTS_CHILD_.value
     if PROPOSED_VARIANTS_PARENT1_.value:
-      parent1_options.proposed_variants_filename = PROPOSED_VARIANTS_PARENT1_.value
+      parent1_options.proposed_variants_filename = (
+          PROPOSED_VARIANTS_PARENT1_.value
+      )
     if PROPOSED_VARIANTS_PARENT2_.value:
-      parent2_options.proposed_variants_filename = PROPOSED_VARIANTS_PARENT2_.value
+      parent2_options.proposed_variants_filename = (
+          PROPOSED_VARIANTS_PARENT2_.value
+      )
 
     if DOWNSAMPLE_FRACTION_CHILD_.value != NO_DOWNSAMPLING:
       child_options.downsample_fraction = DOWNSAMPLE_FRACTION_CHILD_.value
@@ -209,7 +274,9 @@ def trio_samples_from_flags(add_flags=True, flags_obj=None):
     if PILEUP_IMAGE_HEIGHT_CHILD_.value:
       child_options.pileup_height = PILEUP_IMAGE_HEIGHT_CHILD_.value
     if PILEUP_IMAGE_HEIGHT_PARENT_.value:
-      parent1_options.pileup_height = parent2_options.pileup_height = PILEUP_IMAGE_HEIGHT_PARENT_.value
+      parent1_options.pileup_height = (
+          parent2_options.pileup_height
+      ) = PILEUP_IMAGE_HEIGHT_PARENT_.value
 
     if SAMPLE_NAME_TO_TRAIN_.value:
       if SAMPLE_NAME_TO_TRAIN_.value == SAMPLE_NAME_.value:
@@ -218,9 +285,13 @@ def trio_samples_from_flags(add_flags=True, flags_obj=None):
         sample_role_to_train = parent1_options.role
       else:
         errors.log_and_raise(
-            '--sample_name_to_train must match either --sample_name or '
-            '--sample_name_parent1, or it can be unset to default to '
-            '--sample_name.', errors.CommandLineError)
+            (
+                '--sample_name_to_train must match either --sample_name or '
+                '--sample_name_parent1, or it can be unset to default to '
+                '--sample_name.'
+            ),
+            errors.CommandLineError,
+        )
 
   # Ordering here determines the default order of samples, and when a sample
   # above has a custom .order, then this is the list those indices refer to.
@@ -248,22 +319,36 @@ def default_options(add_flags=True, flags_obj=None):
     flags_obj = FLAGS
 
   samples_in_order, sample_role_to_train = trio_samples_from_flags(
-      add_flags=add_flags, flags_obj=flags_obj)
+      add_flags=add_flags, flags_obj=flags_obj
+  )
 
   options = make_examples_options.shared_flags_to_options(
       add_flags=add_flags,
       flags_obj=flags_obj,
       samples_in_order=samples_in_order,
       sample_role_to_train=sample_role_to_train,
-      main_sample_index=MAIN_SAMPLE_INDEX)
+      main_sample_index=MAIN_SAMPLE_INDEX,
+  )
 
   if add_flags:
-    options.bam_fname = os.path.basename(
-        READS_.value) + '|' + (os.path.basename(READS_PARENT1_.value)
-                               if READS_PARENT1_.value else 'None') + '|' + (
-                                   os.path.basename(READS_PARENT2_.value)
-                                   if READS_PARENT2_.value else 'None')
-    options.pic_options.sequencing_type = deepvariant_pb2.PileupImageOptions.TRIO
+    options.bam_fname = (
+        os.path.basename(READS_.value)
+        + '|'
+        + (
+            os.path.basename(READS_PARENT1_.value)
+            if READS_PARENT1_.value
+            else 'None'
+        )
+        + '|'
+        + (
+            os.path.basename(READS_PARENT2_.value)
+            if READS_PARENT2_.value
+            else 'None'
+        )
+    )
+    options.pic_options.sequencing_type = (
+        deepvariant_pb2.PileupImageOptions.TRIO
+    )
     if not options.pic_options.height:
       options.pic_options.height = dt_constants.PILEUP_DEFAULT_HEIGHT
     if not options.pic_options.width:
@@ -277,24 +362,32 @@ def check_options_are_valid(options):
 
   # Check for general flags (shared for DeepVariant and DeepTrio).
   make_examples_options.check_options_are_valid(
-      options, main_sample_index=MAIN_SAMPLE_INDEX)
+      options, main_sample_index=MAIN_SAMPLE_INDEX
+  )
 
   child = options.sample_options[MAIN_SAMPLE_INDEX]
 
   # Sanity check the sample_names (specific to trio).
-  if (child.variant_caller_options.sample_name == FLAGS.sample_name_parent1 or
-      child.variant_caller_options.sample_name == FLAGS.sample_name_parent2):
+  if (
+      child.variant_caller_options.sample_name == FLAGS.sample_name_parent1
+      or child.variant_caller_options.sample_name == FLAGS.sample_name_parent2
+  ):
     errors.log_and_raise(
-        'The sample_name of the child is the same as one of '
-        'the parents.', errors.CommandLineError)
+        'The sample_name of the child is the same as one of the parents.',
+        errors.CommandLineError,
+    )
 
   if options.pic_options.alt_aligned_pileup == 'rows':
-    errors.log_and_raise('--alt_aligned_pileup="rows" cannot be used with '
-                         'DeepTrio because the pileup images would become '
-                         'too tall for InceptionV3.')
+    errors.log_and_raise(
+        '--alt_aligned_pileup="rows" cannot be used with '
+        'DeepTrio because the pileup images would become '
+        'too tall for InceptionV3.'
+    )
 
-  if (options.mode == deepvariant_pb2.MakeExamplesOptions.CANDIDATE_SWEEP and
-      child.candidate_positions is None):
+  if (
+      options.mode == deepvariant_pb2.MakeExamplesOptions.CANDIDATE_SWEEP
+      and child.candidate_positions is None
+  ):
     errors.log_and_raise(
         '--candidate_positions is required when --positions_sweep_mode is set.'
     )
@@ -306,7 +399,9 @@ def main(argv=()):
       errors.log_and_raise(
           'Command line parsing failure: make_examples does not accept '
           'positional arguments but some are present on the command line: '
-          '"{}".'.format(str(argv)), errors.CommandLineError)
+          '"{}".'.format(str(argv)),
+          errors.CommandLineError,
+      )
     del argv  # Unused.
 
     proto_utils.uses_fast_cpp_protos_or_die()