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run_deeptrio_test.py
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# Copyright 2019 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from this
# software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Tests for deepvariant .run_deeptrio."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import sys
if 'google' in sys.modules and 'google.protobuf' not in sys.modules:
del sys.modules['google']
from absl import flags
from absl.testing import absltest
from absl.testing import flagsaver
from absl.testing import parameterized
import six
from deepvariant.opensource_only.scripts import run_deeptrio
FLAGS = flags.FLAGS
# pylint: disable=line-too-long
class RunDeeptrioTest(parameterized.TestCase):
@parameterized.parameters('WGS', 'WES', 'PACBIO')
@flagsaver.flagsaver
def test_call_variants_postprocess_variants_commands(self, model_type):
FLAGS.model_type = model_type
FLAGS.ref = 'your_ref'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.output_gvcf_merged = 'your_gvcf_merged'
FLAGS.num_shards = 64
commands, post_process_commands = run_deeptrio.create_all_commands(
'/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[1], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--checkpoint "/opt/models/deeptrio/{}/child/model.ckpt"'.format(
model_type.lower()))
self.assertEqual(
commands[2], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
'"/tmp/deeptrio_tmp_output/call_variants_output_parent1.tfrecord.gz" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--checkpoint "/opt/models/deeptrio/{}/parent/model.ckpt"'.format(
model_type.lower()))
self.assertEqual(
commands[3], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
'"/tmp/deeptrio_tmp_output/call_variants_output_parent2.tfrecord.gz" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--checkpoint "/opt/models/deeptrio/{}/parent/model.ckpt"'.format(
model_type.lower()))
self.assertEqual(
post_process_commands[0],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--outfile "your_vcf_child" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_child"')
self.assertEqual(
post_process_commands[1],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_parent1.tfrecord.gz" '
'--outfile "your_vcf_parent1" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_parent1"')
self.assertEqual(
post_process_commands[2],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_parent2.tfrecord.gz" '
'--outfile "your_vcf_parent2" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_parent2"')
self.assertLen(commands, 4)
self.assertLen(post_process_commands, 3)
@parameterized.parameters('WGS', 'WES', 'PACBIO')
@flagsaver.flagsaver
def test_duo_call_variants_postprocess_variants_commands(self, model_type):
FLAGS.model_type = model_type
FLAGS.ref = 'your_ref'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_merged = 'your_gvcf_merged'
FLAGS.num_shards = 64
commands, post_process_commands = run_deeptrio.create_all_commands(
'/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[1], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--checkpoint "/opt/models/deeptrio/{}/child/model.ckpt"'.format(
model_type.lower()))
self.assertEqual(
commands[2], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
'"/tmp/deeptrio_tmp_output/call_variants_output_parent1.tfrecord.gz" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--checkpoint "/opt/models/deeptrio/{}/parent/model.ckpt"'.format(
model_type.lower()))
self.assertEqual(
post_process_commands[0],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--outfile "your_vcf_child" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_child"')
self.assertEqual(
post_process_commands[1],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_parent1.tfrecord.gz" '
'--outfile "your_vcf_parent1" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_parent1"')
# pylint: disable=g-generic-assert
self.assertLen(commands, 3)
self.assertLen(post_process_commands, 2)
@parameterized.parameters(
('WGS', '--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '),
('WES', '--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--pileup_image_height_child "100" '
'--pileup_image_height_parent "100" '),
('PACBIO', '--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--noparse_sam_aux_fields '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--nosort_by_haplotypes '
'--vsc_min_fraction_indels "0.12" '))
@flagsaver.flagsaver
def test_make_examples_commands_with_types(self, model_type,
extra_args_plus_gvcf):
FLAGS.model_type = model_type
FLAGS.ref = 'your_ref'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.output_gvcf_merged = 'your_gvcf_merged'
FLAGS.num_shards = 64
commands, _ = run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[0], 'time seq 0 63 '
'| parallel -q --halt 2 --line-buffer '
'/opt/deepvariant/bin/deeptrio/make_examples '
'--mode calling '
'--ref "your_ref" '
'--reads_parent1 "your_bam_parent1" '
'--reads_parent2 "your_bam_parent2" '
'--reads "your_bam_child" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--sample_name "your_sample_child" '
'--sample_name_parent1 "your_sample_parent1" '
'--sample_name_parent2 "your_sample_parent2" '
'%s'
'--task {}' % extra_args_plus_gvcf)
@parameterized.parameters(
('WGS', '--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '),
('WES', '--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--pileup_image_height_child "100" '
'--pileup_image_height_parent "100" '),
('PACBIO', '--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--noparse_sam_aux_fields '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--nosort_by_haplotypes '
'--vsc_min_fraction_indels "0.12" '))
@flagsaver.flagsaver
def test_duo_make_examples_commands_with_types(self, model_type,
extra_args_plus_gvcf):
FLAGS.model_type = model_type
FLAGS.ref = 'your_ref'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_merged = 'your_gvcf_merged'
FLAGS.num_shards = 64
commands, _ = run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[0], 'time seq 0 63 '
'| parallel -q --halt 2 --line-buffer '
'/opt/deepvariant/bin/deeptrio/make_examples '
'--mode calling '
'--ref "your_ref" '
'--reads_parent1 "your_bam_parent1" '
'--reads "your_bam_child" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--sample_name "your_sample_child" '
'--sample_name_parent1 "your_sample_parent1" '
'%s'
'--task {}' % extra_args_plus_gvcf)
@parameterized.parameters(
(None, '--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--noparse_sam_aux_fields '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--nosort_by_haplotypes '
'--vsc_min_fraction_indels "0.12" '),
('alt_aligned_pileup="rows",vsc_min_fraction_indels=0.03',
'--alt_aligned_pileup "rows" '
'--gvcf "/tmp/deeptrio_tmp_output/[email protected]" '
'--noparse_sam_aux_fields '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--nosort_by_haplotypes '
'--vsc_min_fraction_indels "0.03" '),
)
@flagsaver.flagsaver
def test_pacbio_args_overwrite(self, make_examples_extra_args, expected_args):
"""Confirms that adding extra flags can overwrite the default from mode."""
FLAGS.model_type = 'PACBIO'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.regions = None
FLAGS.make_examples_extra_args = make_examples_extra_args
commands, _ = run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[0], 'time seq 0 63 | parallel -q --halt 2 --line-buffer '
'/opt/deepvariant/bin/deeptrio/make_examples --mode calling '
'--ref "your_ref" --reads_parent1 "your_bam_parent1" '
'--reads_parent2 "your_bam_parent2" '
'--reads "your_bam_child" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--sample_name "your_sample_child" '
'--sample_name_parent1 "your_sample_parent1" '
'--sample_name_parent2 "your_sample_parent2" '
'%s'
'--task {}' % expected_args)
@parameterized.parameters(
(None, ('sort_by_haplotypes=true,parse_sam_aux_fields=true'), True),
(True, ('sort_by_haplotypes=true,parse_sam_aux_fields=true'), False),
)
@flagsaver.flagsaver
def test_use_hp_information_conflicts(self, use_hp_information,
make_examples_extra_args, has_conflict):
"""Confirms that PacBio use_hp_information can conflict with HP args."""
FLAGS.model_type = 'PACBIO'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.regions = None
FLAGS.use_hp_information = use_hp_information
FLAGS.make_examples_extra_args = make_examples_extra_args
if has_conflict:
with six.assertRaisesRegex(self, ValueError,
'conflicts with other flags'):
run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
else:
# Otherwise, the command should run without rasing errors.
run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
@parameterized.parameters('WGS', 'WES')
@flagsaver.flagsaver
def test_use_hp_information_only_with_pacbio(self, model_type):
"""Confirms use_hp_information only works for."""
FLAGS.model_type = model_type
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.regions = None
FLAGS.use_hp_information = True
with six.assertRaisesRegex(
self, ValueError, '--use_hp_information can only be used with '
'--model_type="PACBIO"'):
run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
@parameterized.parameters(
('chr1:20-30', '--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--regions "chr1:20-30"'),
('chr1:20-30 chr2:100-200', '--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--regions "chr1:20-30 chr2:100-200"'),
("'chr1:20-30 chr2:100-200'", '--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
"--regions 'chr1:20-30 chr2:100-200'"),
)
def test_make_examples_regions(self, regions, expected_args):
FLAGS.model_type = 'WGS'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.num_shards = 64
FLAGS.regions = regions
commands, _ = run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[0], 'time seq 0 63 | parallel -q --halt 2 --line-buffer '
'/opt/deepvariant/bin/deeptrio/make_examples --mode calling '
'--ref "your_ref" --reads_parent1 "your_bam_parent1" '
'--reads_parent2 "your_bam_parent2" '
'--reads "your_bam_child" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--sample_name "your_sample_child" '
'--sample_name_parent1 "your_sample_parent1" '
'--sample_name_parent2 "your_sample_parent2" '
'%s '
'--task {}' % expected_args)
@flagsaver.flagsaver
def test_make_examples_extra_args_invalid(self):
FLAGS.model_type = 'WGS'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.make_examples_extra_args = 'keep_secondary_alignments'
with six.assertRaisesRegex(self, ValueError, 'not enough values to unpack'):
_, _ = run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
@parameterized.parameters(
('batch_size=1024', '--batch_size "1024"'),
('batch_size=4096,'
'config_string="gpu_options: {per_process_gpu_memory_fraction: 0.5}"',
'--batch_size "4096" '
'--config_string "gpu_options: {per_process_gpu_memory_fraction: 0.5}"'),
)
@flagsaver.flagsaver
def test_call_variants_extra_args(self, call_variants_extra_args,
expected_args):
FLAGS.model_type = 'WGS'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.call_variants_extra_args = call_variants_extra_args
commands, _ = run_deeptrio.create_all_commands('/tmp/deeptrio_tmp_output')
self.assertEqual(
commands[1], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--examples "/tmp/deeptrio_tmp_output/[email protected]" '
'--checkpoint "/opt/models/deeptrio/wgs/child/model.ckpt" '
'%s' % expected_args)
@parameterized.parameters(
('qual_filter=3.0', '--qual_filter "3.0"'),)
@flagsaver.flagsaver
def test_postprocess_variants_extra_args(self,
postprocess_variants_extra_args,
expected_args):
FLAGS.model_type = 'WGS'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.postprocess_variants_extra_args = postprocess_variants_extra_args
_, commands_post_process = run_deeptrio.create_all_commands(
'/tmp/deeptrio_tmp_output')
self.assertEqual(
commands_post_process[0],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--outfile "your_vcf_child" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_child" '
'%s' % expected_args)
@parameterized.parameters(
(True, 'vcf_stats_report=true', '--vcf_stats_report'),
(True, 'vcf_stats_report=false', '--novcf_stats_report'),
# These two cases demonstrate we might end up havig duplicated and
# potentially conflicting flags when using *extra_args.
(False, 'vcf_stats_report=true', '--novcf_stats_report --vcf_stats_report'
),
(False, 'vcf_stats_report=false',
'--novcf_stats_report --novcf_stats_report'),
)
@flagsaver.flagsaver
def test_postprocess_variants_duplicate_extra_args(
self, vcf_stats_report, postprocess_variants_extra_args,
expected_vcf_stats_report):
FLAGS.model_type = 'WGS'
FLAGS.ref = 'your_ref'
FLAGS.sample_name_child = 'your_sample_child'
FLAGS.sample_name_parent1 = 'your_sample_parent1'
FLAGS.sample_name_parent2 = 'your_sample_parent2'
FLAGS.reads_child = 'your_bam_child'
FLAGS.reads_parent1 = 'your_bam_parent1'
FLAGS.reads_parent2 = 'your_bam_parent2'
FLAGS.output_vcf_child = 'your_vcf_child'
FLAGS.output_vcf_parent1 = 'your_vcf_parent1'
FLAGS.output_vcf_parent2 = 'your_vcf_parent2'
FLAGS.output_gvcf_child = 'your_gvcf_child'
FLAGS.output_gvcf_parent1 = 'your_gvcf_parent1'
FLAGS.output_gvcf_parent2 = 'your_gvcf_parent2'
FLAGS.num_shards = 64
FLAGS.vcf_stats_report = vcf_stats_report
FLAGS.postprocess_variants_extra_args = postprocess_variants_extra_args
_, commands_post_process = run_deeptrio.create_all_commands(
'/tmp/deeptrio_tmp_output')
self.assertEqual(
commands_post_process[0],
'time /opt/deepvariant/bin/postprocess_variants '
'--ref "your_ref" '
'--infile '
'"/tmp/deeptrio_tmp_output/call_variants_output_child.tfrecord.gz" '
'--outfile "your_vcf_child" '
'--nonvariant_site_tfrecord_path '
'"/tmp/deeptrio_tmp_output/[email protected]" '
'--gvcf_outfile "your_gvcf_child" '
'%s' % expected_vcf_stats_report)
if __name__ == '__main__':
absltest.main()