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Refactor the test to separate out the commands that differ among types.
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PiperOrigin-RevId: 344166251
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@pichuan
pichuan authored and Copybara-Service committed Nov 25, 2020
1 parent c6a7432 commit 9e03720
Showing 1 changed file with 94 additions and 70 deletions.
164 changes: 94 additions & 70 deletions scripts/run_deeptrio_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ class RunDeeptrioTest(parameterized.TestCase):

@parameterized.parameters('WGS', 'WES', 'PACBIO')
@flagsaver.flagsaver
def test_basic_command(self, model_type):
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'
Expand All @@ -72,41 +72,6 @@ def test_basic_command(self, model_type):
commands, post_process_commands = run_deeptrio.create_all_commands(
'/tmp/deeptrio_tmp_output')

extra_args_plus_gvcf = (
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" ')
if model_type == 'PACBIO':
# --gvcf is added in the middle because the flags are sorted
# alphabetically. PacBio flags here is now mixed with some others.
extra_args_plus_gvcf = (
'--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--vsc_min_fraction_indels "0.12" ')
if model_type == 'WES':
extra_args_plus_gvcf = (
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "100" '
'--pileup_image_height_parent "100" ')

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/make_examples.tfrecord@64.gz" '
'--sample_name "your_sample_child" '
'--sample_name_parent1 "your_sample_parent1" '
'--sample_name_parent2 "your_sample_parent2" '
'%s'
'--task {}' % extra_args_plus_gvcf)
self.assertEqual(
commands[1], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
Expand Down Expand Up @@ -163,7 +128,7 @@ def test_basic_command(self, model_type):

@parameterized.parameters('WGS', 'WES', 'PACBIO')
@flagsaver.flagsaver
def test_duo_command(self, model_type):
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'
Expand All @@ -179,39 +144,6 @@ def test_duo_command(self, model_type):
commands, post_process_commands = run_deeptrio.create_all_commands(
'/tmp/deeptrio_tmp_output')

extra_args_plus_gvcf = (
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" ')
if model_type == 'PACBIO':
# --gvcf is added in the middle because the flags are sorted
# alphabetically. PacBio flags here is now mixed with some others.
extra_args_plus_gvcf = (
'--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--vsc_min_fraction_indels "0.12" ')
if model_type == 'WES':
extra_args_plus_gvcf = (
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "100" '
'--pileup_image_height_parent "100" ')

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/make_examples.tfrecord@64.gz" '
'--sample_name "your_sample_child" '
'--sample_name_parent1 "your_sample_parent1" '
'%s'
'--task {}' % extra_args_plus_gvcf)
self.assertEqual(
commands[1], 'time /opt/deepvariant/bin/call_variants '
'--outfile '
Expand Down Expand Up @@ -250,6 +182,98 @@ def test_duo_command(self, model_type):
self.assertLen(commands, 3)
self.assertLen(post_process_commands, 2)

@parameterized.parameters(
('WGS', '--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '),
('WES', '--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "100" '
'--pileup_image_height_parent "100" '),
('PACBIO', '--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--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/make_examples.tfrecord@64.gz" '
'--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/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '),
('WES', '--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "100" '
'--pileup_image_height_parent "100" '),
('PACBIO', '--alt_aligned_pileup "diff_channels" '
'--gvcf "/tmp/deeptrio_tmp_output/gvcf.tfrecord@64.gz" '
'--pileup_image_height_child "60" '
'--pileup_image_height_parent "40" '
'--norealign_reads '
'--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/make_examples.tfrecord@64.gz" '
'--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/gvcf.tfrecord@64.gz" '
Expand Down

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