This repository has been archived by the owner on Sep 15, 2022. It is now read-only.
forked from hassanfa/autoseq
-
Notifications
You must be signed in to change notification settings - Fork 0
/
test_clinseq_pipeline.py
414 lines (361 loc) · 21.2 KB
/
test_clinseq_pipeline.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
import unittest
import itertools
from mock import patch
from autoseq.pipeline.clinseq import *
from autoseq.util.clinseq_barcode import UniqueCapture
class TestClinseq(unittest.TestCase):
def setUp(self):
self.sample_data = {
"sdid": "P-00202345",
"N": [
"LB-P-00202345-N-03277090-TP20190201-CP20190204"
],
"T": [],
"CFDNA": [
"LB-P-00202345-CFDNA-03277089-TP20190201-CP20190204",
"LB-P-00202345-CFDNA-03277089-TP20190201-CM20190204"
]
}
self.ref_data = {
"bwaIndex": "bwa/test-genome-masked.fasta",
"chrsizes": "genome/test-genome-masked.chrsizes.txt",
"clinvar": "variants/clinvar_20160203.vcf.gz",
"cosmic": "variants/CosmicCodingMuts_v71.vcf.gz",
"dbSNP": "variants/dbsnp142-germline-only.vcf.gz",
"exac": "variants/ExAC.r0.3.1.sites.vep.vcf.gz",
"icgc": "variants/icgc_release_20_simple_somatic_mutation.aggregated.vcf.gz",
"reference_dict": "genome/test-genome-masked.dict",
"reference_genome": "genome/test-genome-masked.fasta",
"swegene_common": "variants/swegen_common.vcf.gz",
"ar_regions": "intervals/ar_regions.bed",
"ts_regions": "intervals/ts_regions.bed",
"fusion_regions": "intervals/fusion_regions.bed",
"1KG":"/nfs/ALASCCA/autoseq-genome/variants/1000G_phase1.indels.b37.vcf.gz",
"Mills_and_1KG_gold_standard": "/nfs/ALASCCA/autoseq-genome/variants/Mills_and_1000G_gold_standard.indels.b37.vcf.gz" ,
"brca_exchange": "/nfs/ALASCCA/autoseq-genome/variants/BrcaExchangeClinvar_15Jan2019_v26_hg19.vcf.gz",
"oncokb": "/nfs/ALASCCA/autoseq-genome/variants/OncoKB_6Mar19_v1.9.txt",
"targets": {
"test-regions": {
"cnvkit-ref": {
"THRUPLEX_PLASMASEQ": {
"CFDNA": "intervals/targets/progression.THRUPLEX_PLASMASEQ.CFDNA.cnn",
"N": "intervals/targets/progression.THRUPLEX_PLASMASEQ.N.cnn"
}
},
"cnvkit-fix": {
"THRUPLEX_PLASMASEQ": {
"CFDNA": "intervals/targets/progression.THRUPLEX_PLASMASEQ.CFDNA.cnvkit-fix.tsv"
}
},
"msisites": "intervals/targets/test-regions.msisites.tsv",
"targets-bed-slopped20": "intervals/targets/test-regions-GRCh37.slopped20.bed",
"targets-interval_list": "intervals/targets/test-regions-GRCh37.slopped20.interval_list",
"targets-interval_list-slopped20": "intervals/targets/test-regions-GRCh37.slopped20.interval_list",
"blacklist-bed": None,
"purecn_targets": "intervals/targets/purecn.bed",
},
"progression": {
"blacklist-bed": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.blacklist.bed",
"cnvkit-fix": {
"THRUPLEX_PLASMASEQ": {
"CFDNA": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.THRUPLEX_PLASMASEQ.CFDNA.cnvkit-fix.tsv"
}
},
"cnvkit-ref": {
"KAPA_HYPERPREP": {
"N": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.KAPA_HYPERPREP.N.cnn",
"T": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.KAPA_HYPERPREP.T.cnn"
},
"THRUPLEX_PLASMASEQ": {
"CFDNA": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.THRUPLEX_PLASMASEQ.CFDNA.cnn",
"N": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.THRUPLEX_PLASMASEQ.N.cnn"
}
},
"msings-baseline": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.msings.baseline",
"msings-bed": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.msings.bed",
"msings-msi_intervals": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.msings.msi_intervals",
"msisites": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.slopped20.msisites.tsv",
"purecn_targets": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.purecn.txt",
"targets-bed-slopped20": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.slopped20.bed.gz",
"targets-interval_list": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.interval_list",
"targets-interval_list-slopped20": "/nfs/ALASCCA/autoseq-genome/intervals/targets/progression.slopped20.interval_list"
},
"monitor": {
"blacklist-bed": "/nfs/ALASCCA/autoseq-genome/intervals/targets/monitor.blacklist.bed",
"msings-baseline": None,
"msings-bed": None,
"msings-msi_intervals": None,
"msisites": "/nfs/ALASCCA/autoseq-genome/intervals/targets/monitor.slopped20.msisites.tsv",
"purecn_targets": None,
"targets-bed-slopped20": "/nfs/ALASCCA/autoseq-genome/intervals/targets/monitor.slopped20.bed.gz",
"targets-interval_list": "/nfs/ALASCCA/autoseq-genome/intervals/targets/monitor.interval_list",
"targets-interval_list-slopped20": "/nfs/ALASCCA/autoseq-genome/intervals/targets/monitor.slopped20.interval_list"
}
},
"contest_vcfs": {
"test-regions": "test_contest.vcf"
},
"vep_dir": "dummy_vep_dir"
}
self.test_single_panel_results = SinglePanelResults()
self.test_cancer_vs_normal_results = CancerVsNormalPanelResults()
self.test_cancer_capture = UniqueCapture("LB", "P-00202345", "CFDNA", "03277089", "TP", "CP")
self.test_normal_capture = UniqueCapture("LB", "P-00202345", "N", "03277090", "TP", "CP")
self.test_monitor_capture = UniqueCapture("LB", "P-00202345", "CFDNA", "03277089", "TP", "CM")
self.test_clinseq_pipeline = ClinseqPipeline(self.sample_data, self.ref_data, {"cov-low-thresh-fraction": 0.8}, "/tmp/liqbio-test/",
"/media/clinseq/disk4/PROBIO/", 'FALSE')
def test_single_panel_results_output(self):
self.assertEquals(self.test_single_panel_results.merged_bamfile, None)
def test_cancer_against_normal_results(self):
self.assertEquals(self.test_cancer_vs_normal_results.somatic_vcf, None)
def test_pipeline_constructor(self):
self.assertEquals(self.test_clinseq_pipeline.job_params, {'cov-low-thresh-fraction': 0.8})
self.assertEquals(self.test_clinseq_pipeline.sampledata["sdid"], "P-00202345")
self.assertEquals(self.test_clinseq_pipeline.refdata["icgc"], "variants/icgc_release_20_simple_somatic_mutation.aggregated.vcf.gz")
def test_get_job_param_set(self):
self.assertEquals(self.test_clinseq_pipeline.get_job_param("cov-low-thresh-fraction"), 0.8)
def test_get_job_param_default(self):
self.assertEquals(self.test_clinseq_pipeline.get_job_param("cov-high-thresh-fold-cov"), 100)
def test_set_germline_vcf(self):
self.test_clinseq_pipeline.set_germline_vcf(self.test_normal_capture, ("test1.vcf", "test2.vcf"))
self.assertEquals(self.test_clinseq_pipeline.normal_capture_to_vcf[self.test_normal_capture],
("test1.vcf", "test2.vcf"))
def test_get_germline_vcf_exists(self):
self.test_clinseq_pipeline.set_germline_vcf(self.test_normal_capture, ("test1.vcf", "test2.vcf"))
self.assertEquals(self.test_clinseq_pipeline.get_germline_vcf(self.test_normal_capture), "test1.vcf")
def test_get_germline_vcf_none(self):
self.assertEquals(self.test_clinseq_pipeline.get_germline_vcf(self.test_normal_capture), None)
def test_get_vepped_germline_vcf(self):
self.test_clinseq_pipeline.set_germline_vcf(self.test_normal_capture, ("test1.vcf", "test2.vcf"))
self.assertEquals(self.test_clinseq_pipeline.get_vepped_germline_vcf(self.test_normal_capture), "test2.vcf")
def test_set_capture_bam(self):
self.test_clinseq_pipeline.set_capture_bam(self.test_cancer_capture, "test.bam", False)
self.assertEquals(self.test_clinseq_pipeline.capture_to_results[self.test_cancer_capture].merged_bamfile,
"test.bam")
self.assertEquals(self.test_clinseq_pipeline.capture_to_results[self.test_cancer_capture].umi_bamfile,
None)
def test_set_capture_cnr(self):
self.test_clinseq_pipeline.set_capture_cnr(self.test_cancer_capture, "test.cnr")
self.assertEquals(self.test_clinseq_pipeline.capture_to_results[self.test_cancer_capture].cnr,
"test.cnr")
def test_set_capture_cns(self):
self.test_clinseq_pipeline.set_capture_cns(self.test_cancer_capture, "test.cns")
self.assertEquals(self.test_clinseq_pipeline.capture_to_results[self.test_cancer_capture].cns,
"test.cns")
def test_get_capture_bam_exists(self):
self.test_clinseq_pipeline.set_capture_bam(self.test_cancer_capture, "test.bam", False)
self.assertEquals(self.test_clinseq_pipeline.get_capture_bam(self.test_cancer_capture, False),
"test.bam")
def test_get_capture_bam_none(self):
self.assertEquals(self.test_clinseq_pipeline.get_capture_bam(self.test_cancer_capture, False ),
None)
@patch('autoseq.pipeline.clinseq.data_available_for_clinseq_barcode')
def test_check_sampledata_all_available(self, mock_data_available_for_clinseq_barcode):
mock_data_available_for_clinseq_barcode.return_value = True
# Test that no changes occur to the sample data if the data is all available:
self.test_clinseq_pipeline.check_sampledata()
self.assertEquals(self.test_clinseq_pipeline.sampledata,
{
"sdid": "P-00202345",
"N": [
"LB-P-00202345-N-03277090-TP20190201-CP20190204"
],
"T": [],
"CFDNA": [
"LB-P-00202345-CFDNA-03277089-TP20190201-CP20190204",
"LB-P-00202345-CFDNA-03277089-TP20190201-CM20190204"
]
})
def test_vep_is_set(self):
self.assertTrue(self.test_clinseq_pipeline.vep_data_is_available())
def test_get_all_unique_capture(self):
self.assertEquals(self.test_clinseq_pipeline.get_mapped_captures_all(), [])
def test_get_unique_normal_captures(self):
self.test_clinseq_pipeline.capture_to_results = {self.test_cancer_capture: 1}
self.assertEquals(self.test_clinseq_pipeline.get_mapped_captures_normal(), [])
def test_get_unique_cancer_captures(self):
self.test_clinseq_pipeline.capture_to_results = {self.test_cancer_capture: 1}
self.assertEquals(self.test_clinseq_pipeline.get_mapped_captures_cancer(), [self.test_cancer_capture])
def test_get_prep_kit_name(self):
self.assertEquals(self.test_clinseq_pipeline.get_prep_kit_name("BN"), "BIOO_NEXTFLEX")
def test_get_capture_name(self):
self.assertEquals(self.test_clinseq_pipeline.get_capture_name("CM"), "monitor")
def test_get_all_clinseq_barcodes(self):
self.assertEquals(self.test_clinseq_pipeline.get_all_clinseq_barcodes(),
[ "LB-P-00202345-N-03277090-TP20190201-CP20190204",
"LB-P-00202345-CFDNA-03277089-TP20190201-CP20190204",
"LB-P-00202345-CFDNA-03277089-TP20190201-CM20190204"
])
def test_get_unique_capture_to_clinseq_barcodes(self):
l1 = list(itertools.chain.from_iterable(self.test_clinseq_pipeline.get_unique_capture_to_clinseq_barcodes().values()))
l2 = [ "LB-P-00202345-N-03277090-TP20190201-CP20190204",
"LB-P-00202345-CFDNA-03277089-TP20190201-CP20190204",
"LB-P-00202345-CFDNA-03277089-TP20190201-CM20190204"
]
self.assertEquals(set(l1),
set(l2))
def test_merge_and_rm_dup(self):
self.test_clinseq_pipeline.merge_and_rm_dup(self.test_cancer_capture, ["test.bam"])
self.assertNotEqual(
self.test_clinseq_pipeline.capture_to_results[self.test_cancer_capture].merged_bamfile,
None)
self.assertEquals(\
len(self.test_clinseq_pipeline.graph.nodes()), 3)
self.assertEquals(\
len(self.test_clinseq_pipeline.qc_files), 1)
@patch('autoseq.pipeline.clinseq.align_library')
@patch('autoseq.pipeline.clinseq.find_fastqs')
def test_configure_align_and_merge(self, mock_find_fastqs, mock_align_library):
mock_align_library.return_value = "dummy_merged.bam"
mock_find_fastqs.return_value = "dummy.fastq.gz"
self.test_clinseq_pipeline.configure_align_and_merge()
self.assertTrue(mock_align_library.called)
self.assertEquals(len(self.test_clinseq_pipeline.qc_files),
len(self.test_clinseq_pipeline.get_unique_capture_to_clinseq_barcodes()))
def test_call_germline_variants(self):
self.test_clinseq_pipeline.call_germline_variants(self.test_normal_capture, "test.bam")
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 5)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.call_germline_variants')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_mapped_captures_cancer')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_panel_analysis_cancer_vs_normal')
def test_configure_panel_analysis_with_normal(self, mock_configure_panel_analysis_cancer_vs_normal,
mock_get_mapped_captures_cancer,
mock_call_germline_variants):
mock_get_mapped_captures_cancer.return_value = [self.test_cancer_capture]
self.test_clinseq_pipeline.configure_panel_analysis_with_normal(self.test_normal_capture)
self.assertTrue(mock_call_germline_variants.called)
self.assertTrue(mock_configure_panel_analysis_cancer_vs_normal.called)
def test_configure_panel_analysis_with_normal_invalid(self):
self.assertRaises(ValueError,
lambda: self.test_clinseq_pipeline.configure_panel_analysis_with_normal(
self.test_cancer_capture))
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_capture_name')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_capture_bam')
def test_configure_single_capture_analysis(self, mock_get_capture_bam,
mock_get_capture_name):
mock_get_capture_name.return_value = "test-regions"
mock_get_capture_bam.return_value = "test.bam"
self.test_clinseq_pipeline.configure_single_capture_analysis(self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 3)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_capture_name')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_capture_bam')
def test_configure_single_capture_analysis_no_ref(self, mock_get_capture_bam,
mock_get_capture_name):
mock_get_capture_name.return_value = "monitor"
mock_get_capture_bam.return_value = "test.bam"
self.test_clinseq_pipeline.configure_single_capture_analysis(self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 0)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_single_capture_analysis')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_panel_analysis_with_normal')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_mapped_captures_no_wgs')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_mapped_captures_normal')
def test_configure_panel_analyses(self, mock_get_mapped_captures_normal,
mock_get_mapped_captures_no_wgs,
mock_configure_panel_analysis_with_normal,
mock_configure_single_capture_analysis):
mock_get_mapped_captures_normal.return_value = [self.test_normal_capture]
mock_get_mapped_captures_no_wgs.return_value = [self.test_cancer_capture]
self.test_clinseq_pipeline.configure_panel_analyses()
self.assertTrue(mock_configure_single_capture_analysis.called)
self.assertTrue(mock_configure_panel_analysis_with_normal.called)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_single_capture_analysis')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_panel_analysis_with_normal')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_mapped_captures_no_wgs')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_mapped_captures_normal')
def test_configure_panel_analyses_cancer_only(self, mock_get_mapped_captures_normal,
mock_get_mapped_captures_no_wgs,
mock_configure_panel_analysis_with_normal,
mock_configure_single_capture_analysis):
mock_get_mapped_captures_normal.return_value = []
mock_get_mapped_captures_no_wgs.return_value = [self.test_cancer_capture]
self.test_clinseq_pipeline.configure_panel_analyses()
self.assertTrue(mock_configure_single_capture_analysis.called)
self.assertFalse(mock_configure_panel_analysis_with_normal.called)
@patch('autoseq.pipeline.clinseq.call_somatic_variants')
def test_configure_somatic_calling(self, mock_call_somatic_variants):
mock_call_somatic_variants.return_value = {"vardict": "test.vcf", "mutect2":"test_mutect.vcf", "varscan_snv": "test_varscan_snv.vcf",\
"varscan_indel": "test_varscan_indel.vcf", "strelka_snvs": "test_strelka_snvs.vcf", \
"strelka_indels": "test_strelka_indels.vcf"}
self.test_clinseq_pipeline.configure_somatic_calling(self.test_normal_capture,
self.test_cancer_capture)
self.assertTrue(mock_call_somatic_variants.called)
stored_vcf = self.test_clinseq_pipeline.normal_cancer_pair_to_results[
(self.test_normal_capture, self.test_cancer_capture)].somatic_vcf
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 1)
def test_configure_vep(self):
self.test_clinseq_pipeline.configure_vep(self.test_normal_capture, self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()) , 2)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.vep_data_is_available')
def test_configure_vep_no_vep_data(self, mock_vep_data_is_available):
mock_vep_data_is_available.return_value = False
self.assertRaises(ValueError, lambda: self.test_clinseq_pipeline.configure_vep(
self.test_normal_capture, self.test_cancer_capture))
def test_configure_msi_sensor(self):
self.test_clinseq_pipeline.configure_msi_sensor(self.test_normal_capture,
self.test_cancer_capture)
self.assertTrue(
self.test_clinseq_pipeline.normal_cancer_pair_to_results[(
self.test_normal_capture, self.test_cancer_capture)].msi_output is not None)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 1)
def test_configure_msings_invalid_refdata(self):
self.assertRaises(InvalidRefDataException,
lambda: self.test_clinseq_pipeline.configure_msings(self.test_monitor_capture))
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_capture_bam')
def test_configure_msings(self, mock_get_capture_bam):
capture_name = 'test-regions'
self.ref_data['targets'][capture_name]['msings-baseline'] = "intervals/targets/test-regions.msings.baseline"
self.ref_data['targets'][capture_name]['msings-bed'] = "intervals/targets/test-regions.msings.bed"
self.ref_data['targets'][capture_name]['msings-msi_intervals'] = "intervals/targets/test-regions.msings.msi_intervals"
test_clinseq_pipeline_2 = ClinseqPipeline(self.sample_data, self.ref_data, {"cov-low-thresh-fraction": 0.8}, "/tmp/liqbio-test/",
"/media/clinseq/disk4/PROBIO/", 'FALSE')
mock_get_capture_bam.return_value = 'dummy.bam'
test_clinseq_pipeline_2.configure_msings(self.test_cancer_capture)
msings_result = test_clinseq_pipeline_2.capture_to_results[self.test_cancer_capture].msings_output
self.assertTrue(msings_result is not None)
self.assertEquals(len(test_clinseq_pipeline_2.graph.nodes()), 1)
def test_configure_contest_vcf_generation(self):
self.test_clinseq_pipeline.configure_contest_vcf_generation(self.test_normal_capture,
self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 1)
def test_configure_contest(self):
self.test_clinseq_pipeline.configure_contest(self.test_normal_capture,
self.test_cancer_capture,
"test.vcf")
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 1)
def test_configure_contam_qc_call(self):
self.test_clinseq_pipeline.configure_contam_qc_call("dummy.txt",
self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 1)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_contest')
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.configure_contam_qc_call')
def test_configure_contamination_estimate(self, mock_configure_contam_qc_call, mock_configure_contest):
mock_configure_contest.side_effect = ["cancer_vs_normal_output.txt", "normal_vs_cancer_output.txt"]
mock_configure_contam_qc_call.return_value = "dummy_call.json"
self.test_clinseq_pipeline.configure_contamination_estimate(self.test_normal_capture,
self.test_cancer_capture)
stored_normal_contest_output = self.test_clinseq_pipeline.normal_cancer_pair_to_results[
(self.test_normal_capture, self.test_cancer_capture)].normal_contest_output
self.assertEquals(stored_normal_contest_output, "normal_vs_cancer_output.txt")
stored_cancer_contest_output = self.test_clinseq_pipeline.normal_cancer_pair_to_results[
(self.test_normal_capture, self.test_cancer_capture)].cancer_contest_output
self.assertEquals(stored_cancer_contest_output, "cancer_vs_normal_output.txt")
stored_cancer_contam_call = self.test_clinseq_pipeline.normal_cancer_pair_to_results[
(self.test_normal_capture, self.test_cancer_capture)].cancer_contam_call
self.assertEquals(stored_cancer_contam_call, "dummy_call.json")
def test_configure_panel_analysis_cancer_vs_normal(self):
self.test_clinseq_pipeline.refdata['vep_dir'] = "dummy_vep_dir"
self.test_clinseq_pipeline.configure_panel_analysis_cancer_vs_normal(self.test_normal_capture,
self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 12)
@patch('autoseq.pipeline.clinseq.ClinseqPipeline.get_mapped_captures_no_wgs')
def test_configure_all_panel_qcs(self, mock_get_mapped_captures_no_wgs):
mock_get_mapped_captures_no_wgs.return_value = [self.test_normal_capture, self.test_cancer_capture]
self.test_clinseq_pipeline.configure_all_panel_qcs()
self.assertEquals(len(self.test_clinseq_pipeline.qc_files), 12)
def test_configure_multi_qc(self):
self.test_clinseq_pipeline.configure_multi_qc()
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 1)
def test_configure_panel_qc(self):
qc_files = self.test_clinseq_pipeline.configure_panel_qc(self.test_cancer_capture)
self.assertEquals(len(self.test_clinseq_pipeline.graph.nodes()), 6)
self.assertEquals(len(qc_files), 6)