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4 files changed

+43
-82
lines changed

4 files changed

+43
-82
lines changed

‎v03_pipeline/lib/misc/family_loading_failures.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -177,9 +177,9 @@ def get_families_failed_sex_check(
177177

178178

179179
def get_families_failed_imputed_sex_ploidy(
180+
families: set[Family],
180181
mt: hl.MatrixTable,
181182
sex_check_ht: hl.Table,
182-
families: set[Family],
183183
) -> dict[Family, str]:
184184
mt = mt.select_cols(
185185
discrepant=(

‎v03_pipeline/lib/misc/family_loading_failures_test.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -317,9 +317,9 @@ def test_get_families_failed_imputed_sex_ploidy(self) -> None:
317317
.key_cols_by('s')
318318
)
319319
failed_families = get_families_failed_imputed_sex_ploidy(
320+
families,
320321
mt,
321322
sex_check_ht,
322-
families,
323323
)
324324
self.assertDictEqual(failed_families, {})
325325

@@ -362,9 +362,9 @@ def test_get_families_failed_imputed_sex_ploidy(self) -> None:
362362
.key_cols_by('s')
363363
)
364364
failed_families = get_families_failed_imputed_sex_ploidy(
365+
families,
365366
mt,
366367
sex_check_ht,
367-
families,
368368
)
369369
self.assertDictEqual(failed_families, {})
370370

@@ -409,9 +409,9 @@ def test_get_families_failed_imputed_sex_ploidy(self) -> None:
409409
.key_cols_by('s')
410410
)
411411
failed_families = get_families_failed_imputed_sex_ploidy(
412+
families,
412413
mt,
413414
sex_check_ht,
414-
families,
415415
)
416416
self.assertCountEqual(
417417
failed_families.values(),
@@ -428,9 +428,9 @@ def test_get_families_failed_imputed_sex_ploidy(self) -> None:
428428
),
429429
}
430430
failed_families = get_families_failed_imputed_sex_ploidy(
431+
families,
431432
mt,
432433
sex_check_ht,
433-
families,
434434
)
435435
self.assertCountEqual(
436436
failed_families.values(),

‎v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -129,20 +129,20 @@ def create_table(self) -> hl.MatrixTable:
129129
relatedness_check_ht,
130130
remap_lookup,
131131
)
132-
families_failed_sex_check = get_families_failed_sex_check(
132+
families_failed_imputed_sex_ploidy = get_families_failed_imputed_sex_ploidy(
133133
families
134134
- families_failed_missing_samples.keys()
135135
- families_failed_relatedness_check.keys(),
136-
sex_check_ht,
137-
remap_lookup,
138-
)
139-
families_failed_imputed_sex_ploidy = get_families_failed_imputed_sex_ploidy(
140136
callset_mt,
141137
sex_check_ht,
138+
)
139+
families_failed_sex_check = get_families_failed_sex_check(
142140
families
143141
- families_failed_missing_samples.keys()
144142
- families_failed_relatedness_check.keys()
145-
- families_failed_sex_check.keys(),
143+
- families_failed_imputed_sex_ploidy.keys(),
144+
sex_check_ht,
145+
remap_lookup,
146146
)
147147

148148
loadable_families = (

‎v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py

Lines changed: 32 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -237,123 +237,84 @@ def test_write_remapped_and_subsetted_callset_task_all_families_failed(
237237
self.assertDictEqual(
238238
json.load(f),
239239
{
240-
'project_guids': [
241-
'R0114_project4',
242-
],
243-
'error_messages': [
244-
'All families failed validation checks',
245-
],
240+
'project_guids': ['R0114_project4'],
241+
'error_messages': ['All families failed validation checks'],
246242
'failed_family_samples': {
247243
'missing_samples': {
248244
'efg_1': {
249-
'samples': [
250-
'NA99999_1',
251-
],
252-
'reasons': [
253-
"Missing samples: {'NA99999_1'}",
254-
],
245+
'samples': ['NA99999_1'],
246+
'reasons': ["Missing samples: {'NA99999_1'}"],
255247
},
256248
},
257249
'relatedness_check': {},
258250
'sex_check': {
259-
'789_1': {
260-
'samples': [
261-
'NA20875_1',
262-
],
251+
'890_1': {
252+
'samples': ['NA20876_1'],
263253
'reasons': [
264-
'Sample NA20875_1 has pedigree sex M but imputed sex F',
254+
'Sample NA20876_1 has pedigree sex M but imputed sex F',
265255
],
266256
},
267257
'456_1': {
268-
'samples': [
269-
'NA20870_1',
270-
],
258+
'samples': ['NA20870_1'],
271259
'reasons': [
272260
'Sample NA20870_1 has pedigree sex M but imputed sex F',
273261
],
274262
},
275263
'123_1': {
276-
'samples': [
277-
'NA19675_1',
278-
],
264+
'samples': ['NA19675_1'],
279265
'reasons': [
280266
'Sample NA19675_1 has pedigree sex M but imputed sex F',
281267
],
282268
},
283-
'cde_1': {
284-
'samples': [
285-
'NA20881_1',
286-
],
269+
'678_1': {
270+
'samples': ['NA20874_1'],
287271
'reasons': [
288-
'Sample NA20881_1 has pedigree sex F but imputed sex M',
272+
'Sample NA20874_1 has pedigree sex M but imputed sex F',
289273
],
290274
},
291-
'901_1': {
292-
'samples': [
293-
'NA20877_1',
294-
],
275+
'789_1': {
276+
'samples': ['NA20875_1'],
295277
'reasons': [
296-
'Sample NA20877_1 has pedigree sex M but imputed sex F',
278+
'Sample NA20875_1 has pedigree sex M but imputed sex F',
297279
],
298280
},
299-
'678_1': {
300-
'samples': [
301-
'NA20874_1',
302-
],
281+
'901_1': {
282+
'samples': ['NA20877_1'],
303283
'reasons': [
304-
'Sample NA20874_1 has pedigree sex M but imputed sex F',
284+
'Sample NA20877_1 has pedigree sex M but imputed sex F',
305285
],
306286
},
307287
'345_1': {
308-
'samples': [
309-
'NA19679_1',
310-
],
288+
'samples': ['NA19679_1'],
311289
'reasons': [
312290
'Sample NA19679_1 has pedigree sex M but imputed sex F',
313291
],
314292
},
315-
'890_1': {
316-
'samples': [
317-
'NA20876_1',
318-
],
319-
'reasons': [
320-
'Sample NA20876_1 has pedigree sex M but imputed sex F',
321-
],
322-
},
323293
'def_1': {
324-
'samples': [
325-
'NA20885_1',
326-
],
294+
'samples': ['NA20885_1'],
327295
'reasons': [
328296
'Sample NA20885_1 has pedigree sex M but imputed sex F',
329297
],
330298
},
299+
},
300+
'ploidy_check': {
301+
'cde_1': {
302+
'samples': ['NA20881_1'],
303+
'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20881_1']",
304+
},
331305
'234_1': {
332-
'samples': [
333-
'NA19678_1',
334-
],
335-
'reasons': [
336-
'Sample NA19678_1 has pedigree sex F but imputed sex M',
337-
],
306+
'samples': ['NA19678_1'],
307+
'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA19678_1']",
338308
},
339309
'bcd_1': {
340-
'samples': [
341-
'NA20878_1',
342-
],
343-
'reasons': [
344-
'Sample NA20878_1 has pedigree sex F but imputed sex M',
345-
],
310+
'samples': ['NA20878_1'],
311+
'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20878_1']",
346312
},
347313
'567_1': {
348-
'samples': [
349-
'NA20872_1',
350-
],
351-
'reasons': [
352-
'Sample NA20872_1 has pedigree sex F but imputed sex M',
353-
],
314+
'samples': ['NA20872_1'],
315+
'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20872_1']",
354316
},
355317
},
356-
'ploidy_check': {},
357318
},
358319
},
359320
)

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