Merge pull request #556 from populationgenomics/resolve-main-conflicts

Resolve main conflicts

scripts/create_test_subset.py

@@ -21,7 +21,6 @@
 import random
 import subprocess
 import traceback
-import typing
 from collections import Counter
 from typing import Optional
 
@@ -97,20 +96,28 @@
     This is in addition to the number of families specified in
     --families and the number of samples specified in -n""",
 )
+@click.option(
+    '--noninteractive',
+    'noninteractive',
+    is_flag=True,
+    default=False,
+    help='Skip interactive confirmation',
+)
 def main(
     project: str,
     samples_n: Optional[int],
     families_n: Optional[int],
     skip_ped: Optional[bool] = True,
     additional_families: Optional[tuple[str]] = None,
     additional_samples: Optional[tuple[str]] = None,
+    noninteractive: Optional[bool] = False,
 ):
     """
     Script creates a test subset for a given project.
     A new project with a prefix -test is created, and for any files in sample/meta,
     sequence/meta, or analysis/output a copy in the -test namespace is created.
     """
-    samples_n, families_n = _validate_opts(samples_n, families_n)
+    samples_n, families_n = _validate_opts(samples_n, families_n, noninteractive)
     _additional_families: list[str] = list(additional_families)
     _additional_samples: list[str] = list(additional_samples)
 
@@ -121,7 +128,7 @@ def main(
         }
     )
     logger.info(f'Found {len(all_samples)} samples')
-    if samples_n and samples_n >= len(all_samples):
+    if (samples_n and samples_n >= len(all_samples)) and not noninteractive:
         resp = str(
             input(
                 f'Requesting {samples_n} samples which is >= '
@@ -440,8 +447,7 @@ def get_map_ipid_esid(
 
     ip_es_map = []
     for ip_is_pair in ip_is_map:
-        samples_per_participant = []
-        samples_per_participant.append(ip_is_pair[0])
+        samples_per_participant = [ip_is_pair[0]]
         for isid in ip_is_pair[1:]:
             if isid in is_es_map:
                 samples_per_participant.append(is_es_map[isid])
@@ -453,10 +459,9 @@ def get_map_ipid_esid(
     return external_sample_internal_participant_map
 
 
-def get_samples_for_families(project: str, additional_families: list[str]):
+def get_samples_for_families(project: str, additional_families: list[str]) -> list[str]:
     """Returns the samples that belong to a list of families"""
 
-    samples: list[str] = []
     full_pedigree = fapi.get_pedigree(
         project=project,
         replace_with_participant_external_ids=False,
@@ -477,17 +482,16 @@ def get_samples_for_families(project: str, additional_families: list[str]):
         }
     )
 
-    samples = [sample['id'] for sample in sample_objects]
+    samples: list[str] = [sample['id'] for sample in sample_objects]
 
     return samples
 
 
 def get_fams_for_samples(
     project: str,
     additional_samples: Optional[list[str]] = None,
-):
+) -> list[str]:
     """Returns the families that a list of samples belong to"""
-    fams: set[str] = set()
     sample_objects = sapi.get_samples(
         body_get_samples={
             'project_ids': [project],
@@ -503,7 +507,7 @@ def get_fams_for_samples(
         replace_with_family_external_ids=True,
     )
 
-    fams = {
+    fams: set[str] = {
         fam['family_id'] for fam in full_pedigree if str(fam['individual_id']) in pids
     }
 
@@ -524,7 +528,7 @@ def _normalise_map(unformatted_map: list[list[str]]) -> dict[str, str]:
 
 
 def _validate_opts(
-    samples_n: int, families_n: int
+    samples_n: int, families_n: int, noninteractive: bool
 ) -> tuple[Optional[int], Optional[int]]:
     if samples_n is not None and families_n is not None:
         raise click.BadParameter('Please specify only one of --samples or --families')
@@ -539,7 +543,7 @@ def _validate_opts(
     if families_n is not None and families_n < 1:
         raise click.BadParameter('Please specify --families higher than 0')
 
-    if families_n is not None and families_n >= 30:
+    if (families_n is not None and families_n >= 30) and not noninteractive:
         resp = str(
             input(
                 f'You requested a subset of {families_n} families. '
@@ -549,7 +553,7 @@ def _validate_opts(
         if resp.lower() != 'y':
             raise SystemExit()
 
-    if samples_n is not None and samples_n >= 100:
+    if (samples_n is not None and samples_n >= 100) and not noninteractive:
         resp = str(
             input(
                 f'You requested a subset of {samples_n} samples. '
@@ -563,7 +567,7 @@ def _validate_opts(
 
 def _print_fam_stats(families: list[dict[str, str]]):
     family_sizes = Counter([fam['family_id'] for fam in families])
-    fam_by_size: typing.Counter[int] = Counter()
+    fam_by_size: Counter[int] = Counter()
     # determine number of singles, duos, trios, etc
     for fam in family_sizes:
         fam_by_size[family_sizes[fam]] += 1