Merge pull request #66 from malariagen/0710-cc-65

Upgrade `cohorts_analysis` to 20210927
malariagen · Oct 14, 2021 · 97c2a67 · 97c2a67
2 parents 9d9eb4c + b61db65
commit 97c2a67
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/malariagen_data/ag3.py b/malariagen_data/ag3.py
@@ -771,7 +771,7 @@ def snp_allele_frequencies(
         self,
         transcript,
         cohorts,
-        cohorts_analysis="20210702",
+        cohorts_analysis="20210927",
         min_cohort_size=10,
         site_mask=None,
         site_filters="dt_20200416",
@@ -1661,7 +1661,7 @@ def gene_cnv_frequencies(
         self,
         contig,
         cohorts,
-        cohorts_analysis="20210702",
+        cohorts_analysis="20210927",
         min_cohort_size=10,
         species_calls=("20200422", "aim"),
         sample_sets="v3_wild",
@@ -1970,7 +1970,7 @@ def _read_cohort_metadata(self, *, sample_set, cohorts_analysis):
             self._cache_cohort_metadata[(sample_set, cohorts_analysis)] = df
             return df
 
-    def sample_cohorts(self, sample_sets="v3_wild", cohorts_analysis="20210702"):
+    def sample_cohorts(self, sample_sets="v3_wild", cohorts_analysis="20210927"):
         """Access cohorts metadata for one or more sample sets.
 
         Parameters

diff --git a/tests/test_ag3.py b/tests/test_ag3.py
@@ -617,20 +617,20 @@ def test_snp_allele_frequencies__str_cohorts():
     df = ag3.snp_allele_frequencies(
         transcript="AGAP004707-RD",
         cohorts=cohorts,
-        cohorts_analysis="20210702",
+        cohorts_analysis="20210927",
         min_cohort_size=10,
         site_mask="gamb_colu",
         sample_sets="v3_wild",
         drop_invariant=True,
     )
-    df_coh = ag3.sample_cohorts(sample_sets="v3_wild", cohorts_analysis="20210702")
+    df_coh = ag3.sample_cohorts(sample_sets="v3_wild", cohorts_analysis="20210927")
     coh_nm = "cohort_" + cohorts
     all_uni = df_coh[coh_nm].dropna().unique().tolist()
     expected_fields = universal_fields + all_uni + ["max_af"]
 
     assert df.columns.tolist() == expected_fields
     assert isinstance(df, pd.DataFrame)
-    assert df.shape == (16639, 101)
+    assert df.shape == (16524, 103)
 
 
 def test_snp_allele_frequencies__dict_cohorts():
@@ -1049,7 +1049,7 @@ def test_gene_cnv_frequencies(contig, cohorts):
             cohort_labels = cohorts.keys()
         if isinstance(cohorts, str):
             df_coh = ag3.sample_cohorts(
-                sample_sets="v3_wild", cohorts_analysis="20210702"
+                sample_sets="v3_wild", cohorts_analysis="20210927"
             )
             coh_nm = "cohort_" + cohorts
             cohort_labels = list(df_coh[coh_nm].dropna().unique())
@@ -1173,7 +1173,7 @@ def test_sample_cohorts(sample_sets):
     )
 
     ag3 = setup_ag3()
-    df_coh = ag3.sample_cohorts(sample_sets=sample_sets, cohorts_analysis="20210702")
+    df_coh = ag3.sample_cohorts(sample_sets=sample_sets, cohorts_analysis="20210927")
     df_meta = ag3.sample_metadata(sample_sets=sample_sets)
 
     assert tuple(df_coh.columns) == expected_cols