More tests and some trimming of the hierarchy in anoph

Author: jonbrenas

malariagen_data/anoph/dipclust.py

@@ -23,14 +23,16 @@
     cnv_params,
 )
 from .snp_frq import AnophelesSnpFrequencyAnalysis
-from .cnv_data import AnophelesCnvData
+from .cnv_frq import AnophelesCnvFrequencyAnalysis
 
 AA_CHANGE_QUERY = (
     "effect in ['NON_SYNONYMOUS_CODING', 'START_LOST', 'STOP_LOST', 'STOP_GAINED']"
 )
 
 
-class AnophelesDipClustAnalysis(AnophelesSnpFrequencyAnalysis, AnophelesCnvData):
+class AnophelesDipClustAnalysis(
+    AnophelesCnvFrequencyAnalysis, AnophelesSnpFrequencyAnalysis
+):
     def __init__(
         self,
         **kwargs,

malariagen_data/anopheles.py

@@ -12,11 +12,6 @@
 import plotly.graph_objects as go  # type: ignore
 from numpydoc_decorator import doc  # type: ignore
 
-from malariagen_data.anoph.snp_frq import (
-    AnophelesSnpFrequencyAnalysis,
-)
-
-from .anoph.cnv_frq import AnophelesCnvFrequencyAnalysis
 
 from .anoph import (
     aim_params,
@@ -31,7 +26,6 @@
 )
 from .anoph.aim_data import AnophelesAimData
 from .anoph.base import AnophelesBase
-from .anoph.cnv_data import AnophelesCnvData
 from .anoph.genome_features import AnophelesGenomeFeaturesData
 from .anoph.genome_sequence import AnophelesGenomeSequenceData
 from .anoph.hap_data import AnophelesHapData, hap_params
@@ -87,8 +81,6 @@ class AnophelesDataResource(
     AnophelesH12Analysis,
     AnophelesG123Analysis,
     AnophelesFstAnalysis,
-    AnophelesCnvFrequencyAnalysis,
-    AnophelesSnpFrequencyAnalysis,
     AnophelesHapFrequencyAnalysis,
     AnophelesDistanceAnalysis,
     AnophelesPca,
@@ -97,7 +89,6 @@ class AnophelesDataResource(
     AnophelesAimData,
     AnophelesHapData,
     AnophelesSnpData,
-    AnophelesCnvData,
     AnophelesSampleMetadata,
     AnophelesGenomeFeaturesData,
     AnophelesGenomeSequenceData,

tests/anoph/test_dipclust.py

@@ -7,6 +7,14 @@
 from malariagen_data.anoph.dipclust import AnophelesDipClustAnalysis
 
 
+def random_transcripts_contig(*, api, contig, n):
+    df_gff = api.genome_features(attributes=["ID", "Parent"])
+    df_transcripts = df_gff.query(f"type == 'mRNA' and contig == '{contig}'")
+    transcript_ids = df_transcripts["ID"].dropna().to_list()
+    transcripts = random.sample(transcript_ids, n)
+    return transcripts
+
+
 @pytest.fixture
 def ag3_sim_api(ag3_sim_fixture):
     return AnophelesDipClustAnalysis(
@@ -98,3 +106,97 @@ def test_plot_diplotype_clustering(
 
     # Run checks.
     api.plot_diplotype_clustering(**dipclust_params)
+
+
+@pytest.mark.parametrize("distance_metric", ["cityblock", "euclidean"])
+@parametrize_with_cases("fixture,api", cases=".")
+def test_plot_diplotype_clustering_advanced(
+    fixture, api: AnophelesDipClustAnalysis, distance_metric
+):
+    # Set up test parameters.
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    linkage_methods = (
+        "single",
+        "complete",
+        "average",
+        "weighted",
+        "centroid",
+        "median",
+        "ward",
+    )
+    sample_queries = (None, "sex_call == 'F'")
+    dipclust_params = dict(
+        region=fixture.random_region_str(region_size=5000),
+        sample_sets=[random.choice(all_sample_sets)],
+        linkage_method=random.choice(linkage_methods),
+        distance_metric=distance_metric,
+        sample_query=random.choice(sample_queries),
+        show=False,
+    )
+
+    # Run checks.
+    api.plot_diplotype_clustering_advanced(**dipclust_params)
+
+
+@pytest.mark.parametrize("n", [1, 2])
+@parametrize_with_cases("fixture,api", cases=".")
+def test_plot_diplotype_clustering_advanced_with_transcript(
+    fixture, api: AnophelesDipClustAnalysis, n
+):
+    # Set up test parameters.
+    contig = fixture.random_contig()
+    transcripts = random_transcripts_contig(api=api, contig=contig, n=n)
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    linkage_methods = (
+        "single",
+        "complete",
+        "average",
+        "weighted",
+        "centroid",
+        "median",
+        "ward",
+    )
+    sample_queries = (None, "sex_call == 'F'")
+    dipclust_params = dict(
+        region=contig,
+        snp_transcripts=transcripts,
+        sample_sets=[random.choice(all_sample_sets)],
+        linkage_method=random.choice(linkage_methods),
+        distance_metric="cityblock",
+        sample_query=random.choice(sample_queries),
+        show=False,
+    )
+
+    # Run checks.
+    api.plot_diplotype_clustering_advanced(**dipclust_params)
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_plot_diplotype_clustering_advanced_with_cnv_region(
+    fixture, api: AnophelesDipClustAnalysis
+):
+    # Set up test parameters.
+    region = fixture.random_region_str(region_size=5000)
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    linkage_methods = (
+        "single",
+        "complete",
+        "average",
+        "weighted",
+        "centroid",
+        "median",
+        "ward",
+    )
+    sample_queries = (None, "sex_call == 'F'")
+    dipclust_params = dict(
+        region=region,
+        cnv_region=region,
+        sample_sets=[random.choice(all_sample_sets)],
+        linkage_method=random.choice(linkage_methods),
+        distance_metric="cityblock",
+        sample_query=random.choice(sample_queries),
+        show=False,
+    )
+
+    # Run checks.
+    api.plot_diplotype_clustering_advanced(**dipclust_params)