Tried to move random_transcript to conftest. WIP.

Author: jonbrenas

tests/anoph/conftest.py

@@ -1013,6 +1013,14 @@ def contigs(self) -> Tuple[str, ...]:
     def random_contig(self):
         return choice(self.contigs)
 
+    def random_transcript_id(self):
+        df_transcripts = self.genome_features.query("type == 'mRNA'")
+        transcript_ids = [
+            t.split(";")[0].split("=")[1] for t in df_transcripts.loc[:, "attributes"]
+        ]
+        transcript_id = choice(transcript_ids)
+        return transcript_id
+
     def random_region_str(self, region_size=None):
         contig = self.random_contig()
         contig_size = self.contig_sizes[contig]

tests/anoph/test_frq.py

@@ -8,8 +8,6 @@
 from malariagen_data import ag3 as _ag3
 from malariagen_data.anoph.snp_frq import AnophelesSnpFrequencyAnalysis
 
-from .test_snp_frq import random_transcript
-
 
 @pytest.fixture
 def ag3_sim_api(ag3_sim_fixture):
@@ -83,7 +81,7 @@ def test_plot_frequencies_heatmap(
     sample_sets = random.choice(all_sample_sets)
     site_mask = random.choice(api.site_mask_ids + (None,))
     min_cohort_size = random.randint(0, 2)
-    transcript = random_transcript(api=api).name
+    transcript = fixture.random_transcript_id()
     cohorts = random.choice(
         ["admin1_year", "admin1_month", "admin2_year", "admin2_month"]
     )
@@ -128,7 +126,7 @@ def test_plot_frequencies_time_series(
     sample_sets = random.choice(all_sample_sets)
     site_mask = random.choice(api.site_mask_ids + (None,))
     min_cohort_size = random.randint(0, 2)
-    transcript = random_transcript(api=api).name
+    transcript = fixture.random_transcript_id()
     area_by = random.choice(["country", "admin1_iso", "admin2_name"])
     period_by = random.choice(["year", "quarter", "month"])
 
@@ -179,7 +177,7 @@ def test_plot_frequencies_time_series_with_taxa(
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = random.choice(all_sample_sets)
     site_mask = random.choice(api.site_mask_ids + (None,))
-    transcript = random_transcript(api=api).name
+    transcript = fixture.random_transcript_id()
     area_by = random.choice(["country", "admin1_iso", "admin2_name"])
     period_by = random.choice(["year", "quarter", "month"])
 
@@ -225,7 +223,7 @@ def test_plot_frequencies_time_series_with_areas(
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = random.choice(all_sample_sets)
     site_mask = random.choice(api.site_mask_ids + (None,))
-    transcript = random_transcript(api=api).name
+    transcript = fixture.random_transcript_id()
     area_by = random.choice(["country", "admin1_iso", "admin2_name"])
     period_by = random.choice(["year", "quarter", "month"])
 
@@ -276,7 +274,7 @@ def test_plot_frequencies_interactive_map(
     sample_sets = random.choice(all_sample_sets)
     site_mask = random.choice(api.site_mask_ids + (None,))
     min_cohort_size = random.randint(0, 2)
-    transcript = random_transcript(api=api).name
+    transcript = fixture.random_transcript_id()
     area_by = random.choice(["country", "admin1_iso", "admin2_name"])
     period_by = random.choice(["year", "quarter", "month"])
 

tests/anoph/test_snp_frq.py

@@ -7,7 +7,6 @@
 from pytest_cases import parametrize_with_cases
 import xarray as xr
 from numpy.testing import assert_allclose, assert_array_equal
-import plotly.graph_objects as go  # type: ignore
 
 from malariagen_data import af1 as _af1
 from malariagen_data import ag3 as _ag3
@@ -1429,248 +1428,3 @@ def test_allele_frequencies_advanced_with_dup_samples(
         api=api,
         sample_sets=sample_sets,
     )
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_plot_frequencies_heatmap(
-    fixture,
-    api: AnophelesSnpFrequencyAnalysis,
-):
-    # Pick test parameters at random.
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.choice(all_sample_sets)
-    site_mask = random.choice(api.site_mask_ids + (None,))
-    min_cohort_size = random.randint(0, 2)
-    transcript = random_transcript(api=api).name
-    cohorts = random.choice(
-        ["admin1_year", "admin1_month", "admin2_year", "admin2_month"]
-    )
-
-    # Set up call params.
-    params = dict(
-        transcript=transcript,
-        cohorts=cohorts,
-        min_cohort_size=min_cohort_size,
-        site_mask=site_mask,
-        sample_sets=sample_sets,
-    )
-
-    # Test SNP allele frequencies.
-    df_snp = api.snp_allele_frequencies(**params)
-    fig = api.plot_frequencies_heatmap(df_snp, show=False, max_len=None)
-    assert isinstance(fig, go.Figure)
-
-    # Test amino acid change allele frequencies.
-    df_aa = api.aa_allele_frequencies(**params)
-    fig = api.plot_frequencies_heatmap(df_aa, show=False, max_len=None)
-    assert isinstance(fig, go.Figure)
-
-    # Test max_len behaviour.
-    with pytest.raises(ValueError):
-        api.plot_frequencies_heatmap(df_snp, show=False, max_len=len(df_snp) - 1)
-
-    # Test index parameter - if None, should use dataframe index.
-    fig = api.plot_frequencies_heatmap(df_snp, show=False, index=None, max_len=None)
-    # Not unique.
-    with pytest.raises(ValueError):
-        api.plot_frequencies_heatmap(df_snp, show=False, index="contig", max_len=None)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_plot_frequencies_time_series(
-    fixture,
-    api: AnophelesSnpFrequencyAnalysis,
-):
-    # Pick test parameters at random.
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.choice(all_sample_sets)
-    site_mask = random.choice(api.site_mask_ids + (None,))
-    min_cohort_size = random.randint(0, 2)
-    transcript = random_transcript(api=api).name
-    area_by = random.choice(["country", "admin1_iso", "admin2_name"])
-    period_by = random.choice(["year", "quarter", "month"])
-
-    # Compute SNP frequencies.
-    ds = api.snp_allele_frequencies_advanced(
-        transcript=transcript,
-        area_by=area_by,
-        period_by=period_by,
-        sample_sets=sample_sets,
-        min_cohort_size=min_cohort_size,
-        site_mask=site_mask,
-    )
-
-    # Trim things down a bit for speed.
-    ds = ds.isel(variants=slice(0, 100))
-
-    # Plot.
-    fig = api.plot_frequencies_time_series(ds, show=False)
-
-    # Test.
-    assert isinstance(fig, go.Figure)
-
-    # Compute amino acid change frequencies.
-    ds = api.aa_allele_frequencies_advanced(
-        transcript=transcript,
-        area_by=area_by,
-        period_by=period_by,
-        sample_sets=sample_sets,
-        min_cohort_size=min_cohort_size,
-    )
-
-    # Trim things down a bit for speed.
-    ds = ds.isel(variants=slice(0, 100))
-
-    # Plot.
-    fig = api.plot_frequencies_time_series(ds, show=False)
-
-    # Test.
-    assert isinstance(fig, go.Figure)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_plot_frequencies_time_series_with_taxa(
-    fixture,
-    api: AnophelesSnpFrequencyAnalysis,
-):
-    # Pick test parameters at random.
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.choice(all_sample_sets)
-    site_mask = random.choice(api.site_mask_ids + (None,))
-    transcript = random_transcript(api=api).name
-    area_by = random.choice(["country", "admin1_iso", "admin2_name"])
-    period_by = random.choice(["year", "quarter", "month"])
-
-    # Pick a random taxon and taxa from valid taxa.
-    sample_sets_taxa = (
-        api.sample_metadata(sample_sets=sample_sets)["taxon"].dropna().unique().tolist()
-    )
-    taxon = random.choice(sample_sets_taxa)
-    taxa = random.sample(sample_sets_taxa, random.randint(1, len(sample_sets_taxa)))
-
-    # Compute SNP frequencies.
-    ds = api.snp_allele_frequencies_advanced(
-        transcript=transcript,
-        area_by=area_by,
-        period_by=period_by,
-        sample_sets=sample_sets,
-        min_cohort_size=1,  # Don't exclude any samples.
-        site_mask=site_mask,
-    )
-
-    # Trim things down a bit for speed.
-    ds = ds.isel(variants=slice(0, 100))
-
-    # Plot with taxon.
-    fig = api.plot_frequencies_time_series(ds, show=False, taxa=taxon)
-
-    # Test taxon plot.
-    assert isinstance(fig, go.Figure)
-
-    # Plot with taxa.
-    fig = api.plot_frequencies_time_series(ds, show=False, taxa=taxa)
-
-    # Test taxa plot.
-    assert isinstance(fig, go.Figure)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_plot_frequencies_time_series_with_areas(
-    fixture,
-    api: AnophelesSnpFrequencyAnalysis,
-):
-    # Pick test parameters at random.
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.choice(all_sample_sets)
-    site_mask = random.choice(api.site_mask_ids + (None,))
-    transcript = random_transcript(api=api).name
-    area_by = random.choice(["country", "admin1_iso", "admin2_name"])
-    period_by = random.choice(["year", "quarter", "month"])
-
-    # Compute SNP frequencies.
-    ds = api.snp_allele_frequencies_advanced(
-        transcript=transcript,
-        area_by=area_by,
-        period_by=period_by,
-        sample_sets=sample_sets,
-        min_cohort_size=1,  # Don't exclude any samples.
-        site_mask=site_mask,
-    )
-
-    # Trim things down a bit for speed.
-    ds = ds.isel(variants=slice(0, 100))
-
-    # Extract cohorts into a DataFrame.
-    cohort_vars = [v for v in ds if str(v).startswith("cohort_")]
-    df_cohorts = ds[cohort_vars].to_dataframe()
-
-    # Pick a random area and areas from valid areas.
-    cohorts_areas = df_cohorts["cohort_area"].dropna().unique().tolist()
-    area = random.choice(cohorts_areas)
-    areas = random.sample(cohorts_areas, random.randint(1, len(cohorts_areas)))
-
-    # Plot with area.
-    fig = api.plot_frequencies_time_series(ds, show=False, areas=area)
-
-    # Test areas plot.
-    assert isinstance(fig, go.Figure)
-
-    # Plot with areas.
-    fig = api.plot_frequencies_time_series(ds, show=False, areas=areas)
-
-    # Test area plot.
-    assert isinstance(fig, go.Figure)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_plot_frequencies_interactive_map(
-    fixture,
-    api: AnophelesSnpFrequencyAnalysis,
-):
-    import ipywidgets  # type: ignore
-
-    # Pick test parameters at random.
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.choice(all_sample_sets)
-    site_mask = random.choice(api.site_mask_ids + (None,))
-    min_cohort_size = random.randint(0, 2)
-    transcript = random_transcript(api=api).name
-    area_by = random.choice(["country", "admin1_iso", "admin2_name"])
-    period_by = random.choice(["year", "quarter", "month"])
-
-    # Compute SNP frequencies.
-    ds = api.snp_allele_frequencies_advanced(
-        transcript=transcript,
-        area_by=area_by,
-        period_by=period_by,
-        sample_sets=sample_sets,
-        min_cohort_size=min_cohort_size,
-        site_mask=site_mask,
-    )
-
-    # Trim things down a bit for speed.
-    ds = ds.isel(variants=slice(0, 100))
-
-    # Plot.
-    fig = api.plot_frequencies_interactive_map(ds)
-
-    # Test.
-    assert isinstance(fig, ipywidgets.Widget)
-
-    # Compute amino acid change frequencies.
-    ds = api.aa_allele_frequencies_advanced(
-        transcript=transcript,
-        area_by=area_by,
-        period_by=period_by,
-        sample_sets=sample_sets,
-        min_cohort_size=min_cohort_size,
-    )
-
-    # Trim things down a bit for speed.
-    ds = ds.isel(variants=slice(0, 100))
-
-    # Plot.
-    fig = api.plot_frequencies_interactive_map(ds)
-
-    # Test.
-    assert isinstance(fig, ipywidgets.Widget)