Merge branch 'master' into GH-1054-add-vcf-export

Author: adilraza99

malariagen_data/anoph/aim_data.py

@@ -341,6 +341,4 @@ def plot_aim_heatmap(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/cnv_data.py

@@ -810,9 +810,7 @@ def plot_cnv_hmm_coverage_track(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -884,9 +882,7 @@ def plot_cnv_hmm_coverage(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -1028,9 +1024,7 @@ def plot_cnv_hmm_heatmap_track(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -1100,6 +1094,4 @@ def plot_cnv_hmm_heatmap(
 
         if show:
             bkplt.show(fig)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/cnv_frq.py

@@ -90,7 +90,11 @@ def _gene_cnv(
         inline_array,
     ):
         # Sanity check.
-        assert isinstance(region, Region)
+        if not isinstance(region, Region):
+            raise TypeError(
+                f"Expected region to be a Region object, "
+                f"got {type(region).__name__}: {region!r}"
+            )
 
         # Access genes within the region of interest.
         df_genome_features = self.genome_features(region=region)
@@ -260,7 +264,11 @@ def _gene_cnv_frequencies(
         debug = self._log.debug
 
         debug("sanity check - this function is one region at a time")
-        assert isinstance(region, Region)
+        if not isinstance(region, Region):
+            raise TypeError(
+                f"Expected region to be a Region object, "
+                f"got {type(region).__name__}: {region!r}"
+            )
 
         debug("get gene copy number data")
         ds_cnv = self.gene_cnv(
@@ -504,7 +512,11 @@ def _gene_cnv_frequencies_advanced(
         debug = self._log.debug
 
         debug("sanity check - here we deal with one region only")
-        assert isinstance(region, Region)
+        if not isinstance(region, Region):
+            raise TypeError(
+                f"Expected region to be a Region object, "
+                f"got {type(region).__name__}: {region!r}"
+            )
 
         debug("access gene CNV calls")
         ds_cnv = self.gene_cnv(

malariagen_data/anoph/dipclust.py

@@ -189,13 +189,11 @@ def plot_diplotype_clustering(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return {
-                "figure": fig,
-                "dendro_sample_id_order": np.asarray(leaf_data["sample_id"].to_list()),
-                "n_snps": n_snps_used,
-            }
+        return {
+            "figure": fig,
+            "dendro_sample_id_order": np.asarray(leaf_data["sample_id"].to_list()),
+            "n_snps": n_snps_used,
+        }
 
     def diplotype_pairwise_distances(
         self,
@@ -800,6 +798,4 @@ def plot_diplotype_clustering_advanced(
 
         if show:
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/distance.py

@@ -614,6 +614,4 @@ def plot_njt(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/frq_base.py

@@ -341,7 +341,11 @@ def plot_frequencies_heatmap(
             for j in range(1, idx_vals.shape[1]):
                 index_col = index_col + ", " + idx_vals[:, j]
         else:
-            assert isinstance(index, str)
+            if not isinstance(index, str):
+                raise TypeError(
+                    f"Expected index to be str or list, "
+                    f"got {type(index).__name__}: {index!r}"
+                )
             index_col = df[index].astype(str)
 
         # Check that index is unique.
@@ -401,9 +405,7 @@ def plot_frequencies_heatmap(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -553,9 +555,7 @@ def plot_frequencies_time_series(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -592,7 +592,11 @@ def plot_frequencies_map_markers(
             ds_variant = ds.isel(variants=variant)
             variant_label = ds["variant_label"].values[variant]
         else:
-            assert isinstance(variant, str)
+            if not isinstance(variant, str):
+                raise TypeError(
+                    f"Expected variant to be int or str, "
+                    f"got {type(variant).__name__}: {variant!r}"
+                )
             ds_variant = ds.set_index(variants="variant_label").sel(variants=variant)
             variant_label = variant
 

malariagen_data/anoph/fst.py

@@ -257,9 +257,7 @@ def plot_fst_gwss_track(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -345,9 +343,7 @@ def plot_fst_gwss(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -590,6 +586,4 @@ def plot_pairwise_average_fst(
 
         if show:  # pragma: no cover
             fig.show(renderer=renderer)
-            return None
-        else:
-            return fig
+        return fig

malariagen_data/anoph/g123.py

@@ -421,9 +421,7 @@ def plot_g123_gwss_track(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -506,9 +504,7 @@ def plot_g123_gwss(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -607,9 +603,7 @@ def plot_g123_calibration(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
 
 def _diplotype_frequencies(gt):

malariagen_data/anoph/genome_features.py

@@ -312,9 +312,7 @@ def plot_transcript(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     @_check_types
     @doc(
@@ -514,9 +512,7 @@ def plot_genes(
 
         if show:  # pragma: no cover
             bokeh.plotting.show(fig)
-            return None
-        else:
-            return fig
+        return fig
 
     def _plot_genes_setup_data(self, *, region):
         attributes = [a for a in self._gff_default_attributes if a != "Parent"]

malariagen_data/anoph/genome_sequence.py

@@ -117,9 +117,13 @@ def genome_sequence(
 
         # Deal with region start and stop.
         slice_start = slice_stop = None
-        if resolved_region.start:
+        if resolved_region.start is not None:
+            if resolved_region.start < 1:
+                raise ValueError("Region start must be >= 1 or None.")
             slice_start = resolved_region.start - 1
-        if resolved_region.end:
+        if resolved_region.end is not None:
+            if resolved_region.end < 1:
+                raise ValueError("Region end must be >= 1 or None.")
             slice_stop = resolved_region.end
         loc_region = slice(slice_start, slice_stop)