Merge branch 'master' into GH940-fix-region-start-zero-truthiness

Author: khushthecoder

malariagen_data/anoph/dipclust.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Optional, Tuple
 
 import allel  # type: ignore
@@ -540,8 +541,9 @@ def _insert_dipclust_snp_trace(
             figures.append(snp_trace)
             subplot_heights.append(snp_row_height * n_snps_transcript)
         else:
-            print(
-                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
+            warnings.warn(
+                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot.",
+                stacklevel=2,
             )
         return figures, subplot_heights, n_snps_transcript
 
@@ -607,8 +609,9 @@ def plot_diplotype_clustering_advanced(
             cnv_colorscale = cnv_params.colorscale_default
         if cohort_size and snp_transcript:
             cohort_size = None
-            print(
-                "Cohort size is not supported with amino acid heatmap. Overriding cohort size to None."
+            warnings.warn(
+                "Cohort size is not supported with amino acid heatmap. Overriding cohort size to None.",
+                stacklevel=2,
             )
 
         res = self.plot_diplotype_clustering(

malariagen_data/anoph/hapclust.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Optional, Tuple
 
 import allel  # type: ignore
@@ -402,8 +403,9 @@ def plot_haplotype_clustering_advanced(
 
         if cohort_size and snp_transcript:
             cohort_size = None
-            print(
-                "Cohort size is not supported with amino acid heatmap. Overriding cohort size to None."
+            warnings.warn(
+                "Cohort size is not supported with amino acid heatmap. Overriding cohort size to None.",
+                stacklevel=2,
             )
 
         res = self.plot_haplotype_clustering(
@@ -709,8 +711,9 @@ def _insert_hapclust_snp_trace(
             figures.append(snp_trace)
             subplot_heights.append(snp_row_height * df_haps.shape[0])
         else:
-            print(
-                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
+            warnings.warn(
+                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot.",
+                stacklevel=2,
             )
         return figures, subplot_heights, n_snps_transcript
 

malariagen_data/anoph/sample_metadata.py

@@ -1534,8 +1534,9 @@ def _setup_cohort_queries(
             if min_cohort_size is not None:
                 cohort_size = min_cohort_size
             if cohort_size is not None and n_samples < cohort_size:
-                print(
-                    f"Cohort ({cohort_label}) has insufficient samples ({n_samples}) for requested cohort size ({cohort_size}), dropping."
+                warnings.warn(
+                    f"Cohort ({cohort_label}) has insufficient samples ({n_samples}) for requested cohort size ({cohort_size}), dropping.",
+                    stacklevel=2,
                 )
             else:
                 cohort_queries_checked[cohort_label] = cohort_query

malariagen_data/veff.py

@@ -356,10 +356,15 @@ def _get_within_cds_effect(ann, base_effect, cds, cdss):
             effect = base_effect._replace(effect="STOP_GAINED", impact="HIGH")
 
         else:
-            # TODO NON_SYNONYMOUS_START and NON_SYNONYMOUS_STOP
-
             # variant causes a codon that produces a different amino acid
             # e.g.: Tgg/Cgg, W/R
+            # N.B. NON_SYNONYMOUS_START and NON_SYNONYMOUS_STOP from the SnpEff
+            # taxonomy do not require separate handling here. Any start codon
+            # mutation that changes the amino acid is already classified as
+            # START_LOST (when ref_aa == "M"). Any stop codon mutation that
+            # changes the amino acid is already classified as STOP_LOST or
+            # STOP_GAINED. There is no reachable case that falls through to here
+            # with ref or alt at a start or stop codon position.
             effect = base_effect._replace(
                 effect="NON_SYNONYMOUS_CODING", impact="MODERATE"
             )