Merge pull request #74 from oxfordmmm/gumpy-1.3.2

bump: use gumpy 1.3.2

gnomonicus/gnomonicus_lib.py

@@ -753,7 +753,11 @@ def minority_population_variants(
                 gene_name.append(gene)
                 g_pos = diff.get_gene_pos(gene, idx, variant)
                 gene_pos.append(g_pos)
-                if diff.genome1.genes[gene]["codes_protein"] and g_pos > 0:
+                if (
+                    diff.genome1.genes[gene]["codes_protein"]
+                    and g_pos is not None
+                    and g_pos > 0
+                ):
                     # Get codon idx
                     nc_idx = diff.genome1.stacked_nucleotide_index[
                         diff.genome1.stacked_gene_name == gene
@@ -785,7 +789,11 @@ def minority_population_variants(
                 g_pos = diff.get_gene_pos(gene, idx, variant)
                 gene_pos.append(g_pos)
 
-                if diff.genome1.genes[gene]["codes_protein"] and g_pos > 0:
+                if (
+                    diff.genome1.genes[gene]["codes_protein"]
+                    and g_pos is not None
+                    and g_pos > 0
+                ):
                     # Get codon idx
                     nc_idx = diff.genome1.stacked_nucleotide_index[
                         diff.genome1.stacked_gene_name == gene

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = gnomonicus
-version = 2.6.4
+version = 2.6.5
 author = Philip W Fowler, Jeremy Westhead
 author_email = philip.fowler@ndm.ox.ac.uk
 description = Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
@@ -16,7 +16,7 @@ package_dir =
 packages = find:
 python_requires = >=3.10
 install_requires = 
-    gumpy>=1.3.1
+    gumpy>=1.3.2
     piezo>=0.8.3
     vcf_subset>=1.1.2
     numpy