fix

.gitignore

@@ -13,3 +13,6 @@ taxonium_backend/latest_public.jsonl.gz.1
 taxonium_component/dist
 taxonium_component/storybook-static/**
 .DS_Store
+**/*.egg-info/**
+**/*.pyc
+**/_version.py

taxoniumtools/src/taxoniumtools/ushertools.py

@@ -97,14 +97,16 @@ def get_mutations(past_nuc_muts_dict,
 
  for mutation in new_nuc_mutations_here:
  zero_indexed_pos = mutation.one_indexed_position - 1
- for codon in nuc_to_codon[zero_indexed_pos]:
- by_codon[codon].append(mutation)
+ if zero_indexed_pos in nuc_to_codon:
+ for codon in nuc_to_codon[zero_indexed_pos]:
+ by_codon[codon].append(mutation)
 
  mutations_here = []
  for gene_codon, mutations in by_codon.items():
 
  # For most of this function we ignore strand - so for negative strand we
  # are actually collecting the reverse complement of the codon
+
  initial_codon = [seq[gene_codon.positions[x]] for x in range(3)]
 
  relevant_past_muts = [(x, past_nuc_muts_dict[x])
@@ -334,7 +336,7 @@ def load_genbank_file(self, genbank_file):
 
  nucleotide_counter = 0
  for part in feature.location.parts:
- for genome_position in range(part.start, part.end + 1):
+ for genome_position in range(part.start, part.end ):
 
  cur_codon_number = nucleotide_counter // 3
  cur_pos_in_codon = nucleotide_counter % 3
@@ -349,6 +351,8 @@ def load_genbank_file(self, genbank_file):
  for codon_index, codon_dict in codons.items():
  codon_obj = Codon(feat_name, codon_index, codon_dict,
  self.genes[feat_name].strand)
+
+ assert len(codon_dict)%3 == 0
  for k, v in codon_dict.items():
  nuc_to_codon[v].append(codon_obj)