fix

taxoniumtools/src/taxoniumtools/ushertools.py

@@ -11,6 +11,8 @@
 
 def reverse_complement(input_string):
  return input_string.translate(str.maketrans("ATCG", "TAGC"))[::-1]
+def complement(input_string):
+ return input_string.translate(str.maketrans("ATCG", "TAGC"))
 
 
 @dataclass(eq=True, frozen=True)
@@ -82,6 +84,8 @@ def get_gene_name(cds):
 def get_genes_dict(cdses):
  genes = {}
  for cds in cdses:
+ print(get_gene_name(cds),cds.strand)
+
  genes[get_gene_name(cds)] = Gene(get_gene_name(cds), cds.strand,
  cds.location.start, cds.location.end)
  return genes
@@ -105,7 +109,7 @@ def get_mutations(past_nuc_muts_dict,
  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
+ # are actually collecting the complement of the codon
 
  initial_codon = [seq[gene_codon.positions[x]] for x in range(3)]
 
@@ -128,9 +132,11 @@ def get_mutations(past_nuc_muts_dict,
  initial_codon = "".join(initial_codon)
  final_codon = "".join(final_codon)
 
+
  if gene_codon.strand == -1:
- initial_codon = reverse_complement(initial_codon)
- final_codon = reverse_complement(final_codon)
+
+ initial_codon = complement(initial_codon)
+ final_codon = complement(final_codon)
 
  initial_codon_trans = codon_table[initial_codon]
  final_codon_trans = codon_table[final_codon]
@@ -329,28 +335,37 @@ def load_genbank_file(self, genbank_file):
  self.genes = get_genes_dict(self.cdses)
 
  by_everything = defaultdict(lambda: defaultdict(dict))
+ total_lengths = {}
 
  for feature in self.cdses:
 
  gene_name = get_gene_name(feature)
+ print(gene_name)
 
  nucleotide_counter = 0
  for part in feature.location.parts:
- for genome_position in range(part.start, part.end):
+ ranger = range(part.start, part.end) if part.strand == 1 else range(part.end -1, part.start-1, -1)
+ print(part)
+ for genome_position in ranger:
+ # print(part.start, part.end, part.strand, genome_position)
+
 
  cur_codon_number = nucleotide_counter // 3
  cur_pos_in_codon = nucleotide_counter % 3
 
  by_everything[gene_name][cur_codon_number][
  cur_pos_in_codon] = genome_position
  nucleotide_counter += 1
+ total_lengths[gene_name] = nucleotide_counter
 
  nuc_to_codon = defaultdict(list)
+ print(self.genes)
 
  for feat_name, codons in by_everything.items():
  for codon_index, codon_dict in codons.items():
  codon_obj = Codon(feat_name, codon_index, codon_dict,
  self.genes[feat_name].strand)
+ print(codon_obj)
 
  assert len(codon_dict) % 3 == 0
  for k, v in codon_dict.items():