[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

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"))
 
@@ -84,8 +86,8 @@ def get_gene_name(cds):
 def get_genes_dict(cdses):
  genes = {}
  for cds in cdses:
- print(get_gene_name(cds),cds.strand)
- 
+ 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
@@ -132,9 +134,8 @@ def get_mutations(past_nuc_muts_dict,
  initial_codon = "".join(initial_codon)
  final_codon = "".join(final_codon)
 
-
  if gene_codon.strand == -1:
- 
+
  initial_codon = complement(initial_codon)
  final_codon = complement(final_codon)
 
@@ -344,11 +345,12 @@ def load_genbank_file(self, genbank_file):
 
  nucleotide_counter = 0
  for part in feature.location.parts:
- ranger = range(part.start, part.end) if part.strand == 1 else range(part.end -1, part.start-1, -1)
+ 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)
-
+ # print(part.start, part.end, part.strand, genome_position)
 
  cur_codon_number = nucleotide_counter // 3
  cur_pos_in_codon = nucleotide_counter % 3