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

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

taxoniumtools/src/taxoniumtools/ushertools.py

@@ -13,8 +13,6 @@ def reverse_complement(input_string):
  return input_string.translate(str.maketrans("ATCG", "TAGC"))[::-1]
 
 
-
-
 @dataclass(eq=True, frozen=True)
 class AAMutation:
  gene: str
@@ -38,16 +36,18 @@ class NucMutation: #hashable
 class Gene:
  name: str
  strand: int
- start: int # zero-indexed
- end: int # 0-indexed
+ start: int  # zero-indexed
+ end: int  # 0-indexed
 
 
 from dataclasses import dataclass
+
+
 @dataclass(eq=True, frozen=True)
 class Codon:
  gene: Gene
- codon_number: int # zero-indexed
- positions: dict # zero-indexed positions e.g. {0:123,1:124,2:125}
+ codon_number: int  # zero-indexed
+ positions: dict  # zero-indexed positions e.g. {0:123,1:124,2:125}
  strand: int
 
 
@@ -88,24 +88,24 @@ def get_mutations(past_nuc_muts_dict,
  by_codon = defaultdict(list)
 
  for mutation in new_nuc_mutations_here:
- zero_indexed_pos  = mutation.one_indexed_position - 1
+ zero_indexed_pos = mutation.one_indexed_position - 1
  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[x] for x in gene_codon.positions]
 
  relevant_past_muts = [(x, past_nuc_muts_dict[x])
  for x in gene_codon.positions
  if x in past_nuc_muts_dict]
- flipped_dict = {position: offset for offset, position in gene_codon.positions.items()}
+ flipped_dict = {
+ position: offset
+ for offset, position in gene_codon.positions.items()
+ }
  for position, value in relevant_past_muts:
  initial_codon[flipped_dict[position]] = value
 
@@ -136,12 +136,14 @@ def get_mutations(past_nuc_muts_dict,
 
  # update past_nuc_muts_dict
  for mutation in mutations:
- past_nuc_muts_dict[mutation.one_indexed_position-1] = mutation.genome_residue
+ past_nuc_muts_dict[mutation.one_indexed_position -
+ 1] = mutation.genome_residue
 
  return mutations_here
 
 
-def recursive_mutation_analysis(node, past_nuc_muts_dict, seq, cdses, pbar, nuc_to_codon):
+def recursive_mutation_analysis(node, past_nuc_muts_dict, seq, cdses, pbar,
+ nuc_to_codon):
  pbar()
 
  new_nuc_mutations_here = node.nuc_mutations
@@ -314,38 +316,35 @@ def load_genbank_file(self, genbank_file):
  # Assert that there are no compound locations and that all strands are positive,
  # and that all CDS features are a multiple of 3
 
-
  self.genes = get_genes_dict(self.cdses)
-
- by_everything = defaultdict( lambda : defaultdict(dict))
 
+ by_everything = defaultdict(lambda: defaultdict(dict))
 
  for feature in self.cdses:
- 
+
  gene_name = get_gene_name(feature)
- 
- nucleotide_counter=0
+
+ nucleotide_counter = 0
  for part in feature.location.parts:
- for genome_position in range(part.start,part.end+1):
- 
- cur_codon_number = nucleotide_counter//3
+ for genome_position in range(part.start, part.end + 1):
+
+ 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
 
+ by_everything[gene_name][cur_codon_number][
+ cur_pos_in_codon] = genome_position
+ nucleotide_counter += 1
 
  nuc_to_codon = defaultdict(list)
 
  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)
- for k,v in codon_dict.items():
+ codon_obj = Codon(feat_name, codon_index, codon_dict,
+ self.genes[feat_name].strand)
+ for k, v in codon_dict.items():
  nuc_to_codon[v].append(codon_obj)
 
  self.nuc_to_codon = nuc_to_codon
-
-
 
  def convert_nuc_mutation(self, usher_mutation):
  new_mut = NucMutation(one_indexed_position=usher_mutation.position,