Skip to content

Commit

Permalink
[pre-commit.ci] auto fixes from pre-commit.com hooks
Browse files Browse the repository at this point in the history
for more information, see https://pre-commit.ci
  • Loading branch information
pre-commit-ci[bot] committed Jul 30, 2023
1 parent a77442b commit 7b5f88c
Showing 1 changed file with 1 addition and 6 deletions.
7 changes: 1 addition & 6 deletions taxoniumtools/src/taxoniumtools/ushertools.py
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,6 @@ def get_gene_name(cds):
def get_genes_dict(cdses):
genes = {}
for cds in cdses:


genes[get_gene_name(cds)] = Gene(get_gene_name(cds), cds.strand,
cds.location.start, cds.location.end)
Expand Down Expand Up @@ -341,7 +340,6 @@ def load_genbank_file(self, genbank_file):
for feature in self.cdses:

gene_name = get_gene_name(feature)


nucleotide_counter = 0
for part in feature.location.parts:
Expand All @@ -350,9 +348,8 @@ def load_genbank_file(self, genbank_file):
) if part.strand == 1 else range(
part.end - 1, part.start - 1, -1
) #(honestly not sure why we need to subtract 1 here but we seem to?)

for genome_position in ranger:


cur_codon_number = nucleotide_counter // 3
cur_pos_in_codon = nucleotide_counter % 3
Expand All @@ -363,13 +360,11 @@ def load_genbank_file(self, genbank_file):
total_lengths[gene_name] = nucleotide_counter

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)


assert len(codon_dict) % 3 == 0
for k, v in codon_dict.items():
Expand Down

0 comments on commit 7b5f88c

Please sign in to comment.