diff --git a/taxoniumtools/src/taxoniumtools/ushertools.py b/taxoniumtools/src/taxoniumtools/ushertools.py index 1b3bede9..3b6c7b69 100644 --- a/taxoniumtools/src/taxoniumtools/ushertools.py +++ b/taxoniumtools/src/taxoniumtools/ushertools.py @@ -86,7 +86,6 @@ 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) @@ -341,7 +340,6 @@ def load_genbank_file(self, genbank_file): for feature in self.cdses: gene_name = get_gene_name(feature) - print(gene_name) nucleotide_counter = 0 for part in feature.location.parts: @@ -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?) - 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 @@ -363,13 +360,11 @@ def load_genbank_file(self, genbank_file): 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():