bb21b3314c57ec4208af8eed8041091cc51ec68a,anvio/profiler.py,BAMProfiler,generate_variabile_codons_table,#BAMProfiler#,288

Before Change

        for contig in self.contigs:
            for gene_callers_id in contig.SCV_profiles:
                for codon_order in contig.SCV_profiles[gene_callers_id]:
                    e = contig.SCV_profiles[gene_callers_id][codon_order]

                    db_entry = {"sample_id": self.sample_id, "corresponding_gene_call": gene_callers_id}
                    db_entry["reference"] = e["reference"]
                    db_entry["coverage"] = e["coverage"]
                    db_entry["departure_from_reference"] = e["departure_from_reference"]
                    db_entry["codon_order_in_gene"] = codon_order
                    for codon in list(constants.codon_to_AA.keys()):
                        db_entry[codon] = e["frequencies"][codon]

                    variable_codons_table.append(db_entry)

        variable_codons_table.store()


    def generate_variabile_nts_table(self):

After Change

            for split in contig.splits:
                for gene_callers_id in split.SCV_profiles:

                    entries = zip(*split.SCV_profiles[gene_callers_id].values())

                    for entry in entries:
                        entry_dict = dict(zip(split.SCV_profiles[gene_callers_id].keys(), entry))
                        variable_codons_table.append(entry_dict)

        variable_codons_table.store()


    def generate_variabile_nts_table(self):

Instances