def merge_variable_codons_tables(self):
variable_codons_table = TableForCodonFrequencies(self.merged_profile_db_path, progress=self.progress)
for input_profile_db_path in self.profile_dbs_info_dict:
sample_profile_db = dbops.ProfileDatabase(input_profile_db_path, quiet=True)
sample_variable_codons_table = sample_profile_db.db.get_table_as_list_of_tuples(tables.variable_codons_table_name, tables.variable_codons_table_structure)
sample_profile_db.disconnect()
for tpl in sample_variable_codons_table:
entry = tuple([variable_codons_table.next_id(tables.variable_codons_table_name)] + list(tpl[1:]))
variable_codons_table.db_entries.append(entry)
variable_codons_table.store()
def merge_variable_codons_tables(self):
variable_codons_table = TableForCodonFrequencies(self.merged_profile_db_path, progress=self.progress)
for input_profile_db_path in self.profile_dbs_info_dict:
sample_profile_db = dbops.ProfileDatabase(input_profile_db_path, quiet=True)
sample_variable_codons_table = sample_profile_db.db.get_table_as_list_of_tuples(tables.variable_codons_table_name, tables.variable_codons_table_structure)
sample_profile_db.disconnect()
for tpl in sample_variable_codons_table:
entry = tuple([variable_codons_table.next_id(tables.variable_codons_table_name)] + list(tpl[1:]))
variable_codons_table.db_entries.append(entry)
variable_codons_table.store()
def generate_variabile_codons_table(self):
if self.skip_SNV_profiling or not self.profile_SCVs:
return
variable_codons_table = TableForCodonFrequencies(
self.profile_db_path, progress=self.progress)
codon_frequencies = bamops.CodonFrequencies()
codons_in_genes_to_profile_SCVs_dict = {}
for gene_callers_id, codon_order in self.codons_in_genes_to_profile_SCVs:
if gene_callers_id not in codons_in_genes_to_profile_SCVs_dict:
codons_in_genes_to_profile_SCVs_dict[gene_callers_id] = set([])
codons_in_genes_to_profile_SCVs_dict[gene_callers_id].add(
codon_order)
gene_caller_ids_to_profile = list(
codons_in_genes_to_profile_SCVs_dict.keys())
for i in range(len(gene_caller_ids_to_profile)):
gene_callers_id = gene_caller_ids_to_profile[i]
codons_to_profile = codons_in_genes_to_profile_SCVs_dict[
gene_callers_id]
gene_call = self.genes_in_contigs_dict[gene_callers_id]
contig_name = gene_call['contig']
codon_frequencies_dict = codon_frequencies.process_gene_call(
self.bam, gene_call,
self.contig_sequences[contig_name]['sequence'],
codons_to_profile)
for codon_order in codon_frequencies_dict:
e = codon_frequencies_dict[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()
# clear contents of set
self.codons_in_genes_to_profile_SCVs.clear()
if len(codon_frequencies.not_reported_items):
items = codon_frequencies.not_reported_items
self.run.warning(
"The profiler of single-codon variants failed to report anything for a\
total of %d items, because they looked weird to anvi'o :( Here is a list\
of those that did ended up being ignored: '%s'."
% (len(items), ', '.join(items)))
def generate_variabile_codons_table(self):
if self.skip_SNV_profiling or not self.profile_SCVs:
return
variable_codons_table = TableForCodonFrequencies(
self.profile_db_path, progress=null_progress)
for contig in self.contigs:
for gene_callers_id in contig.codon_frequencies_dict:
for codon_order in contig.codon_frequencies_dict[
gene_callers_id]:
e = contig.codon_frequencies_dict[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_codons_table(self):
if self.skip_SNV_profiling or not self.profile_SCVs:
return
variable_codons_table = TableForCodonFrequencies(self.profile_db_path, progress=null_progress)
for contig in self.contigs:
for gene_callers_id in contig.codon_frequencies_dict:
for codon_order in contig.codon_frequencies_dict[gene_callers_id]:
e = contig.codon_frequencies_dict[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()