def generate_variabile_nts_table(self):
if self.skip_SNV_profiling:
return
variable_nts_table = TableForVariability(self.profile_db_path,
progress=self.progress)
for contig in self.contigs:
for split in contig.splits:
for column_profile in list(split.column_profiles.values()):
# let's figure out more about this particular variable position
pos_in_contig = column_profile['pos_in_contig']
column_profile['in_partial_gene_call'], \
column_profile['in_complete_gene_call'],\
column_profile['base_pos_in_codon'] = self.get_nt_position_info(contig.name, pos_in_contig)
column_profile['sample_id'] = self.sample_id
column_profile[
'corresponding_gene_call'] = -1 # this means there is no gene call that corresponds to this
# nt position, which will be updated in the following lines.
# yeah, we use '-1', because genecaller ids start from 0 :/
column_profile['codon_order_in_gene'] = -1
# if this particular position (`pos_in_contig`) falls within a COMPLETE gene call,
# we would like to find out which unique gene caller id(s) match to this position.
if column_profile['in_complete_gene_call']:
corresponding_gene_caller_ids = self.get_corresponding_gene_caller_ids_for_base_position(
contig.name, pos_in_contig)
# if there are more than one corresponding gene call, this usually indicates an assembly error
# just to be on the safe side, we will not report a corresopnding unique gene callers id for this
# position
if len(corresponding_gene_caller_ids) == 1:
# if we are here, it means this nucleotide position is in a complete gene call. we will do two things here.
# first, we will store the gene_callers_id that corresponds to this nt position, and then we will store the
# order of the corresponding codon in the gene for this nt position.
gene_callers_id = corresponding_gene_caller_ids[0]
column_profile[
'corresponding_gene_call'] = gene_callers_id
column_profile[
'codon_order_in_gene'] = self.get_corresponding_codon_order_in_gene(
gene_callers_id, contig.name,
pos_in_contig)
# save this information for later use
self.codons_in_genes_to_profile_SCVs.add(
(gene_callers_id,
column_profile['codon_order_in_gene']), )
variable_nts_table.append(column_profile)
variable_nts_table.store()
self.layer_additional_data[
'num_SNVs_reported'] = variable_nts_table.num_entries
self.layer_additional_keys.append('num_SNVs_reported')
def generate_variabile_nts_table(self):
if self.skip_SNV_profiling:
return
variable_nts_table = TableForVariability(self.profile_db_path, progress=null_progress)
for contig in self.contigs:
for split in contig.splits:
for column_profile in list(split.column_profiles.values()):
variable_nts_table.append(column_profile)
variable_nts_table.store()
def generate_variabile_nts_table(self):
if self.skip_SNV_profiling:
return
variable_nts_table = TableForVariability(self.profile_db_path, progress=null_progress)
for contig in self.contigs:
for split in contig.splits:
for column_profile in list(split.column_profiles.values()):
variable_nts_table.append(column_profile)
variable_nts_table.store()