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 profile_contig_worker(self, available_index_queue, output_queue):
bam_file = pysam.Samfile(self.input_file_path, 'rb')
while True:
index = available_index_queue.get(True)
contig_name = self.contig_names[index]
contig = contigops.Contig(contig_name)
contig.length = self.contig_lengths[index]
contig.split_length = self.a_meta['split_length']
contig.min_coverage_for_variability = self.min_coverage_for_variability
contig.skip_SNV_profiling = self.skip_SNV_profiling
contig.report_variability_full = self.report_variability_full
contig.ignore_orphans = not self.include_orphans
contig.max_coverage_depth = self.max_coverage_depth
# populate contig with empty split objects and
for split_name in self.contig_name_to_splits[contig_name]:
s = self.splits_basic_info[split_name]
split_sequence = self.contig_sequences[contig_name][
'sequence'][s['start']:s['end']]
split = contigops.Split(split_name, split_sequence,
contig_name, s['order_in_parent'],
s['start'], s['end'])
contig.splits.append(split)
# analyze coverage for each split
contig.analyze_coverage(bam_file)
# test the mean coverage of the contig.
if contig.coverage.mean < self.min_mean_coverage:
output_queue.put(None)
continue
if not self.skip_SNV_profiling:
contig.analyze_auxiliary(bam_file)
codons_in_genes_to_profile_SCVs = set([])
for split in contig.splits:
for column_profile in list(split.column_profiles.values()):
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
codons_in_genes_to_profile_SCVs.add(
(gene_callers_id,
column_profile['codon_order_in_gene']), )
codon_frequencies = bamops.CodonFrequencies()
codons_in_genes_to_profile_SCVs_dict = {}
for gene_callers_id, codon_order in 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']
contig.codon_frequencies_dict[
gene_callers_id] = codon_frequencies.process_gene_call(
bam_file, gene_call,
self.contig_sequences[contig_name]['sequence'],
codons_to_profile)
output_queue.put(contig)
for split in contig.splits:
del split.coverage
del split.auxiliary
del split
del contig.splits[:]
del contig.coverage
del contig
# we are closing this object here for clarity, although w
# are not really closing it since the code never reaches here
# and the worker is killed by its parent:
bam_file.close()
return