def store_contigs_buffer(self):
for contig in self.contigs:
self.total_length_of_all_contigs += contig.length
self.total_coverage_values_for_all_contigs += contig.coverage.mean * contig.length
# we will divide every abundance after profiling is done.
contig.abundance = contig.coverage.mean
for split in contig.splits:
split.abundance = split.coverage.mean
self.generate_variabile_nts_table()
self.generate_variabile_codons_table()
self.store_split_coverages()
# creating views in the database for atomic data we gathered during the profiling. Meren, please note
# that the first entry has a view_id, and the second one does not have one. I know you will look at this
# and be utterly confused 2 months from now. Please go read the description given in the dbops.py for the
# function create_new_view defined in the class TablesForViews.
view_data_splits, view_data_contigs = contigops.get_atomic_data_dicts(self.sample_id, self.contigs)
TablesForViews(self.profile_db_path).create_new_view(
data_dict=view_data_splits,
table_name='atomic_data_splits',
table_structure=t.atomic_data_table_structure,
table_types=t.atomic_data_table_types,
view_name='single',
append_mode=True)
TablesForViews(self.profile_db_path).create_new_view(
data_dict=view_data_contigs,
table_name='atomic_data_contigs',
table_structure=t.atomic_data_table_structure,
table_types=t.atomic_data_table_types,
view_name=None,
append_mode=True)
def store_contigs_buffer(self):
for contig in self.contigs:
self.total_length_of_all_contigs += contig.length
self.total_coverage_values_for_all_contigs += contig.coverage.mean * contig.length
# we will divide every abundance after profiling is done.
contig.abundance = contig.coverage.mean
for split in contig.splits:
split.abundance = split.coverage.mean
self.generate_variabile_nts_table()
self.generate_variabile_codons_table()
self.store_split_coverages()
# creating views in the database for atomic data we gathered during the profiling. Meren, please note
# that the first entry has a view_id, and the second one does not have one. I know you will look at this
# and be utterly confused 2 months from now. Please go read the description given in the dbops.py for the
# function create_new_view defined in the class TablesForViews.
view_data_splits, view_data_contigs = contigops.get_atomic_data_dicts(self.sample_id, self.contigs)
TablesForViews(self.profile_db_path).create_new_view(
data_dict=view_data_splits,
table_name='atomic_data_splits',
table_structure=t.atomic_data_table_structure,
table_types=t.atomic_data_table_types,
view_name='single',
append_mode=True)
TablesForViews(self.profile_db_path).create_new_view(
data_dict=view_data_contigs,
table_name='atomic_data_contigs',
table_structure=t.atomic_data_table_structure,
table_types=t.atomic_data_table_types,
view_name=None,
append_mode=True)
