Writing a database to file

write_db can be used to write serialised objects to a database instance. In the below example, we use it to write the output of a composed process to disk.

from cogent3 import get_app, open_data_store

dstore = open_data_store("data", suffix="fasta", limit=2)

reader = get_app("load_aligned", format="fasta", moltype="dna")
min_length = get_app("min_length", 300)
out_dstore = open_data_store(f"{path_to_dir}.sqlitedb", mode="w")
writer = get_app("write_db", out_dstore)

process = reader + min_length + writer
result = process.apply_to(dstore)
result.describe

Locked to the current process.

record type	number
completed	0
not_completed	2
logs	1

3 rows x 2 columns

Note that out_dstore and result are the same instance.

out_dstore is result

True