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.. jupyter-execute::
:hide-code:
import set_working_directory
.. _write_db:
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.
.. jupyter-execute::
:hide-code:
from tempfile import TemporaryDirectory
tmpdir = TemporaryDirectory(dir=".")
path_to_dir = tmpdir.name
.. jupyter-execute::
:raises:
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
Note that ``out_dstore`` and ``result`` are the same instance.
.. jupyter-execute::
:raises:
out_dstore is result
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