Sequence Collections Agent tutorial¶

Introduction¶

This tutorial will show you how to use the refget.RefgetDBAgent class to interact with a SQL database of sequence collections.

Under construction

The RefgetDBAgent() is parameterized through environment variables, which will provide the information it needs to connect to a SQL database.

In [ ]:

a_root = "test_fasta"
dbc = RefgetDBAgent()
print(f"SQL Engine: {dbc.engine}")

a_root = "test_fasta" dbc = RefgetDBAgent() print(f"SQL Engine: {dbc.engine}")

You can load some FASTA files into the database like this:

In [ ]:

demo_results = {}
for demo_file in DEMO_FILES:
    f = os.path.join(fa_root, demo_file)
    print("Fasta file to be loaded: {}".format(f))
    demo_results[f] = dbc.seqcol.add_from_fasta_file(f)
    print(demo_results[f])

demo_results = {} for demo_file in DEMO_FILES: f = os.path.join(fa_root, demo_file) print("Fasta file to be loaded: {}".format(f)) demo_results[f] = dbc.seqcol.add_from_fasta_file(f) print(demo_results[f])