def test_basic_search():
client = biosnake.Biosnake()
db = client.databases.create("test", "Test database", TEST_INPUT_FILE)
assert db.description == "Test database"
assert db.name == "test"
search_results = db.search(
[
"ACTAGCTCAGTCAACTAGCTCAGTCCTCAGTCAACTAGCTCAGTCTATATATATACAAC",
"ACTAGCTCAGTCAACTAGCTCAGTCCTCAGTCAACTAGCT",
"ACTAGCTCAGTCAACTAGCT",
"ACTAGCTCAGT",
],
search_type="nucleotides",
headers=[
"query_sequence_id", "target_sequence_id", "sequence_identity",
"target_sequence_aligned"
],
)
search_results.dataframe.to_csv('hujemuje.csv')
import biosnake
#
# Demonstration of basic biosnake2 operations
#
# Create a client
client = biosnake.Biosnake()
# Create a database from fasta file
# Here we specify name of the database, description and input file
# (The input can also be a Seq/SeqRecord list/iterator/etc.)
client.databases.create("test", "Test database", "a.fasta")
# Get description of the database
print(client.databases[0].description)
# Perform search on a database
# Note that the search queries can be a string with a patch to the FASTA file with queries
results = client.databases[0].search(
[
"ACTAGCTCAGTCAACTAGCTCAGTCCTCAGTCAACTAGCTCAGTCTATATATATACAAC",
"ACTAGCTCAGTCAACTAGCTCAGTCCTCAGTCAACTAGCT",
"ACTAGCTCAGTCAACTAGCT",
"ACTAGCTCAGT",
],
search_type="nucleotides",
headers=[
"query_sequence_id", "target_sequence_id", "sequence_identity",
"target_sequence_aligned"
],
def test_empty():
client = biosnake.Biosnake()
client.databases.create("test", "Test database", "./example/a.fasta")