def test_write_db(self):
"""writing with overwrite in MPI should reset db"""
dstore = io_app.get_data_store("data", suffix="fasta")
members = dstore.filtered(
callback=lambda x: "brca1.fasta" not in x.split("/"))
reader = io_app.load_unaligned()
aligner = align_app.align_to_ref()
writer = write_db("delme.tinydb", create=True, if_exists="overwrite")
process = reader + aligner + writer
r = process.apply_to(
members,
logger=False,
show_progress=False,
parallel=True,
par_kw=dict(use_mpi=True),
)
expect = [str(m) for m in process.data_store]
process.data_store.close()
# now get read only and check what's in there
result = io_app.get_data_store("delme.tinydb")
got = [str(m) for m in result]
assert got == expect
def test_apply_to(self):
"""correctly applies iteratively"""
from cogent3.core.alignment import SequenceCollection
dstore = io_app.get_data_store("data", suffix="fasta", limit=3)
reader = io_app.load_unaligned(format="fasta", moltype="dna")
got = reader.apply_to(dstore, show_progress=False)
self.assertEqual(len(got), len(dstore))
# should also be able to apply the results to another composable func
min_length = sample_app.min_length(10)
got = min_length.apply_to(got, show_progress=False, logger=True)
self.assertEqual(len(got), len(dstore))
# should work on a chained function
proc = reader + min_length
got = proc.apply_to(dstore, show_progress=False)
self.assertEqual(len(got), len(dstore))
# and works on a list of just strings
got = proc.apply_to([str(m) for m in dstore], show_progress=False)
self.assertEqual(len(got), len(dstore))
# or a single string
got = proc.apply_to(str(dstore[0]), show_progress=False)
self.assertEqual(len(got), 1)
self.assertIsInstance(got[0], SequenceCollection)
# raises ValueError if empty list
with self.assertRaises(ValueError):
proc.apply_to([])
# raises ValueError if list with empty string
with self.assertRaises(ValueError):
proc.apply_to(["", ""])
def test_load_unaligned(self):
"""load_unaligned returns degapped sequence collections"""
fasta_paths = io_app.get_data_store(self.basedir, suffix=".fasta", limit=2)
fasta_loader = io_app.load_unaligned(format="fasta")
for i, seqs in enumerate(map(fasta_loader, fasta_paths)):
self.assertIsInstance(seqs, SequenceCollection)
self.assertTrue("-" not in "".join(seqs.to_dict().values()))
self.assertEqual(seqs.info.source, fasta_paths[i])
# returns NotCompleted when it's given an alignment/sequence
# collection
got = fasta_loader(seqs)
self.assertIsInstance(got, NotCompleted)
