def test_016_debug(self):
seqann = BioSeqAnn(debug={
"seqann": 5,
"align": 1,
"seq_search": 3,
"refdata": 2
})
self.assertTrue(seqann.debug)
self.assertEqual(seqann.verbosity, 5)
self.assertEqual(seqann.align_verbosity, 1)
self.assertEqual(seqann.seqsearch.verbosity, 3)
self.assertEqual(seqann.refdata.verbosity, 2)
seqann = BioSeqAnn(debug={"seqann": 2, "seq_search": 5})
self.assertTrue(seqann.debug)
self.assertEqual(seqann.verbosity, 2)
self.assertEqual(seqann.align_verbosity, 0)
self.assertEqual(seqann.seqsearch.verbosity, 5)
self.assertEqual(seqann.refdata.verbosity, 0)
seqann = BioSeqAnn(debug={"gfe": 2, "seq_search": 5})
self.assertTrue(seqann.debug)
self.assertTrue(seqann.gfe.verbose)
self.assertEqual(seqann.gfe.verbosity, 2)
self.assertEqual(seqann.seqsearch.verbosity, 5)
self.assertEqual(seqann.refdata.verbosity, 0)
seqann = BioSeqAnn(verbose=True, verbosity=3)
self.assertFalse(seqann.debug)
self.assertEqual(seqann.verbosity, 3)
self.assertEqual(seqann.align_verbosity, 3)
self.assertEqual(seqann.seqsearch.verbosity, 3)
self.assertEqual(seqann.refdata.verbosity, 3)
pass
def gfeNotation_post(sequence, locus, gene):
"""
gfeNotation_post
GFE notations associated with the sequence
:param locus: Valid HLA locus
:param sequence: Valid sequence
:param gene : Kir true or false
:rtype: Feature and gfe
"""
kir = gene
sequence = SeqRecord(seq=Seq(sequence['sequence']))
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter(
'%(asctime)s - %(name)-35s - %(levelname)-5s '
'- %(funcName)s %(lineno)d: - %(message)s')
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
gfe = GFE()
if kir:
seqann = BioSeqAnn(kir=True)
else:
seqann = BioSeqAnn()
try:
annotation = seqann.annotate(sequence)
except Exception as e:
print(e)
log_contents = log_capture_string.getvalue()
return Error("An error occured during the annotation",
log=log_contents.split("\n")), 404
try:
res_feature, res_gfe = gfe.get_gfe(annotation, locus)
except Exception as e:
print(e)
log_contents = log_capture_string.getvalue()
return Error("An error occurred in getting the gfe of annotation",
log=log_contents.split("\n")), 404
feats = []
for f in res_feature:
fn = Feature(accession=f.accession,
rank=f.rank,
term=f.term,
sequence=f.sequence)
feats.append(fn)
return {'gfe': res_gfe, 'feature': feats}
def test_001_align(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
# TODO *** NOT WORKING WITH NO LOCUS ***
# TODO *** FIX 3290 Alignments ***
# TODO *** GET ALIGNMENTS WORKING WITH DB SEQS ***
seqann = BioSeqAnn(server=server, align=True)
input_seq = self.data_dir + '/align_tests.fasta'
for ex in self.expected['align']:
i = int(ex['index'])
ex = self.expected['align'][i]
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
in_seq = list(SeqIO.parse(input_seq, "fasta"))[i]
annotation = seqann.annotate(in_seq, "HLA-A")
align = "".join(
[annotation.aligned[s] for s in annotation.aligned])
for i in range(0, len(align) - 1):
if str(i) in ex['diffs']:
self.assertEqual(list(align)[i], ex['diffs'][str(i)])
else:
if list(align)[i] != list(ex['alignment'])[i]:
print("FAILED:", allele, i,
list(align)[i],
list(ex['alignment'])[i])
self.assertEqual(list(align)[i], list(ex['alignment'])[i])
server.close()
def test_000_pygfe(self):
graph = Graph(neo4jurl, user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb)
seqann = BioSeqAnn(server=server, verbose=False)
seqann = "X"
#else:
# print
# seqann = BioSeqAnn()
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_features=False,
verbose=False,
load_all=True,
loci=["HLA-A"])
self.assertIsInstance(pygfe, pyGFE)
seqs = list(SeqIO.parse(self.data_dir + "/unknown_A.fasta", "fasta"))
typing = pygfe.type_from_seq("HLA-A", str(seqs[1].seq))
#self.assertEqual(typing.gfe, 'HLA-Aw770-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4')
self.assertEqual(typing.hla, 'HLA-A*01:01:01:01')
self.assertEqual(typing.status, "novel")
self.assertIsInstance(typing, Typing)
pass
def test_001_load_features(self):
graph = Graph(neo4jurl, user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=3307)
seqann = BioSeqAnn(server=server)
#else:
# seqann = BioSeqAnn()
pygfe = pyGFE(graph=graph,
seqann=seqann,
verbose=True,
load_features=True,
verbosity=2,
loci=["HLA-A"])
self.assertIsInstance(pygfe, pyGFE)
self.assertGreater(len(pygfe.gfe.structures), 1)
self.assertGreater(len(pygfe.gfe.all_feats), 1)
self.assertTrue('HLA-A' in pygfe.gfe.structures)
self.assertFalse('HLA-Z' in pygfe.gfe.structures)
pass
def test_004_loader3(self):
start = time.time()
graph = Graph(neo4jurl, user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb, port=3307)
seqann = BioSeqAnn(server=server, verbose=True)
pygfe = pyGFE(graph=graph,
seqann=seqann,
verbose=False,
load_features=False,
load_gfe2hla=True,
load_seq2hla=True,
load_gfe2feat=True,
loci=["HLA-A"])
self.assertIsInstance(pygfe, pyGFE)
seqs = list(SeqIO.parse(self.data_dir + "/known_A.fasta", "fasta"))
#typing1 = pygfe.type_from_seq("HLA-A", str(seqs[0].seq), "3.20.0")
typing2 = pygfe.type_from_seq("HLA-A", str(seqs[0].seq), "3.31.0")
server.close()
end = time.time()
time_taken = end - start
print("TIME TAKEN: " + str(time_taken))
self.assertEqual(typing2.hla, 'HLA-A*01:01:01:01')
self.assertEqual(typing2.status, "documented")
self.assertIsInstance(typing2, Typing)
# self.assertEqual(typing1.hla, 'HLA-A*01:01:01:01')
# self.assertEqual(typing1.status, "documented")
# self.assertIsInstance(typing1, Typing)
pass
def test_012_exact(self):
seqann = BioSeqAnn(verbose=False, verbosity=verbosity, pid="007_exact")
input_seq = self.data_dir + '/exact_seqs.fasta'
for ex in self.expected['exact']:
i = int(ex['index'])
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
in_seq = list(SeqIO.parse(input_seq, "fasta"))[i]
annotation = seqann.annotate(in_seq, locus)
self.assertTrue(annotation.exact)
self.assertIsNone(annotation.features)
self.assertEqual(annotation.method, "match")
self.assertIsInstance(annotation, Annotation)
self.assertTrue(annotation.complete_annotation)
self.assertGreater(len(annotation.annotation.keys()), 1)
expected = seqann.refdata.hlaref[allele]
expected_seqs = get_features(expected)
self.assertGreater(len(annotation.structure), 1)
for feat in annotation.structure:
self.assertIsInstance(feat, Feature)
self.assertEqual(annotation.gfe, ex['gfe'])
self.assertGreater(len(expected_seqs.keys()), 1)
self.assertGreater(len(annotation.annotation.keys()), 1)
for feat in expected_seqs:
if feat not in annotation.annotation:
self.assertEqual(feat, None)
else:
self.assertEqual(str(expected_seqs[feat]),
str(annotation.annotation[feat]))
pass
def test_005_A(self):
#start = time.time()
graph = Graph(neo4jurl, user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=3307)
seqann = BioSeqAnn(server=server, dbversion="3200", verbose=True)
pickle_file1 = "unique_db-feats.pickle"
pickle_file2 = "feature-service.pickle"
pickle_gfe2feat = "gfe2feat.pickle"
pickle_file3 = "gfe2hla.pickle"
pickle_file4 = "seq2hla.pickle"
with open(pickle_gfe2feat, 'rb') as handle1:
gfe_feats = pickle.load(handle1)
with open(pickle_file1, 'rb') as handle1:
feats = pickle.load(handle1)
with open(pickle_file2, 'rb') as handle2:
cached_feats = pickle.load(handle2)
with open(pickle_file3, 'rb') as handle3:
gfe2hla = pickle.load(handle3)
with open(pickle_file4, 'rb') as handle:
seq2hla = pickle.load(handle)
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_features=False,
verbose=True,
features=feats,
seq2hla=seq2hla,
gfe2hla=gfe2hla,
gfe_feats=gfe_feats,
cached_features=cached_feats,
loci=["HLA-DQB1"])
self.assertIsInstance(pygfe, pyGFE)
seqs = list(SeqIO.parse(self.data_dir + "/A_fail.fasta", "fasta"))
typing1 = pygfe.type_from_seq("HLA-DQB1", str(seqs[1].seq), "3.20.0")
#typing2 = pygfe.type_from_seq("HLA-DRB1", str(seqs[0].seq), "3.31.0")
#typing2 = pygfe.type_from_seq("HLA-DRB1", str(seqs[0].seq), "3.31.0")
#end = time.time()
#time_taken = end - start
print(typing1)
#print("=====")
#print(typing2)
# self.assertEqual(typing2.hla, 'HLA-A*01:01:01:01')
# self.assertEqual(typing2.status, "documented")
#self.assertIsInstance(typing2, Typing)
# self.assertEqual(typing1.hla, 'HLA-A*01:01:01:01')
# self.assertEqual(typing1.status, "documented")
self.assertIsInstance(typing1, Typing)
pass
def test_020_skip(self):
# import logging
# logging.basicConfig(format='%(asctime)s - %(name)-35s - %(levelname)-5s - %(funcName)s %(lineno)d: - %(message)s',
# datefmt='%m/%d/%Y %I:%M:%S %p',
# level=logging.INFO)
seqann = BioSeqAnn(verbose=False)
refdata = seqann.refdata
test_list = [
'HLA-C*07:241', 'HLA-A*01:07', 'HLA-A*01:01:59',
'HLA-A*01:09:01:01', 'HLA-A*02:545', 'HLA-A*29:13',
'HLA-A*24:03:02', 'HLA-A*02:544', 'HLA-DQA1*04:01:01:01',
'HLA-A*01:217', 'HLA-A*01:22N', 'HLA-B*51:42', 'HLA-C*03:04:05',
'HLA-A*01:01:01:04', 'HLA-A*01:09:01:01', 'HLA-B*82:01'
]
for seqname in refdata.hlaref:
if seqname not in test_list:
continue
print(seqname)
seqrec = refdata.hlaref[seqname]
locus = seqrec.description.split("*")[0]
ann1 = seqann.annotate(seqrec, locus=locus)
ann2 = seqann.annotate(seqrec, locus=locus, skip=[seqname])
self.assertTrue(ann1.exact)
self.assertEqual(len(ann2.annotation), len(ann1.annotation))
self.assertEqual(ann1.gfe, ann2.gfe)
self.assertGreater(len(ann2.structure), 1)
for feat in ann2.structure:
self.assertIsInstance(feat, Feature)
for f in ann1.annotation:
self.assertTrue(f in ann2.annotation)
seq1 = str(ann1.annotation[f])
seq2 = str(ann2.annotation[f].seq)
self.assertEqual(seq1, seq2)
pass
def test_005_picklefiles(self):
graph = Graph("http://ec2-34-207-175-160.compute-1.amazonaws.com:80", user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server, verbose=False)
gfe = GFE()
#cached_feats = gfe.all_feats
# print("Finished loading cached_feats")
# pickle_service = "feature-service.pickle"
# with open(pickle_service, 'wb') as handle2:
# pickle.dump(cached_feats, handle2, protocol=pickle.HIGHEST_PROTOCOL)
feat_df = pd.DataFrame(graph.data(all_feats()))
feat_df['ID'] = feat_df.apply(lambda row: ":".join([row['DB'],
row['LOC'],
str(row['RANK']),
row['TERM'],
row['SEQ']]),
axis=1)
feats = feat_df[['ID', 'ACCESSION']].set_index('ID').to_dict()['ACCESSION']
print("Finished loading feats")
pickle_feats = "unique_db-feats.pickle"
with open(pickle_feats, 'wb') as handle1:
pickle.dump(feats, handle1, protocol=pickle.HIGHEST_PROTOCOL)
gfedb = GfeDB(graph=graph, persist=False, verbose=False)
act = ACT(gfedb=gfedb, seqann=seqann, load_gfe2hla=True,
load_gfe2feat=True,
load_seq2hla=True, gfe=gfe)
print("Finished loading all!!")
gfe2hla = act.gfe2hla
seq2hla = act.seq2hla
gfe2feat = act.gfe_feats
pickle_gfe2feat = "gfe2feat.pickle"
with open(pickle_gfe2feat, 'wb') as handle5:
pickle.dump(gfe2feat, handle5, protocol=pickle.HIGHEST_PROTOCOL)
pickle_gfe2hla = "gfe2hla.pickle"
with open(pickle_gfe2hla, 'wb') as handle3:
pickle.dump(gfe2hla, handle3, protocol=pickle.HIGHEST_PROTOCOL)
pickle_seq2hla = "seq2hla.pickle"
with open(pickle_seq2hla, 'wb') as handle4:
pickle.dump(seq2hla, handle4, protocol=pickle.HIGHEST_PROTOCOL)
pass
def test_002_noserver(self):
seqann = BioSeqAnn(verbose=False,
verbosity=verbosity,
pid="002_noserver")
self.assertIsInstance(seqann, BioSeqAnn)
self.assertIsInstance(seqann.refdata, ReferenceData)
self.assertGreater(len(seqann.refdata.hla_names), 10)
self.assertEqual(seqann.refdata.structure_max['HLA-A'], 17)
self.assertFalse(seqann.refdata.server_avail)
self.assertGreater(len(seqann.refdata.seqref), 0)
self.assertGreater(len(seqann.refdata.hlaref), 0)
pass
def test_009_partialambigserv(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server,
verbose=False,
verbosity=verbosity,
pid="006_partialambig")
input_seq = self.data_dir + '/partial_ambig.fasta'
for ex in self.expected['partial_ambig']:
i = int(ex['index'])
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
print(str(i), allele)
in_seq = list(SeqIO.parse(input_seq, "fasta"))[i]
ann = seqann.annotate(in_seq, locus)
self.assertTrue(ann.complete_annotation)
self.assertEqual(ann.method, ex['method'])
self.assertFalse(ann.blocks)
self.assertIsInstance(ann, Annotation)
self.assertTrue(ann.complete_annotation)
self.assertGreater(len(ann.annotation.keys()), 1)
db = seqann.refdata.server[seqann.refdata.dbversion + "_" + loc]
expected = db.lookup(name=allele)
expected_seqs = get_features(expected)
self.assertGreater(len(expected_seqs.keys()), 1)
self.assertGreater(len(ann.annotation.keys()), 1)
self.assertEqual(ann.gfe, ex['gfe'])
self.assertGreater(len(ann.structure), 1)
for feat in ann.structure:
self.assertIsInstance(feat, Feature)
# Make sure only mapped feats exist
for mf in ex['missing_feats']:
self.assertFalse(mf in ann.annotation)
for feat in ex['feats']:
if feat in ex['diff']:
self.assertNotEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
else:
self.assertEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
server.close()
pass
def test_005_insertionserv(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server,
verbose=False,
verbosity=verbosity,
pid="004_insertion")
input_seq = self.data_dir + '/insertion_seqs.fasta'
for ex in self.expected['insertion']:
i = int(ex['index'])
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
in_seq = list(SeqIO.parse(input_seq, "fasta"))[i]
ann = seqann.annotate(in_seq, locus)
self.assertEqual(ann.method, "nt_search")
self.assertFalse(ann.missing)
self.assertFalse(ann.blocks)
self.assertIsInstance(ann, Annotation)
self.assertTrue(ann.complete_annotation)
self.assertGreater(len(ann.annotation.keys()), 1)
db = seqann.refdata.server[seqann.refdata.dbversion + "_" + loc]
expected = db.lookup(name=allele)
self.assertEqual(ann.gfe, ex['gfe'])
self.assertGreater(len(ann.structure), 1)
for feat in ann.structure:
self.assertIsInstance(feat, Feature)
n_diffs = 0
expected_seqs = get_features(expected)
self.assertGreater(len(expected_seqs.keys()), 1)
for feat in expected_seqs:
if feat not in ann.annotation:
self.assertEqual(feat, None)
else:
if feat in ex['diff']:
n_diffs += 1
self.assertNotEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
diff_len = len(str(ann.annotation[feat].seq)) - \
len(str(expected_seqs[feat]))
self.assertEqual(diff_len, ex['lengths'][feat])
else:
self.assertEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
self.assertEqual(n_diffs, len(ex['diff']))
server.close()
pass
def test_021_stringseq(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server,
verbose=False,
verbosity=verbosity,
pid="015_stringseq")
input_seq = self.data_dir + '/exact_seqs.fasta'
ex = self.expected['exact'][0]
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
in_seqrec = list(SeqIO.parse(input_seq, "fasta"))[0]
in_str = str(in_seqrec.seq)
in_seq = in_seqrec.seq
ann_str = seqann.annotate(in_str, locus)
ann_seq = seqann.annotate(in_seq, locus)
for annotation in [ann_str, ann_seq]:
self.assertTrue(annotation.exact)
self.assertIsNone(annotation.features)
self.assertEqual(annotation.method, "match")
self.assertIsInstance(annotation, Annotation)
self.assertTrue(annotation.complete_annotation)
self.assertGreater(len(annotation.annotation.keys()), 1)
db = seqann.refdata.server[seqann.refdata.dbversion + "_" + loc]
expected = db.lookup(name=allele)
expected_seqs = get_features(expected)
self.assertEqual(annotation.gfe, ex['gfe'])
self.assertGreater(len(expected_seqs.keys()), 1)
self.assertGreater(len(annotation.annotation.keys()), 1)
self.assertGreater(len(annotation.structure), 1)
for feat in annotation.structure:
self.assertIsInstance(feat, Feature)
for feat in expected_seqs:
if feat not in annotation.annotation:
self.assertEqual(feat, None)
else:
self.assertEqual(str(expected_seqs[feat]),
str(annotation.annotation[feat]))
server.close()
pass
def test_001_pygfe(self):
graph = Graph(neo4jurl, user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
pickle_file1 = "unique_db-feats.pickle"
pickle_file2 = "feature-service.pickle"
pickle_gfe2feat = "gfe2feat.pickle"
pickle_file3 = "gfe2hla.pickle"
pickle_file4 = "seq2hla.pickle"
with open(pickle_gfe2feat, 'rb') as handle1:
gfe_feats = pickle.load(handle1)
with open(pickle_file1, 'rb') as handle1:
feats = pickle.load(handle1)
with open(pickle_file2, 'rb') as handle2:
cached_feats = pickle.load(handle2)
with open(pickle_file3, 'rb') as handle3:
gfe2hla = pickle.load(handle3)
with open(pickle_file4, 'rb') as handle:
seq2hla = pickle.load(handle)
seqann = BioSeqAnn(verbose=False, cached_features=cached_feats, align=True)
pygfe = pyGFE(graph=graph,
seqann=seqann,
gfe_feats=gfe_feats,
gfe2hla=gfe2hla,
seq2hla=seq2hla,
features=feats,
verbose=False)
self.assertIsInstance(pygfe, pyGFE)
seqs = list(SeqIO.parse(self.data_dir + "/unknown_A.fasta", "fasta"))
typing = pygfe.type_from_seq("HLA-A", str(seqs[1].seq))
print(typing)
#self.assertEqual(typing.gfe, 'HLA-Aw770-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4')
self.assertEqual(typing.hla, 'HLA-A*01:01:01:01')
self.assertEqual(typing.status, "novel")
self.assertIsInstance(typing, Typing)
pass
def test_015_fail(self):
input_seq = self.data_dir + '/failed_seqs.fasta'
in_seq = list(SeqIO.parse(input_seq, "fasta"))[0]
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server,
verbose=False,
verbosity=verbosity,
pid="011_fail")
self.assertFalse(seqann.refdata.seqref)
self.assertFalse(seqann.refdata.hlaref)
annotation = seqann.annotate(in_seq)
self.assertFalse(annotation)
server.close()
pass
def test_001_seqann(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server,
verbose=False,
verbosity=verbosity,
pid="001_seqann")
self.assertIsInstance(seqann, BioSeqAnn)
self.assertIsInstance(seqann.refdata, ReferenceData)
self.assertIsInstance(seqann.refdata, ReferenceData)
self.assertGreater(len(seqann.refdata.hla_names), 10)
self.assertEqual(seqann.refdata.structure_max['HLA-A'], 17)
self.assertTrue(seqann.refdata.server_avail)
server.close()
pass
def test_013_nomatch(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
seqann = BioSeqAnn(server=server,
verbose=False,
verbosity=verbosity,
pid="009_nomatch")
self.assertIsInstance(seqann, BioSeqAnn)
input_seq = self.data_dir + '/nomatch_seqs.fasta'
in_seq = list(SeqIO.parse(input_seq, "fasta"))[0]
annotation = seqann.annotate(in_seq, "HLA-A")
self.assertIsInstance(annotation, Annotation)
self.assertGreater(len(annotation.annotation.keys()), 1)
self.assertTrue(annotation.complete_annotation)
server.close()
pass
def test_006_insertion(self):
seqann = BioSeqAnn(verbosity=verbosity, pid="004_insertion")
input_seq = self.data_dir + '/insertion_seqs.fasta'
for ex in self.expected['insertion']:
i = int(ex['index'])
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
in_seq = list(SeqIO.parse(input_seq, "fasta"))[i]
ann = seqann.annotate(in_seq, locus)
self.assertEqual(ann.method, "nt_search")
self.assertFalse(ann.missing)
self.assertFalse(ann.blocks)
self.assertIsInstance(ann, Annotation)
self.assertTrue(ann.complete_annotation)
self.assertGreater(len(ann.annotation.keys()), 1)
expected = seqann.refdata.hlaref[allele]
self.assertEqual(ann.gfe, ex['gfe'])
self.assertGreater(len(ann.structure), 1)
for feat in ann.structure:
self.assertIsInstance(feat, Feature)
n_diffs = 0
expected_seqs = get_features(expected)
self.assertGreater(len(expected_seqs.keys()), 1)
for feat in expected_seqs:
if feat not in ann.annotation:
self.assertEqual(feat, None)
else:
if feat in ex['diff']:
n_diffs += 1
self.assertNotEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
diff_len = len(str(ann.annotation[feat].seq)) - \
len(str(expected_seqs[feat]))
self.assertEqual(diff_len, ex['lengths'][feat])
else:
self.assertEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
self.assertEqual(n_diffs, len(ex['diff']))
pass
def test_010_partialambig(self):
seqann = BioSeqAnn(verbose=False,
verbosity=verbosity,
pid="006_partialambig")
input_seq = self.data_dir + '/partial_ambig.fasta'
for ex in self.expected['partial_ambig']:
i = int(ex['index'])
locus = ex['locus']
allele = ex['name']
hla, loc = locus.split("-")
in_seq = list(SeqIO.parse(input_seq, "fasta"))[i]
ann = seqann.annotate(in_seq, locus)
self.assertTrue(ann.complete_annotation)
self.assertEqual(ann.method, ex['method'])
self.assertFalse(ann.blocks)
self.assertIsInstance(ann, Annotation)
self.assertTrue(ann.complete_annotation)
self.assertGreater(len(ann.annotation.keys()), 1)
expected = seqann.refdata.hlaref[allele]
expected_seqs = get_features(expected)
self.assertGreater(len(expected_seqs.keys()), 1)
self.assertGreater(len(ann.annotation.keys()), 1)
self.assertEqual(ann.gfe, ex['gfe'])
self.assertGreater(len(ann.structure), 1)
for feat in ann.structure:
self.assertIsInstance(feat, Feature)
# Make sure only mapped feats exist
for mf in ex['missing_feats']:
self.assertFalse(mf in ann.annotation)
for feat in ex['feats']:
if feat in ex['diff']:
self.assertNotEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
else:
self.assertEqual(str(expected_seqs[feat]),
str(ann.annotation[feat].seq))
pass
def test_017_logging(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
with self.assertLogs(level='INFO') as cm:
seqann = BioSeqAnn(server=server, verbose=True)
input_seq = self.data_dir + '/failed_seqs.fasta'
in_seq = list(SeqIO.parse(input_seq, "fasta"))[0]
annotation = seqann.annotate(in_seq)
self.assertFalse(annotation)
self.assertGreater(len(cm.output), 1)
error = list(cm.output)[len(cm.output) - 1].split(":")[0]
error_msg = list(cm.output)[len(cm.output) - 1].split("-")[1]
self.assertEqual(error, "ERROR")
self.assertEqual(error_msg, " Locus could not be determined!")
server.close()
pass
def test_018_nogfe(self):
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=biosqlport)
with self.assertLogs(level='INFO') as cm:
seqann = BioSeqAnn(server=server, verbose=True)
input_seq = self.data_dir + '/failed_seqs.fasta'
in_seq = list(SeqIO.parse(input_seq, "fasta"))[1]
annotation = seqann.annotate(in_seq)
self.assertFalse(annotation.gfe)
self.assertFalse(annotation.structure)
self.assertTrue(annotation.annotation)
self.assertGreater(len(cm.output), 2)
error = list(cm.output)[0].split(":")[0]
error_msg = list(cm.output)[0].split("-")[1]
self.assertEqual(error, "WARNING")
self.assertEqual(error_msg, " Sequence alphabet contains non DNA")
server.close()
pass
def typeseq_get(sequence,
locus=None,
imgthla_version="3.31.0",
neo4j_url="http://neo4j.b12x.org:80",
user='******',
password='******'): # noqa: E501
"""typeseq_get
Get HLA and GFE from consensus sequence or GFE notation # noqa: E501
:param locus: Valid HLA locus
:type locus: str
:param sequence: Consensus sequence
:type sequence: str
:param imgthla_version: IMGT/HLA DB Version
:type imgthla_version: str
:param neo4j_url: URL for the neo4j graph
:type neo4j_url: str
:param user: Username for the neo4j graph
:type user: str
:param password: Password for the neo4j graph
:type password: str
:param verbose: Flag for running service in verbose
:type verbose: bool
:rtype: Typing
"""
global seqanns
global gfe_feats
global gfe2hla
global seq2hla
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter(
'%(asctime)s - %(name)-35s - %(levelname)-5s - %(funcName)s %(lineno)d: - %(message)s'
)
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
if not re.match(".", imgthla_version):
imgthla_version = ".".join([
list(imgthla_version)[0], "".join(list(imgthla_version)[1:3]),
list(imgthla_version)[3]
])
db = "".join(imgthla_version.split("."))
if db in seqanns:
seqann = seqanns[db]
else:
seqann = BioSeqAnn(verbose=True,
safemode=True,
dbversion=db,
verbosity=3)
seqanns.update({db: seqann})
try:
graph = Graph(neo4j_url, user=user, password=password, bolt=False)
except ServiceUnavailable as err:
log_contents = log_capture_string.getvalue()
log_data = log_contents.split("\n")
log_data.append(str(err))
return Error("Failed to connect to graph", log=log_data), 404
if (not isinstance(gfe_feats, DataFrame)
or not isinstance(seq2hla, DataFrame)):
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_gfe2hla=True,
load_seq2hla=True,
load_gfe2feat=True,
verbose=True)
gfe_feats = pygfe.gfe_feats
seq2hla = pygfe.seq2hla
gfe2hla = pygfe.gfe2hla
else:
pygfe = pyGFE(graph=graph,
seqann=seqann,
gfe2hla=gfe2hla,
gfe_feats=gfe_feats,
seq2hla=seq2hla,
verbose=True)
try:
typing = pygfe.type_from_seq(locus, sequence, imgthla_version)
except:
log_contents = log_capture_string.getvalue()
return Error("Type with alignment failed",
log=log_contents.split("\n")), 404
if isinstance(typing, Error):
log_contents = log_capture_string.getvalue()
typing.log = log_contents.split("\n")
return typing, 404
if not typing:
log_contents = log_capture_string.getvalue()
return Error("Type sequence failed", log=log_contents.split("\n")), 404
typing.gfedb_version = "2.0.0"
return typing
def gfecreate_post(locus,
sequence,
imgt_version,
neo4j_url=neo_dict['neo4j_url'],
user=neo_dict['user'],
password=neo_dict['password']): # noqa: E501
"""gfecreate_post
Get all features associated with a locus
:param locus: Valid HLA locus
:param sequence: Valid sequence
:param imgt_version : db version
:rtype: Typing
"""
imgthla_version = imgt_version
global seqanns
global gfe_feats
global gfe2hla
global seq2hla
pygfe = pyGFE()
sequence = sequence['sequence']
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter('%(asctime)s - %(name)-35s - %(levelname)-5s'
' - %(funcName)s %(lineno)d: - %(message)s')
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
if not re.match(".", imgthla_version):
imgthla_version = ".".join([
list(imgthla_version)[0], "".join(list(imgthla_version)[1:3]),
list(imgthla_version)[3]
])
db = "".join(imgthla_version.split("."))
if db in seqanns:
seqann = seqanns[db]
else:
seqann = BioSeqAnn(verbose=True,
safemode=True,
dbversion=db,
verbosity=3)
seqanns.update({db: seqann})
try:
graph = Graph(neo4j_url, user=user, password=password, bolt=False)
except ServiceUnavailable as err:
log_contents = log_capture_string.getvalue()
log_data = log_contents.split("\n")
log_data.append(str(err))
return Error("Failed to connect to graph", log=log_data), 404
if (not isinstance(gfe_feats, DataFrame)
or not isinstance(seq2hla, DataFrame)):
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_gfe2hla=True,
load_seq2hla=True,
load_gfe2feat=True,
verbose=True)
gfe_feats = pygfe.gfe_feats
seq2hla = pygfe.seq2hla
gfe2hla = pygfe.gfe2hla
else:
pygfe = pyGFE(graph=graph,
seqann=seqann,
gfe2hla=gfe2hla,
gfe_feats=gfe_feats,
seq2hla=seq2hla,
verbose=True)
try:
typing = pygfe.gfe_create(locus=locus,
sequence=sequence,
imgtdb_version=db)
except Exception as e:
print(e)
log_contents = log_capture_string.getvalue()
return Error("Type with alignment failed",
log=log_contents.split("\n")), 404
if isinstance(typing, Error):
log_contents = log_capture_string.getvalue()
typing.log = log_contents.split("\n")
return typing, 404
if not typing:
log_contents = log_capture_string.getvalue()
return Error("Type with alignment failed",
log=log_contents.split("\n")), 404
structute_feats = []
for f in typing['structure']:
fn = Feature(accession=f.accession,
rank=f.rank,
term=f.term,
sequence=f.sequence)
structute_feats.append(fn)
anno_feats = []
for f in typing['annotation'].structure:
fn = Feature(accession=f.accession,
rank=f.rank,
term=f.term,
sequence=f.sequence)
anno_feats.append(fn)
return {
'gfe': typing['gfe'],
'feature': structute_feats,
'annotation_feature': anno_feats
}
def releases_locus_get(imgt_releases,
locus,
neo4j_url=neo_dict['neo4j_url'],
user=neo_dict['user'],
password=neo_dict['password']):
"""releases_locus_get
Get all db releases
:param imgt_releases: Valid imgt releases verion
:param locus: Valid imgt releases verion
:rtype: list of available db
"""
global seqanns
global gfe_feats
global gfe2hla
global seq2hla
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter(
'%(asctime)s - %(name)-35s - %(levelname)-5s '
'- %(funcName)s %(lineno)d: - %(message)s')
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
db = "".join(imgt_releases.split("."))
if db in seqanns:
seqann = seqanns[db]
else:
seqann = BioSeqAnn(verbose=True,
safemode=True,
dbversion=db,
verbosity=3)
seqanns.update({db: seqann})
try:
graph = Graph(neo4j_url, user=user, password=password, bolt=False)
except ServiceUnavailable as err:
log_contents = log_capture_string.getvalue()
log_data = log_contents.split("\n")
log_data.append(str(err))
return Error("Failed to connect to graph", log=log_data), 404
if (not isinstance(gfe_feats, DataFrame)
or not isinstance(seq2hla, DataFrame)):
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_gfe2hla=True,
load_seq2hla=True,
load_gfe2feat=True,
verbose=True)
gfe_feats = pygfe.gfe_feats
seq2hla = pygfe.seq2hla
gfe2hla = pygfe.gfe2hla
else:
pygfe = pyGFE(graph=graph,
seqann=seqann,
gfe2hla=gfe2hla,
gfe_feats=gfe_feats,
seq2hla=seq2hla,
verbose=True)
try:
hla_list = pygfe.list_db_by_locus_imgt(locus, imgt_releases)
except Exception as e:
log_contents = log_capture_string.getvalue()
print("The Error", e)
return Error("hla list failed", log=log_contents.split("\n")), 404
if isinstance(hla_list, Error):
log_contents = log_capture_string.getvalue()
hla_list.log = log_contents.split("\n")
return hla_list, 404
if not hla_list:
log_contents = log_capture_string.getvalue()
return Error("no data record found", log=log_contents.split("\n")), 404
return hla_list
def test_006_align(self):
graph = Graph(neo4jurl, user=neo4juser, password=neo4jpass,
bolt=False)
#if conn():
server = BioSeqDatabase.open_database(driver="pymysql",
user=biosqluser,
passwd=biosqlpass,
host=biosqlhost,
db=biosqldb,
port=3307)
seqann = BioSeqAnn(align=True, server=server, dbversion="3310", verbose=True)
pickle_file1 = "unique_db-feats.pickle"
pickle_file2 = "feature-service.pickle"
pickle_gfe2feat = "gfe2feat.pickle"
pickle_file3 = "gfe2hla.pickle"
pickle_file4 = "seq2hla.pickle"
with open(pickle_gfe2feat, 'rb') as handle1:
gfe_feats = pickle.load(handle1)
with open(pickle_file1, 'rb') as handle1:
feats = pickle.load(handle1)
with open(pickle_file2, 'rb') as handle2:
cached_feats = pickle.load(handle2)
with open(pickle_file3, 'rb') as handle3:
gfe2hla = pickle.load(handle3)
with open(pickle_file4, 'rb') as handle:
seq2hla = pickle.load(handle)
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_features=False,
verbose=True,
features=feats,
seq2hla=seq2hla,
gfe2hla=gfe2hla,
gfe_feats=gfe_feats,
cached_features=cached_feats,
loci=["HLA-A"])
self.assertIsInstance(pygfe, pyGFE)
seqs = list(SeqIO.parse(self.data_dir + "/align_tests.fasta", "fasta"))
typing1 = pygfe.type_from_seq("HLA-A", str(seqs[0].seq), "3.31.0")
typing2 = pygfe.type_from_seq("HLA-A", str(seqs[1].seq), "3.31.0")
typing3 = pygfe.type_from_seq("HLA-A", str(seqs[2].seq), "3.31.0")
typing4 = pygfe.type_from_seq("HLA-A", str(seqs[3].seq), "3.31.0")
self.assertEqual(typing1.hla, 'HLA-A*02:01:01:12')
self.assertEqual(typing2.hla, 'HLA-A*02:01:01:12')
self.assertEqual(typing3.hla, 'HLA-A*02:01:01:12')
self.assertEqual(typing4.hla, 'HLA-A*02:01:01:12')
#end = time.time()
#time_taken = end - start
#print(typing1)
#print(typing1.aligned.keys())
#print(typing1.novel_features)
#difss = pygfe.hla_seqdiff("HLA-A","3.31.0","HLA-A*01:01:01:01","HLA-A*01:01:01:07")
#self.assertIsInstance(typing1, Typing)
pass
def gfeAnnotation_post(sequence, locus, gene=None, imgtdb_version="3.31.0"):
"""gfeAnnotation_post
Get all kir associated with a GFE # noqa: E501
:param sequence: Valid sequence fasta
:param gene: the KIR param true or false
:param locus: Valid Locus
:param imgtdb_version:
:rtype: Typing
"""
global seqanns
typing = Typing()
sequence = SeqRecord(seq=Seq(sequence['sequence']))
if not re.match(".", imgtdb_version):
imgtdb_version = ".".join([list(imgtdb_version)[0],
"".join(list(imgtdb_version)[1:3]),
list(imgtdb_version)[3]])
db = "".join(imgtdb_version.split("."))
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p',
level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter(
'%(asctime)s - %(name)-35s - %(levelname)-5s '
'- %(funcName)s %(lineno)d: - %(message)s')
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
# TODO: Use `gene` or locus to figure out the gene-family
if db in seqanns:
seqann = seqanns[db]
elif gene:
if gene.upper() == 'KIR':
seqann = BioSeqAnn(verbose=True, safemode=True,
dbversion=db, verbosity=3, kir=True)
seqanns.update({db: seqann})
else:
# Defaults to HLA
seqann = BioSeqAnn(verbose=True, safemode=True,
dbversion=db, verbosity=3)
seqanns.update({db: seqann})
try:
annotation = seqann.annotate(sequence, locus)
except Exception as e:
print(e)
log_contents = log_capture_string.getvalue()
return Error("An error occurred during the annotation",
log=log_contents.split("\n")), 404
if not annotation:
log_contents = log_capture_string.getvalue()
return Error("No annotation could be produced",
log=log_contents.split("\n")), 404
if not hasattr(annotation, 'structure'):
log_contents = log_capture_string.getvalue()
return Error("No structure was produced",
log=log_contents.split("\n")), 404
feats = []
for f in annotation.structure:
fn = Feature(accession=f.accession, rank=f.rank,
term=f.term, sequence=f.sequence)
feats.append(fn)
typing.features = feats
typing.gfe = annotation.gfe
typing.imgtdb_version = imgtdb_version
return typing
def annotate_get(sequence, locus=None, imgthla_version="3.31.0"): # noqa: E501
"""annotate_get
Find the sequence differences between two GFE # noqa: E501
:param sequence: Valid consensus sequence
:type sequence: str
:param locus: Valid locus
:type locus: str
:param imgthla_version: IMGT/HLA DB Version
:type imgthla_version: str
:param verbose: Flag for running service in verbose
:type verbose: bool
:rtype: Typing
"""
global seqanns
typing = Typing()
sequence = SeqRecord(seq=Seq(sequence))
if not re.match(".", imgthla_version):
imgthla_version = ".".join([
list(imgthla_version)[0], "".join(list(imgthla_version)[1:3]),
list(imgthla_version)[3]
])
db = "".join(imgthla_version.split("."))
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter(
'%(asctime)s - %(name)-35s - %(levelname)-5s - %(funcName)s %(lineno)d: - %(message)s'
)
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
if db in seqanns:
seqann = seqanns[db]
else:
seqann = BioSeqAnn(verbose=True,
safemode=True,
dbversion=db,
verbosity=3)
seqanns.update({db: seqann})
try:
annotation = seqann.annotate(sequence, locus)
except:
log_contents = log_capture_string.getvalue()
return Error("An error occured during the annotation",
log=log_contents.split("\n")), 404
if not annotation:
log_contents = log_capture_string.getvalue()
return Error("No annotation could be produced",
log=log_contents.split("\n")), 404
if not hasattr(annotation, 'structure'):
log_contents = log_capture_string.getvalue()
return Error("No structure was produced",
log=log_contents.split("\n")), 404
feats = []
for f in annotation.structure:
fn = Feature(accession=f.accession,
rank=f.rank,
term=f.term,
sequence=f.sequence)
feats.append(fn)
typing.features = feats
typing.gfe = annotation.gfe
typing.imgtdb_version = imgthla_version
return typing
def findkir_get(gfe,
neo4j_url=neo_dict['neo4j_url'],
user=neo_dict['user'],
password=neo_dict['password']): # noqa: E501
"""findkir_get
Get all kir associated with a GFE # noqa: E501
:param gfe: Valid gfe of locus
:rtype: Typing
"""
global seqanns
global gfe_feats
global gfe2hla
global seq2hla
log_capture_string = io.StringIO()
logger = logging.getLogger('')
logging.basicConfig(datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
# create console handler and set level to debug
ch = logging.StreamHandler(log_capture_string)
formatter = logging.Formatter(
'%(asctime)s - %(name)-35s - %(levelname)-5s '
'- %(funcName)s %(lineno)d: - %(message)s')
ch.setFormatter(formatter)
ch.setLevel(logging.INFO)
logger.addHandler(ch)
seqann = BioSeqAnn()
try:
graph = Graph(neo4j_url, user=user, password=password, bolt=False)
except ServiceUnavailable as err:
log_contents = log_capture_string.getvalue()
log_data = log_contents.split("\n")
log_data.append(str(err))
return Error("Failed to connect to graph", log=log_data), 404
if (not isinstance(gfe_feats, DataFrame)
or not isinstance(seq2hla, DataFrame)):
pygfe = pyGFE(graph=graph,
seqann=seqann,
load_gfe2hla=True,
load_seq2hla=True,
load_gfe2feat=True,
verbose=True)
gfe_feats = pygfe.gfe_feats
seq2hla = pygfe.seq2hla
gfe2hla = pygfe.gfe2hla
else:
pygfe = pyGFE(graph=graph,
seqann=seqann,
gfe2hla=gfe2hla,
gfe_feats=gfe_feats,
seq2hla=seq2hla,
verbose=True)
try:
typing = pygfe.find_gfe_kir(gfe, pygfe.breakup_gfe(gfe))
except Exception as e:
print(e)
log_contents = log_capture_string.getvalue()
return Error("Type with alignment failed",
log=log_contents.split("\n")), 404
if isinstance(typing, Error):
log_contents = log_capture_string.getvalue()
typing.log = log_contents.split("\n")
return typing, 404
if not typing:
log_contents = log_capture_string.getvalue()
return Error("Type with alignment failed",
log=log_contents.split("\n")), 404
return typing