def test_diff3():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.8, 'SOX4': 0.75})
gs2 = GeneSignature(name="test1", gene2weight={'TP53': 0.3, 'SOX2': 0.60})
gsu = gs1.difference(gs2)
assert 'SOX4' in gsu
assert gsu.gene2weight['SOX4'] == 0.75
assert len(gsu) == 1
def test_intersection3():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.8, 'SOX4': 0.75})
gs2 = GeneSignature(name="test1", gene2weight={'TP53': 0.3, 'SOX2': 0.60})
gsu = gs1.intersection(gs2)
assert len(gsu) == 1
assert 'TP53' in gsu
assert gsu.gene2weight['TP53'] == 0.8
def test_union1():
gs1 = GeneSignature(name="test1", gene2weight=['TP53', 'SOX4'])
gs2 = GeneSignature(name="test1", gene2weight=['TP53', 'SOX2'])
gsu = gs1.union(gs2)
assert 'TP53' in gsu
assert 'SOX4' in gsu
assert 'SOX2' in gsu
assert len(gsu) == 3
def test_union3():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.8, 'SOX4': 0.75})
gs2 = GeneSignature(name="test1", gene2weight={'TP53': 0.3, 'SOX2': 0.60})
gsu = gs1.union(gs2)
assert 'TP53' in gsu
assert gsu.gene2weight['TP53'] == 0.8
assert 'SOX4' in gsu
assert gsu.gene2weight['SOX4'] == 0.75
assert 'SOX2' in gsu
assert gsu.gene2weight['SOX2'] == 0.6
assert len(gsu) == 3
def test_init1():
gs1 = GeneSignature(name="test1", gene2weight=['TP53', 'SOX4'])
assert 'TP53' in gs1
assert 'SOX4' in gs1
assert gs1.name == 'test1'
assert len(gs1) == 2
assert gs1.gene2weight['TP53'] == 1.0
assert gs1.gene2weight['SOX4'] == 1.0
def test_init2():
gs1 = GeneSignature(name="test1", gene2weight=[('TP53', 0.5), ('SOX4', 0.75)])
assert 'TP53' in gs1
assert 'SOX4' in gs1
assert gs1.name == 'test1'
assert len(gs1) == 2
assert gs1.gene2weight['TP53'] == 0.5
assert gs1.gene2weight['SOX4'] == 0.75
def test_init3():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.5, 'SOX4': 0.75})
assert 'TP53' in gs1
assert 'SOX4' in gs1
assert gs1.name == 'test1'
assert len(gs1) == 2
assert gs1.gene2weight['TP53'] == 0.5
assert gs1.gene2weight['SOX4'] == 0.75
def test_head():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.8, 'SOX4': 0.75})
gs2 = gs1.head(1)
assert gs2['TP53'] == 0.8
assert len(gs2) == 1
gs2 = gs1.head(2)
assert gs2['TP53'] == 0.8
assert gs2['SOX4'] == 0.75
assert len(gs2) == 2
def test_rename():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.5, 'SOX4': 0.75})
gs2 = gs1.rename('test2')
assert 'TP53' in gs2
assert 'SOX4' in gs2
assert gs2.name == 'test2'
assert len(gs2) == 2
assert gs2.gene2weight['TP53'] == 0.5
assert gs2.gene2weight['SOX4'] == 0.75
def test_aucell_mismatch(exp_matrix, gs):
percentiles = derive_auc_threshold(exp_matrix)
gss = [
GeneSignature(name="test",
gene2weight=list(map("FAKE{}".format, range(100))))
] + gs
aucs_mtx = aucell(exp_matrix,
gss,
auc_threshold=percentiles[0.01],
num_workers=1)
print(aucs_mtx.head())
def test_noweights():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.8, 'SOX4': 0.75})
gs2 = gs1.noweights()
assert gs1['TP53'] == 0.8
assert gs2['TP53'] == 1.0
reg1 = Regulon(name='TP53 regulon', gene2weight={'TP53': 0.8, 'SOX4': 0.75}, transcription_factor="TP53", gene2occurrence={"TP53": 1})
reg2 = reg1.noweights()
assert reg1['TP53'] == 0.8
assert reg2['TP53'] == 1.0
assert isinstance(reg2, Regulon)
def calculate_regulon_enrichment(self):
# Calculate regulon enrichment per cell using AUCell.
# Create regulons with weight based on given key
print("Using {} to weight the genes when running AUCell.".format(
self.auc_regulon_weights_key))
regulon_signatures = list(
map(
lambda x: GeneSignature(
name=x.name,
gene2weight=self.get_regulon_gene_data(
x, self.auc_regulon_weights_key),
),
self.regulons,
))
auc_mtx = aucell(
self.ex_mtx, regulon_signatures,
num_workers=self.num_workers) # (n_cells x n_regulons)
auc_mtx = auc_mtx.loc[self.ex_mtx.index]
return auc_mtx
def signatures():
for gene_sig_file_path in gene_sig_file_paths:
gene_sig = pd.read_csv(gene_sig_file_path,
sep='\t',
header=None,
index_col=None)
fname = ntpath.basename(gene_sig_file_path)
regulon = os.path.splitext(fname)[0]
# Check if the file is the regulon frequency file
if regulon == 'regulons':
continue
# Do some sanity checks
if len(gene_sig.columns) == 0:
raise Exception(
f"{gene_sig_file_path} has 0 columns. Requires .tsv with 1 or 2 columns. First column should be genes (required), second (optional) are weight for the given genes."
)
if len(gene_sig.columns) > 2:
raise Exception(
f"{gene_sig_file_path} has more than 2 columns. Requires .tsv with 1 or 2 columns. First column should be genes, second (optional) are weight for the given genes."
)
if len(gene_sig.columns) == 1 or noweights:
gene2weight = gene_sig[0]
if len(gene_sig.columns) == 2 and not noweights:
# Filter the genes based on the given weight_threshold
# 1st column: genes
# 2nd column: weights
gene_sig = gene_sig[gene_sig[1] > weight_threshold]
if len(gene_sig.index) == 0:
if show_warnings:
warnings.warn(
"{0} is empty after apply filter with weight_threshold > {1}"
.format(regulon, weight_threshold))
continue
gene2weight = [tuple(x) for x in gene_sig.values]
yield GeneSignature(name=regulon, gene2weight=gene2weight)
def doGeneSetEnrichment(self, request, context):
gene_set_file_path = os.path.join(self.dfh.get_gene_sets_dir(),
request.geneSetFilePath)
loom = self.lfh.get_loom(loom_file_path=request.loomFilePath)
gse = _gse.GeneSetEnrichment(scope=self,
method="AUCell",
loom=loom,
gene_set_file_path=gene_set_file_path,
annotation='')
# Running AUCell...
yield gse.update_state(step=-1,
status_code=200,
status_message="Running AUCell...",
values=None)
time.sleep(1)
# Reading gene set...
yield gse.update_state(step=0,
status_code=200,
status_message="Reading the gene set...",
values=None)
with open(gse.gene_set_file_path, 'r') as f:
# Skip first line because it contains the name of the signature
gs = GeneSignature(name='Gene Signature #1',
gene2weight=[
line.strip() for idx, line in enumerate(f)
if idx > 0
])
time.sleep(1)
if not gse.has_AUCell_rankings():
# Creating the matrix as DataFrame...
yield gse.update_state(step=1,
status_code=200,
status_message="Creating the matrix...",
values=None)
loom = self.lfh.get_loom(loom_file_path=request.loomFilePath)
dgem = np.transpose(loom.get_connection()[:, :])
ex_mtx = pd.DataFrame(data=dgem,
index=loom.get_ca_attr_by_name("CellID"),
columns=loom.get_genes())
# Creating the rankings...
start_time = time.time()
yield gse.update_state(step=2.1,
status_code=200,
status_message="Creating the rankings...",
values=None)
rnk_mtx = create_rankings(ex_mtx=ex_mtx)
# Saving the rankings...
yield gse.update_state(step=2.2,
status_code=200,
status_message="Saving the rankings...",
values=None)
lp.create(gse.get_AUCell_ranking_filepath(), rnk_mtx.as_matrix(),
{"CellID": loom.get_cell_ids()},
{"Gene": loom.get_genes()})
print("Debug: %s seconds elapsed ---" % (time.time() - start_time))
else:
# Load the rankings...
yield gse.update_state(
step=2,
status_code=200,
status_message="Rankings exists: loading...",
values=None)
rnk_loom = self.lfh.get_loom_connection(
gse.get_AUCell_ranking_filepath())
rnk_mtx = pd.DataFrame(data=rnk_loom[:, :],
index=rnk_loom.ra.CellID,
columns=rnk_loom.ca.Gene)
# Calculating AUCell enrichment...
start_time = time.time()
yield gse.update_state(
step=3,
status_code=200,
status_message="Calculating AUCell enrichment...",
values=None)
aucs = enrichment(rnk_mtx, gs).loc[:, "AUC"].values
print("Debug: %s seconds elapsed ---" % (time.time() - start_time))
yield gse.update_state(step=4,
status_code=200,
status_message=gse.get_method() +
" enrichment done!",
values=aucs)
def test_diff1():
gs1 = GeneSignature(name="test1", gene2weight=['TP53', 'SOX4'])
gs2 = GeneSignature(name="test1", gene2weight=['TP53', 'SOX2'])
gsu = gs1.difference(gs2)
assert 'SOX4' in gsu
assert len(gsu) == 1
def test_immut():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.5, 'SOX4': 0.75})
with pytest.raises(attr.exceptions.FrozenInstanceError):
gs1.name = 'rename'
with pytest.raises(TypeError):
gs1.gene2weight['TP53'] = 0.6
def test_genes():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.5, 'SOX4': 0.75})
assert gs1.genes == ('SOX4', 'TP53')
def test_dict():
gs1 = GeneSignature(name="test1", gene2weight={'TP53': 0.5, 'SOX4': 0.75})
assert gs1['TP53'] == 0.5
assert gs1['SOX4'] == 0.75
