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_create_rankings():
ex_mtx = exp_matrix()
df_rnk = create_rankings(ex_mtx)
n_genes = ex_mtx.shape[1]
assert len(df_rnk.sum(axis=1).unique()) == 1
assert (df_rnk + 1).sum(axis=1).unique()[0] == (n_genes * (n_genes+1))/2.0