v0.0.8

jmschrei · Sep 15, 2022 · cf6a791 · cf6a791
1 parent 1df5847
commit cf6a791
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Showing 3 changed files with 11 additions and 10 deletions.
diff --git a/modiscolite/__init__.py b/modiscolite/__init__.py
@@ -7,3 +7,5 @@
 from . import tfmodisco
 from . import cluster
 from . import report
+
+__version__ = '0.0.8'
diff --git a/modiscolite/gapped_kmer.py b/modiscolite/gapped_kmer.py
@@ -14,8 +14,8 @@
 @njit(parallel=True)
 def _extract_gkmers(X, min_k, max_k, max_gap, max_len, max_entries):
 	nx = X.shape[0]
-	keys = np.zeros((nx, max_entries), dtype='int64') - 1
-	scores = np.zeros((nx, max_entries), dtype='float64') - 1.0
+	keys = np.zeros((nx, max_entries), dtype='int64')
+	scores = np.zeros((nx, max_entries), dtype='float64')
 
 	for xi in prange(nx):
 		n = X.shape[1]
@@ -74,7 +74,6 @@ def _extract_gkmers(X, min_k, max_k, max_gap, max_len, max_entries):
 						if k >= min_k:
 							gkmer_attrs[new_gkmer_hash] = gkmer_attrs.get(new_gkmer_hash, 0) + new_gkmer_attr / k
 
-
 				if len(gkmers_) == 0:
 					last_k_gkmers[j] = np.zeros(0, dtype='int32')
 					last_k_gkmers_attrs[j] = np.zeros(0, dtype='float64')
@@ -83,7 +82,6 @@ def _extract_gkmers(X, min_k, max_k, max_gap, max_len, max_entries):
 					last_k_gkmers[j] = np.array(gkmers_, dtype='int32')
 					last_k_gkmers_attrs[j] = np.array(gkmer_attrs_, dtype='float64')
 					last_k_gkmers_hashes[j] = np.array(gkmer_hashes_, dtype='int64')
-
 
 		ny = len(gkmer_attrs)
 		keys_ = np.empty(ny, dtype='int64')
@@ -100,8 +98,6 @@ def _extract_gkmers(X, min_k, max_k, max_gap, max_len, max_entries):
 
 	return keys, scores
 
-
-
 def _seqlet_to_gkmers(seqlets, topn, min_k, max_k, max_gap, max_len, 
 	max_entries, take_fwd, sign):
 
@@ -126,9 +122,8 @@ def _seqlet_to_gkmers(seqlets, topn, min_k, max_k, max_gap, max_len,
 		Xs.append(X_)
 
 	X = np.array(Xs)
-	keys, scores = _extract_gkmers(X, min_k=min_k, 
-		max_k=max_k, max_gap=max_gap, max_len=max_len, max_entries=max_entries)
-
+	keys, scores = _extract_gkmers(X, min_k=min_k, max_k=max_k, 
+		max_gap=max_gap, max_len=max_len, max_entries=max_entries)
 
 	row_idxs = np.repeat(range(keys.shape[0]), keys.shape[1])
 	csr_mat = scipy.sparse.csr_matrix((scores.flatten(), 

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
 	name='modisco-lite',
-	version='0.0.6',
+	version='0.0.8',
 	author='Jacob Schreiber',
 	author_email='[email protected]',
 	packages=['modiscolite'],
@@ -18,5 +18,9 @@
 		'leidenalg == 0.8.10',
 		'igraph == 0.9.11',
 		'tqdm >= 4.38.0',
+		'pandas >= 1.4.3',
+		'logomaker >= 0.8',
+		'h5py >= 3.7.0',
+		'hdf5plugin'
 	]
 )