PyTFBS 1.0.4__tar.gz → 1.0.5__tar.gz

{pytfbs-1.0.4 → pytfbs-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTFBS
-Version: 1.0.4
+Version: 1.0.5
 Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT

{pytfbs-1.0.4 → pytfbs-1.0.5}/PyTFBS/predict.py

@@ -232,6 +232,31 @@ def predict_seq():
 			motif = motifs_all[motif_name][0]
 			predict_llrs(seq, motif, seq_name, motif_name)
 
+def seq2llr(seq_in, motif_len, motif, base_freq):
+	poss = []
+	j_tmps = []
+	llr_matrix = []
+	seq_len = len(seq_in)
+	dseq = sequence_to_numbers(seq_in)
+	for si in range(seq_len - motif_len + 1):
+		llr_sum = 0.0
+		llrs = []
+		for mi in range(motif_len):
+			base = dseq[si + mi]
+			if base == 4:
+				llr = 0.0
+			else:
+				llr = math.log(motif[mi][base] / base_freq[base]);
+			llr_sum += llr
+			# print(motif[mi][base], base_freq[base])
+			llrs.append(llr)
+		j_tmp = llr_sum / motif_len
+		if j_tmp > 0.0:
+			llr_matrix.append(llrs)
+			j_tmps.append(j_tmp)
+			poss.append(si)
+	return llr_matrix, poss, j_tmps
+
 def seq2onehot(seq_in, motif_len, motif, base_freq):
 	datas = []
 	poss = []
@@ -361,7 +386,7 @@ def script(motif_id, model_id, seq_file, out_file, data_dir=None):
 		print(seq_file, 'not exist!')
 		exit(1)
 	motif_name, motif = read_motif_single(motif_file)
-	data_dim = [len(motif) * 5, 1]
+	data_dim = [len(motif), 1]
 	#model = loade_model_pars(model_file, data_dim)
 	model = loade_model_trace(model_file)
 	# run predict
@@ -375,8 +400,8 @@ def script(motif_id, model_id, seq_file, out_file, data_dir=None):
 		seq = fasta[seq_name].upper()
 		if has_non_acgtn_upper(seq):
 			continue
-		data_onehot, poss, j_tmps = seq2onehot(seq, motif_len, motif, seq_freq)
-		data = torch.tensor(data_onehot)
+		data_llr, poss, j_tmps = seq2llr(seq, motif_len, motif, seq_freq)
+		data = torch.tensor(data_llr)
 		data = data.view(-1, data_dim[0])
 		logits = model(data).flatten().tolist()
 		#indices = torch.nonzero(logits > 0.5, as_tuple=False).squeeze().tolist()

{pytfbs-1.0.4 → pytfbs-1.0.5}/PyTFBS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTFBS
-Version: 1.0.4
+Version: 1.0.5
 Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT

{pytfbs-1.0.4 → pytfbs-1.0.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyTFBS"
-version = "1.0.4"
+version = "1.0.5"
 license = "MIT"  # SPDX expression
 description = "PyTFBS: A Python Package for Transcription Factor Binding Site Prediction"
 readme = "README.md"