PyTFBS 1.0.12__tar.gz → 1.0.14__tar.gz

{pytfbs-1.0.12 → pytfbs-1.0.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTFBS
-Version: 1.0.12
+Version: 1.0.14
 Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT
@@ -94,7 +94,7 @@ for tf_cname in tf_cnames[tf_code]:
 	tar_exps = {idx: row.tolist() for idx, row in df_rexps_tars.iterrows()}
 	rcis = clink.rci(tar_exps, tf_exp)
 	for rci in rcis:
-		score = rci[1] + (random.uniform(1E-10, 1E-15) * random.choice([1, -1]))
+		score = rci[1] + (random.uniform(1E-15, 1E-10) * random.choice([1, -1]))
 		print(tf_cname[0] + '\t' + rci[0] + '\t' + str(score))
 
 ```

{pytfbs-1.0.12 → pytfbs-1.0.14}/PyTFBS/clink.py

@@ -162,7 +162,7 @@ def read_rexp_file(file=None, data_dir=None):
 	return df_rexps
 
 def read_PyTFBS_output(file):
-	tf_tars = set()
+	tar_scores = {}
 	for line in open(file):
 		if line[0] == '#':
 			continue
@@ -171,8 +171,13 @@ def read_PyTFBS_output(file):
 		score = float(lblocks[3])
 		jindex = float(lblocks[2])
 		if score > 0.8 and jindex > 0.3:
-			tf_tars.add(gene_name)
-	return tf_tars
+			if gene_name in tar_scores:
+				if tar_scores[gene_name] < score:
+					tar_scores[gene_name] = score
+			else:
+				tar_scores[gene_name] = score
+	sorted_tars = sorted(tar_scores, key=tar_scores.get, reverse=True)
+	return sorted_tars[:8000]
 
 def get_rexp_files(species=None, data_dir=None):
 	if data_dir == None:
@@ -210,5 +215,5 @@ if __name__ == '__main__':
 		tar_exps = {idx: row.tolist() for idx, row in df_rexps_tars.iterrows()}
 		rcis = rci(tar_exps, tf_exp)
 		for rci in rcis:
-			score = rci[1] + (random.uniform(1E-10, 1E-15) * random.choice([1, -1]))
+			score = rci[1] + (10 ** random.uniform(-15, -10) * random.choice([1, -1]))
 			print(tf_cname[0] + '\t' + rci[0] + '\t' + str(score))

{pytfbs-1.0.12 → pytfbs-1.0.14}/PyTFBS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTFBS
-Version: 1.0.12
+Version: 1.0.14
 Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT
@@ -94,7 +94,7 @@ for tf_cname in tf_cnames[tf_code]:
 	tar_exps = {idx: row.tolist() for idx, row in df_rexps_tars.iterrows()}
 	rcis = clink.rci(tar_exps, tf_exp)
 	for rci in rcis:
-		score = rci[1] + (random.uniform(1E-10, 1E-15) * random.choice([1, -1]))
+		score = rci[1] + (random.uniform(1E-15, 1E-10) * random.choice([1, -1]))
 		print(tf_cname[0] + '\t' + rci[0] + '\t' + str(score))
 
 ```

{pytfbs-1.0.12 → pytfbs-1.0.14}/README.md

@@ -59,7 +59,7 @@ for tf_cname in tf_cnames[tf_code]:
 	tar_exps = {idx: row.tolist() for idx, row in df_rexps_tars.iterrows()}
 	rcis = clink.rci(tar_exps, tf_exp)
 	for rci in rcis:
-		score = rci[1] + (random.uniform(1E-10, 1E-15) * random.choice([1, -1]))
+		score = rci[1] + (random.uniform(1E-15, 1E-10) * random.choice([1, -1]))
 		print(tf_cname[0] + '\t' + rci[0] + '\t' + str(score))
 
 ```

{pytfbs-1.0.12 → pytfbs-1.0.14}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyTFBS"
-version = "1.0.12"
+version = "1.0.14"
 license = "MIT"  # SPDX expression
 description = "PyTFBS: A Python Package for Transcription Factor Binding Site Prediction"
 readme = "README.md"