PyOVERCAST 1.0.9__tar.gz → 1.0.11__tar.gz

{pyovercast-1.0.9 → pyovercast-1.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyOVERCAST
-Version: 1.0.9
+Version: 1.0.11
 Summary: A Python package for mining key transcription factors from transcriptome data.
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT

{pyovercast-1.0.9 → pyovercast-1.0.11}/PyOVERCAST/predict.py

@@ -526,27 +526,23 @@ def permutation(gene_set, gene_list):
 	gene_list0 = gene_list[gene_list.index.isin(gene_set0.index)]
 
 	diff_idx = list(gene_list.index.difference(gene_list0.index))
-	if len(diff_idx) == 0:
-		gene_sample = []
-	else:
-		gene_sample = random.sample(diff_idx, gene_set0.shape[0])
+	gene_sample = random.sample(diff_idx, min(gene_set0.shape[0], len(diff_idx)))
 	
 	set1_values = []
-	set0_max, set0_min = gene_set0[gene_set0.columns[1]].max(), gene_set0[gene_set0.columns[1]].min()
+	col1 = gene_set0.columns[1]
+	set0_max, set0_min = gene_set0.loc[gene_set0[col1] >= 0.0, col1].min(), gene_set0.loc[gene_set0[col1] <= 0.0, col1].max()
 	set0_range = set0_max - set0_min
 	if set0_range < 0.0:
-		set0_range = set0_min
-	for gene in gene_sample:
-		set1_values.append(random.uniform(set0_min - set0_range, set0_min))
-	
-	if len(gene_sample) == 0:
-		gene_set_pt = gene_set0
-		gene_list_pt = gene_list0
+		for gene in gene_sample:
+			set1_values.append(random.uniform(set0_max, set0_min) + (random.uniform(1E-10, 1E-15) * random.choice([1, -1])))
 	else:
-		gene_set1 = pd.DataFrame({"gene": gene_sample, "logFC": set1_values}, index=gene_sample)
-		gene_set_pt = pd.concat([gene_set0, gene_set1], axis=0)
-		gene_list1 = gene_list[gene_list.index.isin(gene_sample)]
-		gene_list_pt = pd.concat([gene_list0, gene_list1], axis=0)
+		for gene in gene_sample:
+			set1_values.append(random.uniform(set0_min, set0_max) + (random.uniform(1E-10, 1E-15) * random.choice([1, -1])))
+	
+	gene_set1 = pd.DataFrame({"gene": gene_sample, "logFC": set1_values}, index=gene_sample)
+	gene_set_pt = pd.concat([gene_set0, gene_set1], axis=0)
+	gene_list1 = gene_list[gene_list.index.isin(gene_sample)]
+	gene_list_pt = pd.concat([gene_list0, gene_list1], axis=0)
 
 	return gene_set_pt, gene_list_pt
 

{pyovercast-1.0.9 → pyovercast-1.0.11}/PyOVERCAST.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyOVERCAST
-Version: 1.0.9
+Version: 1.0.11
 Summary: A Python package for mining key transcription factors from transcriptome data.
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT

{pyovercast-1.0.9 → pyovercast-1.0.11}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyOVERCAST"
-version = "1.0.9"
+version = "1.0.11"
 license = "MIT"  # SPDX expression
 description = "A Python package for mining key transcription factors from transcriptome data."
 readme = "README.md"