cpgtools 2.0.3__tar.gz → 2.0.4__tar.gz

{cpgtools-2.0.3 → cpgtools-2.0.4}/PKG-INFO

@@ -1,35 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: cpgtools
-Version: 2.0.3
+Version: 2.0.4
 Summary: Tools to analyze and visualize DNA methylation data
 Author-email: Liguo Wang <wangliguo78@gmail.com>
 Maintainer-email: Liguo Wang <wangliguo78@gmail.com>
-License: Copyright (c) 2024 The Python Packaging Authority
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License-Expression: MIT
 Project-URL: Documentation, https://cpgtools.readthedocs.io/en/latest/index.html
 Project-URL: Repository, https://github.com/liguowang/cpgtools.git
 Keywords: DNA methylation,EPIC,450K,850K,935K,RRBS,WGBS
 Classifier: Programming Language :: Python :: 3
 Classifier: Development Status :: 4 - Beta
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: MacOS :: MacOS X
@@ -37,7 +17,7 @@ Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.5
 Description-Content-Type: text/markdown
-License-File: LICENSE
+License-File: LICENSE.txt
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: scikit-learn
@@ -46,6 +26,8 @@ Requires-Dist: bx-python
 Requires-Dist: pandas
 Requires-Dist: umap-learn
 Requires-Dist: fancyimpute
+Requires-Dist: pycombat
+Dynamic: license-file
 
 ## Install CpGtools using [pip](https://pip.pypa.io/en/stable/)
 

{cpgtools-2.0.3 → cpgtools-2.0.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 #Project's meta data
 [project]
-version = "2.0.3"
+version = "2.0.4"
 name = "cpgtools"
 authors = [
   {name="Liguo Wang", email="wangliguo78@gmail.com"},
@@ -15,7 +15,7 @@ maintainers = [
 ]
 description = "Tools to analyze and visualize DNA methylation data"
 readme = "README.md"
-license = {file = "LICENSE"}
+license = "MIT"
 requires-python = ">=3.5"
 
 dependencies = [
@@ -27,12 +27,12 @@ dependencies = [
 	"pandas",
 	"umap-learn",
 	"fancyimpute",
+	"pycombat",
 ]
 
 classifiers=[
 	"Programming Language :: Python :: 3",
 	'Development Status :: 4 - Beta',
-	"License :: OSI Approved :: MIT License",
 	'Environment :: Console',
 	'Intended Audience :: Science/Research',
 	'Operating System :: MacOS :: MacOS X',

{cpgtools-2.0.3 → cpgtools-2.0.4}/scripts/beta_PCA.py

@@ -73,7 +73,10 @@ def main():
 		print (__doc__)
 		parser.print_help()
 		sys.exit(101)
-	
+	if not (options.group_file):
+		print (__doc__)
+		parser.print_help()
+		sys.exit(101)	
 	if not (options.out_file):
 		print (__doc__)
 		parser.print_help()

cpgtools-2.0.4/scripts/beta_remove_batch_effects.py

@@ -0,0 +1,138 @@
+#!/usr/bin/env python3
+
+"""
+Description
+-----------
+This program corrects batch effect.
+
+Example of input data file
+---------------------------
+CpG_ID	Sample_01	Sample_02	Sample_03	Sample_04
+cg_001	0.831035	0.878022	0.794427	0.880911
+cg_002	0.249544	0.209949	0.234294	0.236680
+cg_003	0.845065	0.843957	0.840184	0.824286
+...
+
+Example of batch file
+-------------------------------
+Sample,Group
+Sample_01,plate_1
+Sample_02,plate_1
+Sample_03,plate_2
+Sample_04,plate_2
+...
+
+Notes
+-----
+* Rows with missing values will be removed
+
+"""
+
+
+import sys
+import subprocess
+from optparse import OptionParser
+from cpgmodule.utils import *
+from cpgmodule._version import __version__
+import pandas as pd
+#from sklearn.preprocessing import StandardScaler
+#from sklearn.decomposition import PCA
+from collections import Counter
+from combat.pycombat import pycombat
+import matplotlib.pyplot as plt
+import matplotlib.colors as mcolors
+
+__author__ = "Liguo Wang"
+__copyright__ = "Copyleft"
+__credits__ = []
+__license__ = "GPL"
+__maintainer__ = "Liguo Wang"
+__email__ = "wang.liguo@mayo.edu"
+__status__ = "Development"
+
+def pick_colors(n):
+	my_colors = list(mcolors.CSS4_COLORS.keys())
+	if n > len(my_colors):
+		print ("Too many colors requested", file = sys.stderr)
+		sys.exit()
+	return my_colors[0:n]
+
+def box_plot(df, s_colors,  out_png, ylab="Beta values", title=""):
+	s_names = df.columns
+	fig, ax = plt.subplots()
+	bplot = ax.boxplot(df, patch_artist=True, tick_labels = s_names)
+	for patch, color in zip(bplot['boxes'], s_colors):
+		patch.set_facecolor(color)
+	ax.set_xticklabels(s_names, rotation='vertical')
+	plt.ylabel(ylab)
+	plt.title(title)
+	plt.savefig(out_png)
+
+def main():
+	
+	usage="%prog [options]" + "\n"
+	parser = OptionParser(usage,version="%prog " + __version__)
+	parser.add_option("-i","--input_file",action="store",type="string",dest="input_file",help="Tab-separated data frame file containing beta values with the 1st row containing sample IDs and the 1st column containing CpG IDs.")
+	parser.add_option("-g","--group",action="store",type="string",dest="group_file",help="Comma-separated group file defining the batch groups of each sample.")
+	parser.add_option("-o","--output",action="store",type='string', dest="out_file",help="The prefix of the output file.")
+	(options,args)=parser.parse_args()
+	
+	print ()
+	if not (options.input_file):
+		print (__doc__)
+		parser.print_help()
+		sys.exit(101)
+	if not (options.group_file):
+		print (__doc__)
+		parser.print_help()
+		sys.exit(101)	
+	if not (options.out_file):
+		print (__doc__)
+		parser.print_help()
+		sys.exit(103)	
+
+	beta_out = options.out_file + '.combat.tsv'
+	beta_boxplot_before = options.out_file + '.boxplot.png'
+	beta_boxplot_after = options.out_file + '.boxplot_combat.png'
+	
+	printlog("Reading input file: \"%s\" ..." % (options.input_file))
+	df1 = pd.read_csv(options.input_file, index_col = 0, sep="\t")
+	
+	#remove NA and transpose
+	df2 = df1.dropna(axis=0, how='any')
+	printlog("%d rows with missing values were removed." % (len(df1.index) - len(df2.index)))
+
+	printlog("Reading group file: \"%s\" ..." % (options.group_file))
+	group = pd.read_csv(options.group_file, index_col=0, names=['Sample_ID', 'Group_ID'])
+	#check if sample IDs are unique
+	if len(group.index) != len(group.index.unique()):
+		print ("Sample IDs are not unique", file = sys.stderr)
+		sys.exit()	
+	group.index = group.index.map(str)
+	printlog("Group/batch \"%s\" contains %d samples" % (options.group_file, len(group.index)))
+	
+	# a list of unique group names, and their frequencies
+	group_info = Counter(group['Group_ID'])
+	print(list(group['Group_ID']))
+	# a list of unique colors
+	color_names = pick_colors(len(group_info))	
+	color_list = []
+	for name,count in zip(color_names, list(group_info.values())):
+		color_list.extend([name]*count)
+
+	printlog("Generate boxplot before correction. Save to '%s'" % beta_boxplot_before)
+	box_plot(df2, s_colors=color_list, out_png=beta_boxplot_before, title="Before batch effects correction")
+
+	# remove batch effect
+	printlog("Removing batch effect ...")
+	df_corrected = pycombat(df2, list(group['Group_ID']))
+	
+
+	df_corrected.to_csv(beta_out,sep="\t")
+
+	printlog("Generate boxplot after correction. Save to '%s'" % beta_boxplot_after)
+	box_plot(df_corrected, s_colors=color_list, out_png=beta_boxplot_after, title="After batch effects correction")
+
+
+if __name__=='__main__':
+	main()	

{cpgtools-2.0.3 → cpgtools-2.0.4}/setup.py

@@ -21,6 +21,7 @@ script_files = [
 "scripts/beta_tSNE.py",
 "scripts/beta_topN.py",
 "scripts/beta_trichotmize.py",
+"scripts/beta_remove_batch_effects.py",
 "scripts/dmc_Bayes.py",
 "scripts/dmc_bb.py",
 "scripts/dmc_fisher.py",

{cpgtools-2.0.3 → cpgtools-2.0.4}/src/cpgtools.egg-info/PKG-INFO

@@ -1,35 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: cpgtools
-Version: 2.0.3
+Version: 2.0.4
 Summary: Tools to analyze and visualize DNA methylation data
 Author-email: Liguo Wang <wangliguo78@gmail.com>
 Maintainer-email: Liguo Wang <wangliguo78@gmail.com>
-License: Copyright (c) 2024 The Python Packaging Authority
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License-Expression: MIT
 Project-URL: Documentation, https://cpgtools.readthedocs.io/en/latest/index.html
 Project-URL: Repository, https://github.com/liguowang/cpgtools.git
 Keywords: DNA methylation,EPIC,450K,850K,935K,RRBS,WGBS
 Classifier: Programming Language :: Python :: 3
 Classifier: Development Status :: 4 - Beta
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: MacOS :: MacOS X
@@ -37,7 +17,7 @@ Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.5
 Description-Content-Type: text/markdown
-License-File: LICENSE
+License-File: LICENSE.txt
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: scikit-learn
@@ -46,6 +26,8 @@ Requires-Dist: bx-python
 Requires-Dist: pandas
 Requires-Dist: umap-learn
 Requires-Dist: fancyimpute
+Requires-Dist: pycombat
+Dynamic: license-file
 
 ## Install CpGtools using [pip](https://pip.pypa.io/en/stable/)
 

{cpgtools-2.0.3 → cpgtools-2.0.4}/src/cpgtools.egg-info/SOURCES.txt

@@ -1,4 +1,4 @@
-LICENSE
+LICENSE.txt
 MANIFEST.in
 README.md
 distribute_setup.py
@@ -20,6 +20,7 @@ scripts/beta_jitter_plot.py
 scripts/beta_m_conversion.py
 scripts/beta_profile_gene_centered.py
 scripts/beta_profile_region.py
+scripts/beta_remove_batch_effects.py
 scripts/beta_selectNBest.py
 scripts/beta_stacked_barplot.py
 scripts/beta_stats.py

{cpgtools-2.0.3 → cpgtools-2.0.4}/src/cpgtools.egg-info/requires.txt

@@ -6,3 +6,4 @@ bx-python
 pandas
 umap-learn
 fancyimpute
+pycombat