cpgtools 2.0.2__tar.gz → 2.0.4__tar.gz

{cpgtools-2.0.2 → cpgtools-2.0.4}/MANIFEST.in

@@ -4,8 +4,8 @@ include PKG-INFO
 include LICENSE
 
 include distribute_setup.py
-recursive-include lib *.pyx
-recursive-include lib *.py
-recursive-include lib *.pkl
-recursive-include bin *
+recursive-include src *.pyx
+recursive-include src *.py
+recursive-include src *.pkl
+recursive-include scripts *
 recursive-include doc *

{cpgtools-2.0.2 → cpgtools-2.0.4}/PKG-INFO

@@ -1,35 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: cpgtools
-Version: 2.0.2
+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-2.0.2 → cpgtools-2.0.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 #Project's meta data
 [project]
-version = "2.0.2"
+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-2.0.2 → 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-2.0.2 → cpgtools-2.0.4}/scripts/dmc_ttest.py

@@ -189,7 +189,7 @@ def main():
 			else:
 				continue
 		line_num += 1
-
+	
 	printlog("Perfrom Benjamini-Hochberg (aka FDR) correction ...")
 	adjusted_p = {}
 	q_list =  padjust.multiple_testing_correction(p_list)
@@ -204,6 +204,10 @@ def main():
 		else:
 			f = l.split()
 			probe_ID = f[0]
+			if probe_ID in delta_beta:
+				pass
+			else:
+				delta_beta[probe_ID] = 'n/a'
 			try:
 				print (l + '\t' + str(delta_beta[probe_ID]) + '\t' + adjusted_p[probe_ID], file=FOUT)
 			except:

cpgtools-2.0.2/scripts/beta_imputation.py → cpgtools-2.0.4/scripts/predict_missing.py

@@ -20,6 +20,7 @@ from impyute.cs.em import em
 from impyute.ops.util import toy_df,insert_na
 from impyute.cs.random import random_impute
 from impyute.cs.buck_iterative import buck_iterative
+from impyute.ts.moving_window import moving_window
 from missingpy import MissForest
 
 #use pip to install fancyimpute
@@ -64,6 +65,7 @@ def nafiller():
                     the same row or column.",
         'FillRef': "Impute missing values using values from an external \
                     reference dataset.",
+        'MW': "Interpolate the missing values with moving window.",
         'KNN': "Impute missing values using scikit-learn's KNNImputer function. \
                 Note: slow for large datasets.",
         'KNN2': "Impute missing values using KNN2",
@@ -98,6 +100,7 @@ def nafiller():
     FillMax_parser = sub_parsers.add_parser('FillMax', help=commands['FillMax'])
     FillRand_parser = sub_parsers.add_parser('FillRand', help=commands['FillRand'])
     FillRef_parser = sub_parsers.add_parser('FillRef', help=commands['FillRef'])
+    MW_parser = sub_parsers.add_parser('MW', help=commands['MW'])
     KNN_parser = sub_parsers.add_parser('KNN', help=commands['KNN'])
     fKNN_parser = sub_parsers.add_parser('fKNN', help=commands['fKNN'])
     EM_parser = sub_parsers.add_parser('EM', help=commands['EM'])
@@ -116,7 +119,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     DropNA_parser.add_argument(
-        '-a', '--axis', type=int, choices=range(2), default=0,
+        '--axis', type=int, choices=range(2), default=0,
         help="0 : drop rows with any missing values, 1 : drop columns with \
             missing values. Default: 0")
     DropNA_parser.add_argument(
@@ -130,7 +133,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillValue_parser.add_argument(
-        '-s', '--score', type=float, default=0.0,
+        '--score', type=float, default=0.0,
         help="The value uesd to fill all NAs.")
     FillValue_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -143,7 +146,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillMean_parser.add_argument(
-        '-a', '--axis', type=int, choices=range(2), default=1,
+        '--axis', type=int, choices=range(2), default=1,
         help="0 means column, 1 means row. Default: fill NAs with row means")
     FillMean_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -156,7 +159,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillMedian_parser.add_argument(
-        '-a', '--axis', type=int, choices=range(2), default=1,
+        '--axis', type=int, choices=range(2), default=1,
         help="0 means column, 1 means row. Default: fill NAs with row medians")
     FillMedian_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -169,7 +172,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillMin_parser.add_argument(
-        '-a', '--axis', type=int, choices=range(2), default=1,
+        '--axis', type=int, choices=range(2), default=1,
         help="0 means column, 1 means row. Default: fill NAs with the minimum value of the rows.")
     FillMin_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -182,7 +185,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillMax_parser.add_argument(
-        '-a', '--axis', type=int, choices=range(2), default=1,
+        '--axis', type=int, choices=range(2), default=1,
         help="0 means column, 1 means row. Default: fill NAs with the maximum value of the rows.")
     FillMax_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -195,7 +198,7 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillRand_parser.add_argument(
-        '-a', '--axis', type=int, choices=range(2), default=1,
+        '--axis', type=int, choices=range(2), default=1,
         help="0 means column, 1 means row. Default: fill NAs with values randomly selected from rows.")
     FillRand_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -208,12 +211,50 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     FillRef_parser.add_argument(
-        '-r', '--ref', type=str,
+        '--ref', type=str,
         help="File name of the external reference.")
     FillRef_parser.add_argument(
         '--decimal', type=int, default=5,
         help="Number of decimal places to round each column to. default: %(default)s")
 
+    MW_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    MW_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    MW_parser.add_argument(
+        '--nindex', type=int, choices=[0, -1, None],
+        default=None,
+        help="Null index. Index of the null value inside the moving average window. \
+            See impyute documentation for details. default: %(default)s")
+    MW_parser.add_argument(
+        '--wsize', type=int, default=5,
+        help="Size of the moving average window/area of values being used \
+            for each local imputation. This number includes the missing value. \
+            default: %(default)s")
+    MW_parser.add_argument(
+        '--errors', type=str, choices=["raise", "coerce", "ignore"], 
+        default='coerce',
+        help="Errors will occur with the indexing of the windows - for \
+            example if there is a nan at data[x][0] and `nindex` is set to \
+            -1 or there is a nan at data[x][-1] and `nindex` is set to 0. `\
+            'raise' will raise an error, `coerce` will try again using an \
+            nindex set to the middle and `ignore` will just leave it as a \
+            nan  default: %(default)s")
+    MW_parser.add_argument(
+        '--func', type=str, choices=["mean", "median"], 
+        default='mean',
+        help="Function to summerzie values within the moving window. \
+            default: %(default)s")
+    MW_parser.add_argument(
+        '--axis', type=int, choices=range(2), default=1,
+        help="0 means column, 1 means row. Default: fill missing value \
+            with windows moving on rows.")
+    MW_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
     KNN_parser.add_argument(
         'input', type=str, metavar='input_df',
         help="Input data frame.")
@@ -306,20 +347,28 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Name of the output data frame.")
     ToyDf_parser.add_argument(
-        '-r', '--nrow', type=int, default=10,
+        '--nrow', type=int, default=10,
         help="Number of rows. default: %(default)s")
     ToyDf_parser.add_argument(
-        '-c', '--ncol', type=int, default=10,
+        '--ncol', type=int, default=10,
         help="Number of columns. default: %(default)s")
     ToyDf_parser.add_argument(
-        '--na', type=int, default=5,
+        '--nmiss', type=float, default=5,
         help="Number of missing values ingested into the dataframe. default: %(default)s")
     ToyDf_parser.add_argument(
-        '-s', '--seed', type=int, default=123,
+        '--seed', type=int, default=123,
         help="Seed used to initialize a pseudorandom number generator. default: %(default)s")
     ToyDf_parser.add_argument(
         '--prefix', type=str, default='s',
-        help="Prefix of the column names, a series numbers will be appended to the prefix. default: %(default)s")
+        help="Prefix of the column names, a series numbers will be appended to \
+            the prefix. If this is set to None, as np.ndarray rather than pd.dataframe \
+            will be returned. default: %(default)s")
+    ToyDf_parser.add_argument(
+        '--min', type=float, default=0.0, 
+        help="The minimum value. default: %(default)s")
+    ToyDf_parser.add_argument(
+        '--max', type=float, default=1.0, 
+        help="The maximum value. default: %(default)s")
     ToyDf_parser.add_argument(
         '--decimal', type=int, default=5,
         help="Number of decimal places to round each column to. default: %(default)s")
@@ -331,10 +380,10 @@ def nafiller():
         'output', type=str, metavar='out_df',
         help="Output data frame.")
     InsertNA_parser.add_argument(
-        '--na', type=int,
+        '--nmiss', type=int,
         help="Number of missing values ingested into the dataframe.")
     InsertNA_parser.add_argument(
-        '-s', '--seed', type=int, default=123,
+        '--seed', type=int, default=123,
         help="Seed used to initialize a pseudorandom number generator. default: %(default)s")
     InsertNA_parser.add_argument(
         '--decimal', type=int, default=5,
@@ -483,6 +532,25 @@ def nafiller():
                     continue
             output_df = input_df
             output_df = output_df.round(args.decimal)
+            output_df.to_csv(args.output, sep="\t", na_rep="NaN")
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.output, output_df.isna().sum().sum()))
+        elif command.lower() == 'mw':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            logging.info("Replace missing values using moving window on %s ..." % axis_name[args.axis])
+            if args.axis == 1:
+                output_df = moving_window(
+                    input_df, nindex = args.nindex, wsize=args.wsize, 
+                    errors=args.errors, func=getattr(np, args.func))
+                output_df = output_df.round(args.decimal)
+            elif args.axis == 0:
+                output_df = moving_window(
+                    input_df.T, nindex = args.nindex, wsize=args.wsize, 
+                    errors=args.errors, func=getattr(np, args.func))
+                output_df = output_df.round(args.decimal).T
+           
             output_df.to_csv(args.output, sep="\t", na_rep="NaN")
             logging.info("File \"%s\" contains %d missing values ..." %
                         (args.output, output_df.isna().sum().sum()))
@@ -576,9 +644,10 @@ def nafiller():
 
         elif command.lower() == 'toydf':
             logging.info("Generate toy dataframe ...")
-            output_df = toy_df(nrow = args.nrow, ncol = args.ncol, 
-                               n_miss = args.na, sample_prefix=args.prefix,
-                               seed=args.seed)
+            output_df = toy_df(n_rows = args.nrow, n_cols = args.ncol, 
+                               missingness = args.nmiss, sample_prefix=args.prefix,
+                               min_val = args.min, max_val = args.max, 
+                               rand_seed=args.seed)
             #print(output_df)
             output_df = output_df.round(args.decimal)
             output_df.to_csv(args.output, sep="\t", na_rep="NaN")
@@ -589,7 +658,7 @@ def nafiller():
             logging.info("File \"%s\" contains %d missing values ..." %
                          (args.input, input_df.isna().sum().sum()))
             logging.info("Insert %d NAs into dataframe ..." % args.na)
-            output_df = insert_na(df=input_df, n_miss=args.na, seed=args.seed)
+            output_df = insert_na(df=input_df, n_miss=args.nmiss, seed=args.seed)
             output_df = output_df.round(args.decimal)
             output_df.to_csv(args.output, sep="\t", na_rep="NaN")
             logging.info("File \"%s\" contains %d missing values ..." %

{cpgtools-2.0.2 → cpgtools-2.0.4}/setup.py

@@ -11,7 +11,6 @@ script_files = [
 "scripts/CpG_to_gene.py",
 "scripts/beta_PCA.py",
 "scripts/beta_UMAP.py",
-"scripts/beta_imputation.py",
 "scripts/beta_jitter_plot.py",
 "scripts/beta_m_conversion.py",
 "scripts/beta_profile_gene_centered.py",
@@ -22,6 +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",
@@ -30,6 +30,7 @@ script_files = [
 "scripts/dmc_nonparametric.py",
 "scripts/dmc_ttest.py",
 "scripts/predict_sex.py",
+"scripts/predict_missing.py",
 ]
 
 if __name__ == "__main__":

{cpgtools-2.0.2 → 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: 2.0.2
+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-2.0.2 → cpgtools-2.0.4}/src/cpgtools.egg-info/SOURCES.txt

@@ -1,9 +1,10 @@
-LICENSE
+LICENSE.txt
 MANIFEST.in
 README.md
 distribute_setup.py
 pyproject.toml
 setup.py
+scripts/.DS_Store
 scripts/CpG_aggregation.py
 scripts/CpG_anno_position.py
 scripts/CpG_anno_probe.py
@@ -15,11 +16,11 @@ scripts/CpG_logo.py
 scripts/CpG_to_gene.py
 scripts/beta_PCA.py
 scripts/beta_UMAP.py
-scripts/beta_imputation.py
 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
@@ -33,6 +34,7 @@ scripts/dmc_glm.py
 scripts/dmc_logit.py
 scripts/dmc_nonparametric.py
 scripts/dmc_ttest.py
+scripts/predict_missing.py
 scripts/predict_sex.py
 src/cpgmodule/BED.py
 src/cpgmodule/MI.py
@@ -46,6 +48,25 @@ src/cpgmodule/methylClock.py
 src/cpgmodule/padjust.py
 src/cpgmodule/region2gene.py
 src/cpgmodule/utils.py
+src/cpgmodule/data/AltumAge_cpg.pkl
+src/cpgmodule/data/AltumAge_multi_platform_cpgs.pkl
+src/cpgmodule/data/AltumAge_scaler.pkl
+src/cpgmodule/data/GA_Bohlin.pkl
+src/cpgmodule/data/GA_Haftorn.pkl
+src/cpgmodule/data/GA_Knight.pkl
+src/cpgmodule/data/GA_Lee_CPC.pkl
+src/cpgmodule/data/GA_Lee_RPC.pkl
+src/cpgmodule/data/GA_Lee_refined_RPC.pkl
+src/cpgmodule/data/GA_Mayne.pkl
+src/cpgmodule/data/Hannum.pkl
+src/cpgmodule/data/Horvath_2013.pkl
+src/cpgmodule/data/Horvath_2018.pkl
+src/cpgmodule/data/Levine.pkl
+src/cpgmodule/data/Lu_DNAmTL.pkl
+src/cpgmodule/data/Ped_McEwen.pkl
+src/cpgmodule/data/Ped_Wu.pkl
+src/cpgmodule/data/Zhang_BLUP.pkl
+src/cpgmodule/data/Zhang_EN.pkl
 src/cpgmodule/data/__init__.py
 src/cpgtools.egg-info/PKG-INFO
 src/cpgtools.egg-info/SOURCES.txt

{cpgtools-2.0.2 → cpgtools-2.0.4}/src/cpgtools.egg-info/requires.txt

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

{cpgtools-2.0.2 → cpgtools-2.0.4}/src/impyute/ops/util.py

@@ -41,20 +41,40 @@ def execute_fn_with_args_and_or_kwargs(fn, args, kwargs):
     except TypeError:
         return fn(*args)
 
-def toy_df(nrow, ncol, n_miss, sample_prefix, seed):
-    """
-    Make a dataFrame (nrow x ncol) with random values between 0 and 1, add
-    some missing values (n_miss). Generate a toy dataframe for testing purposes.
-    """
-    np.random.seed(seed)
-    data = np.random.rand(nrow*ncol).reshape((nrow, ncol)).astype(float)
-    x_ind = np.random.choice(nrow, n_miss)
-    y_ind = np.random.choice(ncol, n_miss)
-    for x,y in zip(x_ind, y_ind):
-        data[x][y] =  np.nan
-    colNames = [sample_prefix + '_' + str(i) for i in range(0,ncol)]
-    df = pd.DataFrame(data, columns=colNames)
-    return df
+def toy_df(n_rows=20, n_cols=5, missingness=0.2, min_val=0, max_val=1,
+              missing_value=np.nan, rand_seed=1234, sample_prefix=None):
+    """Generate an array or DataFrame with NaNs"""
+    np.random.seed(rand_seed)
+    X = np.random.uniform(
+        low = min_val, high = max_val, size = n_rows * n_cols).reshape(n_rows, n_cols).astype(
+        float)
+    # check missingness
+    if missingness > 0:
+        # If missingness >= 1 then use it as approximate (see below) count
+        if missingness >= 1:
+            n_missing = int(missingness)
+        else:
+            n_missing = int(missingness * n_rows * n_cols)
+            print(n_missing)
+    
+    # Introduce NaNs until n_miss "NAs" are inserted.
+    missing_count = 0
+    for i,j in zip(np.random.choice(n_rows, n_missing), np.random.choice(n_cols, n_missing)):
+        if np.isnan(X[i][j]):
+            continue
+        else:
+            X[i][j] = missing_value
+            missing_count += 1
+        if missing_count >= n_missing:
+            break
+
+    # check sample_prefix
+    if sample_prefix is None:
+        return X
+    else:
+        colNames = [sample_prefix + '_' + str(i) for i in range(0, n_cols)]
+        return pd.DataFrame(X, columns=colNames)
+    
 
 def insert_na(df, n_miss, seed):
     np.random.seed(seed)