cpgtools 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

cpgtools-2.0.2.data/scripts/beta_imputation.py

@@ -0,0 +1,604 @@
+#!python
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Sep 20 21:14:40 2024
+
+@author: m102324
+"""
+
+import sys
+import pandas as pd
+import numpy as np
+import logging
+import argparse
+from sklearn.impute import KNNImputer
+#from sklearn.experimental import enable_iterative_imputer
+#from sklearn.impute import IterativeImputer
+
+from impyute.cs.fast_knn import fast_knn
+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 missingpy import MissForest
+
+#use pip to install fancyimpute
+from fancyimpute import NuclearNormMinimization, SoftImpute, BiScaler
+
+from cpgmodule._version import __version__
+
+
+__author__ = "Liguo Wang"
+__copyright__ = "Copyleft"
+__credits__ = []
+__license__ = "MIT"
+__maintainer__ = "Liguo Wang"
+__email__ = "wang.liguo@mayo.edu"
+__status__ = "Development"
+
+logging.basicConfig(
+    format="%(asctime)s [%(levelname)s]  %(message)s",
+    datefmt='%Y-%m-%d %I:%M:%S', level=logging.DEBUG)
+            
+def read_df(infile):
+    logging.info("Read input file \"%s\" as a data frame ..." % infile)
+    df = pd.read_csv(infile, index_col=0, sep=None, engine='python')
+    return df
+
+def nafiller():
+    """
+    Generic and Specific Methods for DNA Methylation Missing Value Imputation.
+    """
+   
+    general_help = "DNA methylation data imputation package"
+
+    # sub commands and help.
+    commands = {
+        'DropNA': "Drop rows or columns with NAs.",
+        'FillValue': "Replace missing values with a given value.",
+        'FillMean': "Impute missing values with row-wise or column-wise means..",
+        'FillMedian': "Impute missing values with row-wise or column-wise medians.",
+        'FillMin': "Impute missing values with row-wise or column-wise minimum values.",
+        'FillMax': "Impute missing values with row-wise or column-wise maximum values",
+        'FillRand': "Impute missing values with randomly selected values from \
+                    the same row or column.",
+        'FillRef': "Impute missing values using values from an external \
+                    reference dataset.",
+        'KNN': "Impute missing values using scikit-learn's KNNImputer function. \
+                Note: slow for large datasets.",
+        'KNN2': "Impute missing values using KNN2",
+        'fKNN': "Impute missing values using Impyute's fast KNN (fKNN) method.",
+        'EM': "Impute missing values using the Expectation Maximization (EM) \
+                algorithm.",
+        'Buck': "Impute missing values using Buck's method.",
+        'NNM': "Impute missing values using Nuclear Norm Minimization (NNM).",
+        'SoftImpute': "Impute missing values by iterative soft thresholding of SVD decompositions.",
+        'RF': "Impute missing values using Random Forest (RF) prediction.",
+        'ToyDf': "Generate a toy dataframe with specified missing values for testing.",
+        'InsertNA': "Insert n missing values into an exist dataframe.",
+         }
+    # create parse
+    parser = argparse.ArgumentParser(
+        description=general_help, epilog='',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+        )
+    parser.add_argument(
+        '-v', '--version', action='version', version='%s %s' %
+        ('nafiller', __version__)
+        )
+
+    # create sub-parser
+    sub_parsers = parser.add_subparsers(help='Sub-command description:')
+    
+    DropNA_parser = sub_parsers.add_parser('DropNA', help=commands['DropNA'])
+    FillValue_parser = sub_parsers.add_parser('FillValue', help=commands['FillValue'])
+    FillMean_parser = sub_parsers.add_parser('FillMean', help=commands['FillMean'])
+    FillMedian_parser = sub_parsers.add_parser('FillMedian', help=commands['FillMedian'])
+    FillMin_parser = sub_parsers.add_parser('FillMin', help=commands['FillMin'])
+    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'])
+    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'])
+    Buck_parser = sub_parsers.add_parser('Buck', help=commands['Buck'])
+    NNM_parser = sub_parsers.add_parser('NNM', help=commands['NNM'])
+    SoftImpute_parser = sub_parsers.add_parser('SoftImpute', help=commands['SoftImpute'])
+    RF_parser = sub_parsers.add_parser('RF', help=commands['RF'])
+    ToyDf_parser = sub_parsers.add_parser('ToyDf', help=commands['ToyDf'])
+    InsertNA_parser = sub_parsers.add_parser('InsertNA', help=commands['InsertNA'])
+    
+    
+    DropNA_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    DropNA_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    DropNA_parser.add_argument(
+        '-a', '--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(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    FillValue_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillValue_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillValue_parser.add_argument(
+        '-s', '--score', type=float, default=0.0,
+        help="The value uesd to fill all NAs.")
+    FillValue_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    FillMean_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillMean_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillMean_parser.add_argument(
+        '-a', '--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,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    FillMedian_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillMedian_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillMedian_parser.add_argument(
+        '-a', '--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,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    FillMin_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillMin_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillMin_parser.add_argument(
+        '-a', '--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,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
+    FillMax_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillMax_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillMax_parser.add_argument(
+        '-a', '--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,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
+    FillRand_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillRand_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillRand_parser.add_argument(
+        '-a', '--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,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    FillRef_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    FillRef_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    FillRef_parser.add_argument(
+        '-r', '--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")
+
+    KNN_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    KNN_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    KNN_parser.add_argument(
+        '-k', '--neighbours', type=int,
+        help="Number of neighboring samples to use for imputation. If k is \
+            None, k = sqrt(n) where n is the \"total number of samples\".")
+    KNN_parser.add_argument(
+        '-w', '--weightfunction', type=str,
+        choices=['uniform', 'distance'],
+        default='distance',
+        help="Weight function used in predictionaction.")
+    KNN_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    fKNN_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    fKNN_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    fKNN_parser.add_argument(
+        '-k', '--neighbours', type=int,
+        help="Number of neighboring samples to use for imputation. If k is \
+            None, k = sqrt(n) where n is the \"total number of samples\".")
+    fKNN_parser.add_argument(
+        '--eps', type=float,
+        default=0,
+        help="Refer to the docs for [`scipy.spatial.KDTree.query`]. Must be\
+            non-negative float number.")
+    fKNN_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    EM_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    EM_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    EM_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
+    Buck_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    Buck_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    Buck_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
+    NNM_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    NNM_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    NNM_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    SoftImpute_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    SoftImpute_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    SoftImpute_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    RF_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    RF_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    RF_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+
+    ToyDf_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Name of the output data frame.")
+    ToyDf_parser.add_argument(
+        '-r', '--nrow', type=int, default=10,
+        help="Number of rows. default: %(default)s")
+    ToyDf_parser.add_argument(
+        '-c', '--ncol', type=int, default=10,
+        help="Number of columns. default: %(default)s")
+    ToyDf_parser.add_argument(
+        '--na', type=int, default=5,
+        help="Number of missing values ingested into the dataframe. default: %(default)s")
+    ToyDf_parser.add_argument(
+        '-s', '--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")
+    ToyDf_parser.add_argument(
+        '--decimal', type=int, default=5,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
+    InsertNA_parser.add_argument(
+        'input', type=str, metavar='input_df',
+        help="Input data frame.")
+    InsertNA_parser.add_argument(
+        'output', type=str, metavar='out_df',
+        help="Output data frame.")
+    InsertNA_parser.add_argument(
+        '--na', type=int,
+        help="Number of missing values ingested into the dataframe.")
+    InsertNA_parser.add_argument(
+        '-s', '--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,
+        help="Number of decimal places to round each column to. default: %(default)s")
+    
+    axis_name = {0:'columns', 1:'rows'}
+    args = parser.parse_args()
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(0)
+    elif len(sys.argv) >= 2:
+        command = sys.argv[1]
+        if command.lower() == 'dropna':
+            input_df = read_df(args.input)
+            #reset
+            axis_name = {0:'rows', 1:'columns'}
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            logging.info("Remove %s with any missing values ..." % axis_name[args.axis])
+            output_df = input_df.dropna(axis=args.axis, how='any').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() == 'fillvalue':
+            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 with \"%f\" ..." % args.score)
+            output_df = input_df.fillna(args.score).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() == 'fillmean':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            if args.axis == 0:
+                logging.info("Replace missing values with COLUMN means ...")
+                output_df = input_df.fillna(input_df.mean())
+            elif args.axis == 1:
+                logging.info("Replace missing values with ROW means ...")
+                input_df = input_df.T
+                output_df = input_df.fillna(input_df.mean()).T
+                logging.info("Unknown parameter.")
+                pass
+            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() == 'fillmedian':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            if args.axis == 0:
+                logging.info("Replace missing values with COLUMN medians ...")
+                output_df = input_df.fillna(input_df.median())
+            elif args.axis == 1:
+                logging.info("Replace missing values with ROW medians ...")
+                input_df = input_df.T
+                output_df = input_df.fillna(input_df.median()).T
+            else:
+                logging.info("Unknown parameter.")
+                pass
+            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() == 'fillmin':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            if args.axis == 0:
+                logging.info("Replace missing values with COLUMN minimums ...")
+                output_df = input_df.fillna(input_df.min())
+            elif args.axis == 1:
+                logging.info("Replace missing values with ROW minimums ...")
+                input_df = input_df.T
+                output_df = input_df.fillna(input_df.min()).T
+            else:
+                logging.info("Unknown parameter.")
+                pass
+            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() == 'fillmax':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            if args.axis == 0:
+                logging.info("Replace missing values with COLUMN maximums ...")
+                output_df = input_df.fillna(input_df.max())
+            elif args.axis == 1:
+                logging.info("Replace missing values with ROW maximums ...")
+                input_df = input_df.T
+                output_df = input_df.fillna(input_df.max()).T
+            else:
+                logging.info("Unknown parameter.")
+                pass
+            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() == 'fillrand':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+            if args.axis == 0:
+                logging.info("Replace missing values with values randomly selected  from the same column ...")
+                output_df = random_impute(input_df)
+            elif args.axis == 1:
+                logging.info("Replace missing values with values randomly selected  from the same row ...")
+                input_df = input_df.T
+                output_df = random_impute(input_df).T
+            else:
+                logging.info("Unknown parameter.")
+                pass
+            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() == 'fillref':
+            input_df = read_df(args.input)
+            logging.info("File \"%s\" contains %d missing values ..." %
+                        (args.input, input_df.isna().sum().sum()))
+
+            input_df.index = input_df.index.map(str)
+            external_ref = {}
+            logging.info("Read external reference file \"%s\" ..." % args.ref)
+            for l in open(args.ref,'r'):
+                l = l.strip()
+                f = l.split()
+                try:
+                    external_ref[f[0]] = float(f[1])
+                except ValueError:
+                    pass
+            logging.info("Replace missing values with values from external reference ...")
+            for ID, betas in input_df.iterrows():
+                if betas.isnull().values.any():
+                    if ID in external_ref:
+                        ref_beta = external_ref[ID]
+                        input_df.loc[ID, :] = betas.fillna(ref_beta)
+                    else:
+                        continue
+                else:
+                    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() == 'knn':
+            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 scikit-learn's KNNImputer function ...")
+            if args.neighbours is None:
+                nb = int(input_df.shape[1]**0.5)
+            else:
+                nb = args.neighbours
+            imputer = KNNImputer(n_neighbors=nb, weights=args.weightfunction)
+            after = imputer.fit_transform(input_df)
+            output_df = pd.DataFrame(after, index = input_df.index,
+                                     columns = input_df.columns)
+            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() == 'fknn':
+            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 Impyute's fast KNN (fKNN) method ...")
+            if args.neighbours is None:
+                nb = int(input_df.shape[1]**0.5)
+            else:
+                nb = args.neighbours
+            output_df = fast_knn(input_df, k=nb, eps=args.eps, p=2, 
+                                 distance_upper_bound=np.inf, leafsize=10)
+            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() == 'em':
+            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 EM algorithem ...")
+            output_df = em(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() == 'buck':
+            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 Buck's method ...")
+            output_df = buck_iterative(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() == 'nnm':
+            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 nuclear norm minimization ...")
+            X_filled = NuclearNormMinimization().fit_transform(input_df.to_numpy())
+            output_df = pd.DataFrame(X_filled, index=input_df.index, columns=input_df.columns)
+            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() == 'softimpute':
+            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 SoftImpute ...")
+            X_filled = SoftImpute().fit_transform(input_df.to_numpy())
+            output_df = pd.DataFrame(X_filled, index=input_df.index, columns=input_df.columns)
+            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() == 'rf':
+            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 Random Forest ...")
+            imputer = MissForest()
+            X_filled = imputer.fit_transform(input_df.to_numpy())
+            output_df = pd.DataFrame(X_filled, index=input_df.index, columns=input_df.columns)
+            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() == '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)
+            #print(output_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() == 'insertna':
+            input_df = read_df(args.input)
+            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 = 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()))
+
+    else:
+        print("Unknown command!")
+        parser.print_help(sys.stderr)
+        sys.exit(0)
+
+if __name__=='__main__':
+    nafiller()

{cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_jitter_plot.py

@@ -26,6 +26,7 @@ import sys,os
 import collections
 import subprocess
 import numpy as np
+from cpgmodule._version import __version__
 from optparse import OptionParser
 from cpgmodule import ireader
 from cpgmodule.utils import *
@@ -36,7 +37,6 @@ __author__ = "Liguo Wang"
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPL"
-__version__="2.0.0"
 __maintainer__ = "Liguo Wang"
 __email__ = "wang.liguo@mayo.edu"
 __status__ = "Development"

{cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_m_conversion.py

@@ -18,6 +18,7 @@ import sys,os
 import collections
 import numpy as np
 from scipy import stats
+from cpgmodule._version import __version__
 from optparse import OptionParser
 from cpgmodule import ireader
 from cpgmodule.utils import *
@@ -26,7 +27,6 @@ __author__ = "Liguo Wang"
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPL"
-__version__="2.0.0"
 __maintainer__ = "Liguo Wang"
 __email__ = "wang.liguo@mayo.edu"
 __status__ = "Development"

{cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_profile_gene_centered.py

@@ -21,6 +21,7 @@ import collections
 import subprocess
 import numpy as np
 from optparse import OptionParser
+from cpgmodule._version import __version__
 from cpgmodule import ireader
 from cpgmodule.utils import *
 from cpgmodule import BED
@@ -29,7 +30,6 @@ __author__ = "Liguo Wang"
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPL"
-__version__="2.0.0"
 __maintainer__ = "Liguo Wang"
 __email__ = "wang.liguo@mayo.edu"
 __status__ = "Development"

{cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_profile_region.py

@@ -25,6 +25,7 @@ import collections
 import subprocess
 import numpy as np
 from optparse import OptionParser
+from cpgmodule._version import __version__
 from cpgmodule import ireader
 from cpgmodule.utils import *
 from cpgmodule import BED
@@ -33,7 +34,6 @@ __author__ = "Liguo Wang"
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPL"
-__version__="2.0.0"
 __maintainer__ = "Liguo Wang"
 __email__ = "wang.liguo@mayo.edu"
 __status__ = "Development"