annotate normalize_dataset.py @ 0:72633301cc0d draft default tip

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/normalize_dataset commit 21b25425f77162c0edae4dd87b3a9e33608c5a95-dirty

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os
import argparse
import re

def isfloat(value):
  try:
    float(value)
    return True
  except ValueError:
    return False

def normalize_dataset(args):
    with open(args.input_file, 'r') as input_file:
        input_file_content = input_file.readlines()
        if args.normalization == 'column':
            column_number = len(input_file_content[0][:-1].split('\t'))
            column_sum = [0] * column_number

        with open(args.output_file, 'w') as output_file:
            for line in input_file_content:
                split_line = line[:-1].split('\t')

                if args.normalization == 'row':
                    row_sum = 0

                    for col in split_line:
                        if isfloat(col):
                            row_sum += float(col) 

                    sep = ''
                    for col in split_line:
                        if isfloat(col):
                            if args.format == 'percentage':
                                output_file.write(sep + str(100*float(col)/row_sum))
                            else:
                                output_file.write(sep + str(float(col)/row_sum))
                        else:
                            output_file.write(sep + col)
                        sep = '\t'
                    output_file.write('\n')

                elif args.normalization == 'column':
                    for i in range(len(split_line)):
                        if isfloat(split_line[i]):
                            column_sum[i] += float(split_line[i]) 

            if args.normalization == 'column':
                for line in input_file_content:
                    split_line = line[:-1].split('\t')
                    sep = ''
                    for i in range(len(split_line)):
                        if isfloat(split_line[i]):
                            if args.format == 'percentage':
                                output_file.write(sep + str(100*float(split_line[i])/column_sum[i]))
                            else:
                                output_file.write(sep + str(float(split_line[i])/column_sum[i]))
                        else:
                            output_file.write(sep + split_line[i])
                        sep = '\t'
                    output_file.write('\n')

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--input_file', required=True)
    parser.add_argument('--output_file', required=True)
    parser.add_argument('--normalization', required=True, 
        choices= ['column','row'])
    parser.add_argument('--format', required=True, 
        choices= ['proportion','percentage'])
    args = parser.parse_args()
    normalize_dataset(args)