annotate Marea/marea.py @ 37:2495c7772ca8 draft

Uploaded
author bimib
date Mon, 25 Nov 2019 11:57:57 -0500
parents 7b1971251c63
children 3af9d394367c
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bimib
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1 from __future__ import division
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bimib
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2 import sys
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bimib
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3 import pandas as pd
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bimib
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4 import itertools as it
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bimib
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5 import scipy.stats as st
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bimib
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6 import collections
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bimib
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7 import lxml.etree as ET
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bimib
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8 import pickle as pk
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bimib
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9 import math
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bimib
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10 import os
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bimib
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11 import argparse
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bimib
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12 from svglib.svglib import svg2rlg
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bimib
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13 from reportlab.graphics import renderPDF
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bimib
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14
16
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bimib
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15 ########################## argparse ##########################################
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16
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bimib
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17 def process_args(args):
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18 parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
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bimib
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19 description = 'process some value\'s'+
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bimib
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20 ' genes to create a comparison\'s map.')
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bimib
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21 parser.add_argument('-rs', '--rules_selector',
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bimib
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22 type = str,
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bimib
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23 default = 'HMRcore',
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bimib
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24 choices = ['HMRcore', 'Recon', 'Custom'],
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bimib
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25 help = 'chose which type of dataset you want use')
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bimib
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26 parser.add_argument('-cr', '--custom',
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bimib
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27 type = str,
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bimib
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28 help='your dataset if you want custom rules')
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bimib
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29 parser.add_argument('-na', '--names',
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bimib
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30 type = str,
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bimib
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31 nargs = '+',
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bimib
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32 help = 'input names')
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bimib
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33 parser.add_argument('-n', '--none',
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bimib
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34 type = str,
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bimib
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35 default = 'true',
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bimib
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36 choices = ['true', 'false'],
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bimib
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37 help = 'compute Nan values')
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38 parser.add_argument('-pv' ,'--pValue',
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bimib
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39 type = float,
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bimib
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40 default = 0.05,
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bimib
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41 help = 'P-Value threshold (default: %(default)s)')
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42 parser.add_argument('-fc', '--fChange',
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bimib
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43 type = float,
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bimib
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44 default = 1.5,
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bimib
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45 help = 'Fold-Change threshold (default: %(default)s)')
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46 parser.add_argument('-td', '--tool_dir',
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bimib
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47 type = str,
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bimib
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48 required = True,
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bimib
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49 help = 'your tool directory')
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50 parser.add_argument('-op', '--option',
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51 type = str,
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52 choices = ['datasets', 'dataset_class', 'datasets_rasonly'],
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53 help='dataset or dataset and class')
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54 parser.add_argument('-ol', '--out_log',
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55 help = "Output log")
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56 parser.add_argument('-ids', '--input_datas',
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bimib
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57 type = str,
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bimib
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58 nargs = '+',
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bimib
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59 help = 'input datasets')
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bimib
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60 parser.add_argument('-id', '--input_data',
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61 type = str,
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bimib
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62 help = 'input dataset')
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63 parser.add_argument('-ic', '--input_class',
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64 type = str,
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bimib
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65 help = 'sample group specification')
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66 parser.add_argument('-cm', '--custom_map',
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67 type = str,
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bimib
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68 help = 'custom map')
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69 parser.add_argument('-yn', '--yes_no',
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70 type = str,
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bimib
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71 choices = ['yes', 'no'],
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bimib
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72 help = 'if make or not custom map')
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73 parser.add_argument('-gs', '--generate_svg',
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74 type = str,
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bimib
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75 default = 'true',
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76 choices = ['true', 'false'],
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77 help = 'generate svg map')
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78 parser.add_argument('-gp', '--generate_pdf',
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79 type = str,
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80 default = 'true',
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81 choices = ['true', 'false'],
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82 help = 'generate pdf map')
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83 parser.add_argument('-gr', '--generate_ras',
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84 type = str,
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85 default = 'true',
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86 choices = ['true', 'false'],
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bimib
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87 help = 'generate reaction activity score')
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88 parser.add_argument('-sr', '--single_ras_file',
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89 type = str,
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bimib
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90 help = 'file that will contain ras')
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91
0
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bimib
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92 args = parser.parse_args()
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bimib
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93 return args
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bimib
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94
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bimib
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95 ########################### warning ###########################################
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96
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bimib
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97 def warning(s):
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98 args = process_args(sys.argv)
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bimib
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99 with open(args.out_log, 'a') as log:
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bimib
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100 log.write(s)
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101
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bimib
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102 ############################ dataset input ####################################
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103
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104 def read_dataset(data, name):
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105 try:
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106 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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107 except pd.errors.EmptyDataError:
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108 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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109 if len(dataset.columns) < 2:
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110 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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111 return dataset
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112
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113 ############################ dataset name #####################################
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114
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115 def name_dataset(name_data, count):
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116 if str(name_data) == 'Dataset':
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117 return str(name_data) + '_' + str(count)
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118 else:
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bimib
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119 return str(name_data)
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120
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121 ############################ load id e rules ##################################
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122
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123 def load_id_rules(reactions):
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124 ids, rules = [], []
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125 for key, value in reactions.items():
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126 ids.append(key)
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127 rules.append(value)
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128 return (ids, rules)
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bimib
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129
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130 ############################ check_methods ####################################
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131
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132 def gene_type(l, name):
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133 if check_hgnc(l):
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134 return 'hugo_id'
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bimib
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135 elif check_ensembl(l):
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136 return 'ensembl_gene_id'
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bimib
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137 elif check_symbol(l):
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138 return 'symbol'
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bimib
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139 elif check_entrez(l):
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bimib
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140 return 'entrez_id'
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bimib
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141 else:
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bimib
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142 sys.exit('Execution aborted:\n' +
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143 'gene ID type in ' + name + ' not supported. Supported ID'+
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144 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n')
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145
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146 def check_hgnc(l):
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147 if len(l) > 5:
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148 if (l.upper()).startswith('HGNC:'):
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149 return l[5:].isdigit()
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150 else:
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bimib
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151 return False
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bimib
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152 else:
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bimib
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153 return False
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154
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155 def check_ensembl(l):
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156 if len(l) == 15:
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157 if (l.upper()).startswith('ENS'):
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bimib
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158 return l[4:].isdigit()
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159 else:
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bimib
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160 return False
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161 else:
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bimib
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162 return False
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163
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164 def check_symbol(l):
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165 if len(l) > 0:
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bimib
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166 if l[0].isalpha() and l[1:].isalnum():
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bimib
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167 return True
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bimib
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168 else:
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bimib
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169 return False
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bimib
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170 else:
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bimib
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171 return False
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172
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173 def check_entrez(l):
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174 if len(l) > 0:
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bimib
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175 return l.isdigit()
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176 else:
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bimib
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177 return False
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178
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bimib
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179 def check_bool(b):
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bimib
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180 if b == 'true':
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bimib
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181 return True
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bimib
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182 elif b == 'false':
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183 return False
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184
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185 ############################ resolve_methods ##################################
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186
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187 def replace_gene_value(l, d):
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188 tmp = []
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bimib
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189 err = []
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bimib
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190 while l:
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bimib
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191 if isinstance(l[0], list):
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192 tmp_rules, tmp_err = replace_gene_value(l[0], d)
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193 tmp.append(tmp_rules)
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bimib
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194 err.extend(tmp_err)
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bimib
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195 else:
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bimib
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196 value = replace_gene(l[0], d)
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bimib
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197 tmp.append(value)
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bimib
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198 if value == None:
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bimib
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199 err.append(l[0])
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bimib
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200 l = l[1:]
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bimib
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201 return (tmp, err)
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202
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203
0
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204 def replace_gene(l, d):
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205 if l =='and' or l == 'or':
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206 return l
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207 else:
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208 value = d.get(l, None)
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bimib
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209 if not(value == None or isinstance(value, (int, float))):
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210 sys.exit('Execution aborted: ' + value + ' value not valid\n')
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bimib
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211 return value
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212
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213 def computes(val1, op, val2, cn):
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bimib
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214 if val1 != None and val2 != None:
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bimib
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215 if op == 'and':
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bimib
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216 return min(val1, val2)
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217 else:
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bimib
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218 return val1 + val2
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bimib
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219 elif op == 'and':
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bimib
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220 if cn is True:
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bimib
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221 if val1 != None:
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bimib
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222 return val1
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bimib
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223 elif val2 != None:
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bimib
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224 return val2
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bimib
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225 else:
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bimib
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226 return None
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bimib
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227 else:
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bimib
parents:
diff changeset
228 return None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
229 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
230 if val1 != None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
231 return val1
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
232 elif val2 != None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
233 return val2
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
234 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
235 return None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
236
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
237 def control(ris, l, cn):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
238 if len(l) == 1:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
239 if isinstance(l[0], (float, int)) or l[0] == None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
240 return l[0]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
241 elif isinstance(l[0], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
242 return control(None, l[0], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
243 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
244 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
245 elif len(l) > 2:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
246 return control_list(ris, l, cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
247 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
248 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
249
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
250 def control_list(ris, l, cn):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
251 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
252 if len(l) == 1:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
253 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
254 elif (isinstance(l[0], (float, int)) or
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
255 l[0] == None) and l[1] in ['and', 'or']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
256 if isinstance(l[2], (float, int)) or l[2] == None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
257 ris = computes(l[0], l[1], l[2], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
258 elif isinstance(l[2], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
259 tmp = control(None, l[2], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
260 if tmp is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
261 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
262 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
263 ris = computes(l[0], l[1], tmp, cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
264 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
265 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
266 l = l[3:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
267 elif l[0] in ['and', 'or']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
268 if isinstance(l[1], (float, int)) or l[1] == None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
269 ris = computes(ris, l[0], l[1], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
270 elif isinstance(l[1], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
271 tmp = control(None,l[1], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
272 if tmp is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
273 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
274 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
275 ris = computes(ris, l[0], tmp, cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
276 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
277 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
278 l = l[2:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
279 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
280 if isinstance(l[2], (float, int)) or l[2] == None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
281 tmp = control(None, l[0], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
282 if tmp is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
283 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
284 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
285 ris = computes(tmp, l[1], l[2], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
286 elif isinstance(l[2], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
287 tmp = control(None, l[0], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
288 tmp2 = control(None, l[2], cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
289 if tmp is False or tmp2 is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
290 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
291 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
292 ris = computes(tmp, l[1], tmp2, cn)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
293 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
294 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
295 l = l[3:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
296 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
297 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
298 return ris
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
299
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
300 ############################ map_methods ######################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
301
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
302 def fold_change(avg1, avg2):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
303 if avg1 == 0 and avg2 == 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
304 return 0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
305 elif avg1 == 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
306 return '-INF'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
307 elif avg2 == 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
308 return 'INF'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
309 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
310 return math.log(avg1 / avg2, 2)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
311
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
312 def fix_style(l, col, width, dash):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
313 tmp = l.split(';')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
314 flag_col = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
315 flag_width = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
316 flag_dash = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
317 for i in range(len(tmp)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
318 if tmp[i].startswith('stroke:'):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
319 tmp[i] = 'stroke:' + col
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
320 flag_col = True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
321 if tmp[i].startswith('stroke-width:'):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
322 tmp[i] = 'stroke-width:' + width
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
323 flag_width = True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
324 if tmp[i].startswith('stroke-dasharray:'):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
325 tmp[i] = 'stroke-dasharray:' + dash
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
326 flag_dash = True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
327 if not flag_col:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
328 tmp.append('stroke:' + col)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
329 if not flag_width:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
330 tmp.append('stroke-width:' + width)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
331 if not flag_dash:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
332 tmp.append('stroke-dasharray:' + dash)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
333 return ';'.join(tmp)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
334
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
335 def fix_map(d, core_map, threshold_P_V, threshold_F_C, max_F_C):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
336 maxT = 12
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
337 minT = 2
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
338 grey = '#BEBEBE'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
339 blue = '#0000FF'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
340 red = '#E41A1C'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
341 for el in core_map.iter():
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
342 el_id = str(el.get('id'))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
343 if el_id.startswith('R_'):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
344 tmp = d.get(el_id[2:])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
345 if tmp != None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
346 p_val = tmp[0]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
347 f_c = tmp[1]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
348 if p_val < threshold_P_V:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
349 if not isinstance(f_c, str):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
350 if abs(f_c) < math.log(threshold_F_C, 2):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
351 col = grey
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
352 width = str(minT)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
353 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
354 if f_c < 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
355 col = blue
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
356 elif f_c > 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
357 col = red
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
358 width = str(max((abs(f_c) * maxT) / max_F_C, minT))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
359 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
360 if f_c == '-INF':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
361 col = blue
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
362 elif f_c == 'INF':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
363 col = red
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
364 width = str(maxT)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
365 dash = 'none'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
366 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
367 dash = '5,5'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
368 col = grey
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
369 width = str(minT)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
370 el.set('style', fix_style(el.get('style'), col, width, dash))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
371 return core_map
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
372
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
373 ############################ make recon #######################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
374
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
375 def check_and_doWord(l):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
376 tmp = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
377 tmp_genes = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
378 count = 0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
379 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
380 if count >= 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
381 if l[0] == '(':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
382 count += 1
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
383 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
384 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
385 elif l[0] == ')':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
386 count -= 1
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
387 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
388 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
389 elif l[0] == ' ':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
390 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
391 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
392 word = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
393 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
394 if l[0] in [' ', '(', ')']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
395 break
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
396 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
397 word.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
398 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
399 word = ''.join(word)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
400 tmp.append(word)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
401 if not(word in ['or', 'and']):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
402 tmp_genes.append(word)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
403 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
404 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
405 if count == 0:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
406 return (tmp, tmp_genes)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
407 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
408 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
409
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
410 def brackets_to_list(l):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
411 tmp = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
412 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
413 if l[0] == '(':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
414 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
415 tmp.append(resolve_brackets(l))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
416 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
417 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
418 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
419 return tmp
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
420
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
421 def resolve_brackets(l):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
422 tmp = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
423 while l[0] != ')':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
424 if l[0] == '(':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
425 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
426 tmp.append(resolve_brackets(l))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
427 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
428 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
429 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
430 l.pop(0)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
431 return tmp
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
432
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
433 def priorityAND(l):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
434 tmp = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
435 flag = True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
436 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
437 if len(l) == 1:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
438 if isinstance(l[0], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
439 tmp.append(priorityAND(l[0]))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
440 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
441 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
442 l = l[1:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
443 elif l[0] == 'or':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
444 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
445 flag = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
446 l = l[1:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
447 elif l[1] == 'or':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
448 if isinstance(l[0], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
449 tmp.append(priorityAND(l[0]))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
450 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
451 tmp.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
452 tmp.append(l[1])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
453 flag = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
454 l = l[2:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
455 elif l[1] == 'and':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
456 tmpAnd = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
457 if isinstance(l[0], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
458 tmpAnd.append(priorityAND(l[0]))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
459 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
460 tmpAnd.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
461 tmpAnd.append(l[1])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
462 if isinstance(l[2], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
463 tmpAnd.append(priorityAND(l[2]))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
464 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
465 tmpAnd.append(l[2])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
466 l = l[3:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
467 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
468 if l[0] == 'and':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
469 tmpAnd.append(l[0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
470 if isinstance(l[1], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
471 tmpAnd.append(priorityAND(l[1]))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
472 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
473 tmpAnd.append(l[1])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
474 l = l[2:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
475 elif l[0] == 'or':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
476 flag = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
477 break
13
e96f3b85e5a0 Uploaded
bimib
parents: 12
diff changeset
478 if flag == True: #when there are only AND in list
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
479 tmp.extend(tmpAnd)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
480 elif flag == False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
481 tmp.append(tmpAnd)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
482 return tmp
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
483
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
484 def checkRule(l):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
485 if len(l) == 1:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
486 if isinstance(l[0], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
487 if checkRule(l[0]) is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
488 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
489 elif len(l) > 2:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
490 if checkRule2(l) is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
491 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
492 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
493 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
494 return True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
495
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
496 def checkRule2(l):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
497 while l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
498 if len(l) == 1:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
499 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
500 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
501 if checkRule(l[0]) is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
502 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
503 if isinstance(l[2], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
504 if checkRule(l[2]) is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
505 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
506 l = l[3:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
507 elif l[1] in ['and', 'or']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
508 if isinstance(l[2], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
509 if checkRule(l[2]) is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
510 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
511 l = l[3:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
512 elif l[0] in ['and', 'or']:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
513 if isinstance(l[1], list):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
514 if checkRule(l[1]) is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
515 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
516 l = l[2:]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
517 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
518 return False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
519 return True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
520
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
521 def do_rules(rules):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
522 split_rules = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
523 err_rules = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
524 tmp_gene_in_rule = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
525 for i in range(len(rules)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
526 tmp = list(rules[i])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
527 if tmp:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
528 tmp, tmp_genes = check_and_doWord(tmp)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
529 tmp_gene_in_rule.extend(tmp_genes)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
530 if tmp is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
531 split_rules.append([])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
532 err_rules.append(rules[i])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
533 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
534 tmp = brackets_to_list(tmp)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
535 if checkRule(tmp):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
536 split_rules.append(priorityAND(tmp))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
537 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
538 split_rules.append([])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
539 err_rules.append(rules[i])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
540 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
541 split_rules.append([])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
542 if err_rules:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
543 warning('Warning: wrong format rule in ' + str(err_rules) + '\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
544 return (split_rules, list(set(tmp_gene_in_rule)))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
545
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
546 def make_recon(data):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
547 try:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
548 import cobra as cb
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
549 import warnings
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
550 with warnings.catch_warnings():
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
551 warnings.simplefilter('ignore')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
552 recon = cb.io.read_sbml_model(data)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
553 react = recon.reactions
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
554 rules = [react[i].gene_reaction_rule for i in range(len(react))]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
555 ids = [react[i].id for i in range(len(react))]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
556 except cb.io.sbml3.CobraSBMLError:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
557 try:
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
558 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('')
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
559 if len(data.columns) < 2:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
560 sys.exit('Execution aborted: wrong format of '+
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
561 'custom datarules\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
562 if not len(data.columns) == 2:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
563 warning('Warning: more than 2 columns in custom datarules.\n' +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
564 'Extra columns have been disregarded\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
565 ids = list(data.iloc[:, 0])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
566 rules = list(data.iloc[:, 1])
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
567 except pd.errors.EmptyDataError:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
568 sys.exit('Execution aborted: wrong format of custom datarules\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
569 except pd.errors.ParserError:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
570 sys.exit('Execution aborted: wrong format of custom datarules\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
571 split_rules, tmp_genes = do_rules(rules)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
572 gene_in_rule = {}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
573 for i in tmp_genes:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
574 gene_in_rule[i] = 'ok'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
575 return (ids, split_rules, gene_in_rule)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
576
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
577 ############################ gene #############################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
578
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
579 def data_gene(gene, type_gene, name, gene_custom):
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
580 args = process_args(sys.argv)
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
581 for i in range(len(gene)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
582 tmp = gene.iloc[i, 0]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
583 if tmp.startswith(' ') or tmp.endswith(' '):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
584 gene.iloc[i, 0] = (tmp.lstrip()).rstrip()
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
585 gene_dup = [item for item, count in
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
586 collections.Counter(gene[gene.columns[0]]).items() if count > 1]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
587 pat_dup = [item for item, count in
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
588 collections.Counter(list(gene.columns)).items() if count > 1]
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
589
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
590 if gene_dup:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
591 if gene_custom == None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
592 if args.rules_selector == 'HMRcore':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
593 gene_in_rule = pk.load(open(args.tool_dir +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
594 '/local/HMRcore_genes.p', 'rb'))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
595 elif args.rules_selector == 'Recon':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
596 gene_in_rule = pk.load(open(args.tool_dir +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
597 '/local/Recon_genes.p', 'rb'))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
598 gene_in_rule = gene_in_rule.get(type_gene)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
599 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
600 gene_in_rule = gene_custom
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
601 tmp = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
602 for i in gene_dup:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
603 if gene_in_rule.get(i) == 'ok':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
604 tmp.append(i)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
605 if tmp:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
606 sys.exit('Execution aborted because gene ID '
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
607 +str(tmp)+' in '+name+' is duplicated\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
608 if pat_dup:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
609 warning('Warning: duplicated label\n' + str(pat_dup) + 'in ' + name +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
610 '\n')
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
611
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
612 return (gene.set_index(gene.columns[0])).to_dict()
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
613
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
614 ############################ resolve ##########################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
615
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
616 def resolve(genes, rules, ids, resolve_none, name):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
617 resolve_rules = {}
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
618 names_array = []
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
619 not_found = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
620 flag = False
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
621 for key, value in genes.items():
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
622 tmp_resolve = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
623 for i in range(len(rules)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
624 tmp = rules[i]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
625 if tmp:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
626 tmp, err = replace_gene_value(tmp, value)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
627 if err:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
628 not_found.extend(err)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
629 ris = control(None, tmp, resolve_none)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
630 if ris is False or ris == None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
631 tmp_resolve.append(None)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
632 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
633 tmp_resolve.append(ris)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
634 flag = True
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
635 else:
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
636 tmp_resolve.append(None)
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
637 resolve_rules[key] = tmp_resolve
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
638 if flag is False:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
639 warning('Warning: no computable score (due to missing gene values)' +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
640 'for class ' + name + ', the class has been disregarded\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
641 return (None, None)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
642 return (resolve_rules, list(set(not_found)))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
643
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
644 ############################ split class ######################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
645
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
646 def split_class(classes, resolve_rules):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
647 class_pat = {}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
648 for i in range(len(classes)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
649 classe = classes.iloc[i, 1]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
650 if not pd.isnull(classe):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
651 l = []
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
652 for j in range(i, len(classes)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
653 if classes.iloc[j, 1] == classe:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
654 pat_id = classes.iloc[j, 0]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
655 tmp = resolve_rules.get(pat_id, None)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
656 if tmp != None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
657 l.append(tmp)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
658 classes.iloc[j, 1] = None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
659 if l:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
660 class_pat[classe] = list(map(list, zip(*l)))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
661 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
662 warning('Warning: no sample found in class ' + classe +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
663 ', the class has been disregarded\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
664 return class_pat
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
665
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
666 ############################ create_ras #######################################
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
667
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
668 def create_ras (resolve_rules, dataset_name, single_ras, rules, ids):
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
669
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
670 if resolve_rules == None:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
671 warning("Couldn't generate RAS for current dataset: " + dataset_name)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
672
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
673 for geni in resolve_rules.values():
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
674 for i, valori in enumerate(geni):
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
675 if valori == None:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
676 geni[i] = 'None'
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
677
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
678 output_ras = pd.DataFrame.from_dict(resolve_rules)
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
679
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
680 output_ras.insert(0, 'Reactions', ids)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
681 output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False)
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
682
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
683 if (single_ras):
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
684 args = process_args(sys.argv)
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
685 text_file = open(args.single_ras_file, "w")
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
686 else:
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
687 text_file = open("ras/Reaction_Activity_Score_Of_" + dataset_name + ".tsv", "w")
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
688
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
689 text_file.write(output_to_csv)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
690 text_file.close()
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
691
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
692 ############################ map ##############################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
693
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
694 def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C, create_svg, create_pdf):
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
695 args = process_args(sys.argv)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
696 if (not class_pat) or (len(class_pat.keys()) < 2):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
697 sys.exit('Execution aborted: classes provided for comparisons are ' +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
698 'less than two\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
699 for i, j in it.combinations(class_pat.keys(), 2):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
700 tmp = {}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
701 count = 0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
702 max_F_C = 0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
703 for l1, l2 in zip(class_pat.get(i), class_pat.get(j)):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
704 try:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
705 stat_D, p_value = st.ks_2samp(l1, l2)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
706 avg = fold_change(sum(l1) / len(l1), sum(l2) / len(l2))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
707 if not isinstance(avg, str):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
708 if max_F_C < abs(avg):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
709 max_F_C = abs(avg)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
710 tmp[ids[count]] = [float(p_value), avg]
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
711 count += 1
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
712 except (TypeError, ZeroDivisionError):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
713 count += 1
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
714 tab = 'result/' + i + '_vs_' + j + ' (Tabular Result).tsv'
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
715 tmp_csv = pd.DataFrame.from_dict(tmp, orient = "index")
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
716 tmp_csv = tmp_csv.reset_index()
31
944e15aa970a Uploaded
bimib
parents: 28
diff changeset
717 header = ['ids', 'P_Value', 'Log2(fold change)']
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
718 tmp_csv.to_csv(tab, sep = '\t', index = False, header = header)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
719
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
720 if create_svg or create_pdf:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
721 if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom'
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
722 and args.yes_no == 'yes'):
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
723 fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
724 file_svg = 'result/' + i + '_vs_' + j + ' (SVG Map).svg'
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
725 with open(file_svg, 'wb') as new_map:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
726 new_map.write(ET.tostring(core_map))
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
727
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
728
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
729 if create_pdf:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
730 file_pdf = 'result/' + i + '_vs_' + j + ' (PDF Map).pdf'
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
731 renderPDF.drawToFile(svg2rlg(file_svg), file_pdf)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
732
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
733 if not create_svg:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
734 #Ho utilizzato il file svg per generare il pdf,
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
735 #ma l'utente non ne ha richiesto il ritorno, quindi
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
736 #lo elimino
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
737 os.remove('result/' + i + '_vs_' + j + ' (SVG Map).svg')
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
738
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
739 return None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
740
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
741 ############################ MAIN #############################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
742
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
743 def main():
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
744 args = process_args(sys.argv)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
745
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
746 create_svg = check_bool(args.generate_svg)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
747 create_pdf = check_bool(args.generate_pdf)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
748 generate_ras = check_bool(args.generate_ras)
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
749
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
750 os.makedirs('result')
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
751
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
752 if generate_ras:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
753 os.makedirs('ras')
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
754
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
755 if args.rules_selector == 'HMRcore':
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
756 recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb'))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
757 elif args.rules_selector == 'Recon':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
758 recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb'))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
759 elif args.rules_selector == 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
760 ids, rules, gene_in_rule = make_recon(args.custom)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
761
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
762 resolve_none = check_bool(args.none)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
763
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
764 class_pat = {}
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
765
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
766 if args.option == 'datasets_rasonly':
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
767 name = "RAS Dataset"
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
768 dataset = read_dataset(args.input_datas[0],"dataset")
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
769
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
770 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
771
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
772 type_gene = gene_type(dataset.iloc[0, 0], name)
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
773
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
774 if args.rules_selector != 'Custom':
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
775 genes = data_gene(dataset, type_gene, name, None)
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
776 ids, rules = load_id_rules(recon.get(type_gene))
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
777 elif args.rules_selector == 'Custom':
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
778 genes = data_gene(dataset, type_gene, name, gene_in_rule)
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
779
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
780 resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
781
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
782 create_ras(resolve_rules, name, True, rules, ids)
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
783
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
784 if err != None and err:
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
785 warning('Warning: gene\n' + str(err) + '\nnot found in class '
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
786 + name + ', the expression level for this gene ' +
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
787 'will be considered NaN\n')
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
788
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
789 print('execution succeded')
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
790 return None
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
791
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
792
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
793 elif args.option == 'datasets':
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
794 num = 1
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
795 for i, j in zip(args.input_datas, args.names):
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
796
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
797 name = name_dataset(j, num)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
798 dataset = read_dataset(i, name)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
799
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
800 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
801
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
802 type_gene = gene_type(dataset.iloc[0, 0], name)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
803
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
804 if args.rules_selector != 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
805 genes = data_gene(dataset, type_gene, name, None)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
806 ids, rules = load_id_rules(recon.get(type_gene))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
807 elif args.rules_selector == 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
808 genes = data_gene(dataset, type_gene, name, gene_in_rule)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
809
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
810
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
811 resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
812
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
813 if generate_ras:
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
814 create_ras(resolve_rules, name, False, rules, ids)
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
815
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
816 if err != None and err:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
817 warning('Warning: gene\n' + str(err) + '\nnot found in class '
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
818 + name + ', the expression level for this gene ' +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
819 'will be considered NaN\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
820 if resolve_rules != None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
821 class_pat[name] = list(map(list, zip(*resolve_rules.values())))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
822 num += 1
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
823 elif args.option == 'dataset_class':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
824 name = 'RNAseq'
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
825 dataset = read_dataset(args.input_data, name)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
826 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
827 type_gene = gene_type(dataset.iloc[0, 0], name)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
828 classes = read_dataset(args.input_class, 'class')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
829 if not len(classes.columns) == 2:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
830 warning('Warning: more than 2 columns in class file. Extra' +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
831 'columns have been disregarded\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
832 classes = classes.astype(str)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
833 if args.rules_selector != 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
834 genes = data_gene(dataset, type_gene, name, None)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
835 ids, rules = load_id_rules(recon.get(type_gene))
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
836 elif args.rules_selector == 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
837 genes = data_gene(dataset, type_gene, name, gene_in_rule)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
838 resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
839 if err != None and err:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
840 warning('Warning: gene\n'+str(err)+'\nnot found in class '
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
841 + name + ', the expression level for this gene ' +
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
842 'will be considered NaN\n')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
843 if resolve_rules != None:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
844 class_pat = split_class(classes, resolve_rules)
34
1a97d1537623 Lot of bug fixes
bimib
parents: 31
diff changeset
845 if generate_ras:
35
7b1971251c63 Uploaded
bimib
parents: 34
diff changeset
846 create_ras(resolve_rules, name, False, rules, ids)
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
847
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 16
diff changeset
848
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
849 if args.rules_selector == 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
850 if args.yes_no == 'yes':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
851 try:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
852 core_map = ET.parse(args.custom_map)
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
853 except (ET.XMLSyntaxError, ET.XMLSchemaParseError):
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
854 sys.exit('Execution aborted: custom map in wrong format')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
855 elif args.yes_no == 'no':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
856 core_map = ET.parse(args.tool_dir + '/local/HMRcoreMap.svg')
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
857 else:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
858 core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg')
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
859
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
860 maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf)
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
861
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
862 print('Execution succeded')
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
863
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
864 return None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
865
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
866 ###############################################################################
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
867
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
868 if __name__ == "__main__":
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
869 main()