Mercurial > repos > proteore > proteore_filter_keywords_values
annotate filter_kw_val.py @ 1:cb9555653b09 draft
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author | proteore |
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date | Fri, 21 Sep 2018 06:03:25 -0400 |
parents | a55e8b137c6b |
children | 52a7afd01c6d |
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1 import argparse, re, csv |
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2 |
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3 def options(): |
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4 """ |
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5 Parse options: |
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6 -i, --input Input filename and boolean value if the file contains header ["filename,true/false"] |
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7 --kw Keyword to be filtered, the column number where this filter applies, |
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8 boolean value if the keyword should be filtered in exact ["keyword,ncol,true/false"]. |
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9 This option can be repeated: --kw "kw1,c1,true" --kw "kw2,c1,false" --kw "kw3,c2,true" |
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10 --kwfile A file that contains keywords to be filter, the column where this filter applies and |
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11 boolean value if the keyword should be filtered in exact ["filename,ncol,true/false"] |
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12 --value The value to be filtered, the column number where this filter applies and the |
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13 operation symbol ["value,ncol,=/>/>=/</<=/!="] |
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14 --values_range range of values to be keep, example : --values_range 5 20 c1 true |
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15 --operator The operator used to filter with several keywords/values : AND or OR |
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16 --o --output The output filename |
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17 --filtered_file The file contains removed lines |
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18 -s --sort_col Used column to sort the file, ",true" for reverse sorting, ",false" otherwise example : c1,false |
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19 """ |
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20 parser = argparse.ArgumentParser() |
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21 parser.add_argument("-i", "--input", help="Input file", required=True) |
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22 parser.add_argument("--kw", nargs="+", action="append", help="") |
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23 parser.add_argument("--kw_file", nargs="+", action="append", help="") |
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24 parser.add_argument("--value", nargs="+", action="append", help="") |
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25 parser.add_argument("--values_range", nargs="+", action="append", help="") |
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26 parser.add_argument("--operator", default="OR", type=str, choices=['AND','OR'],help='') |
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27 parser.add_argument("-o", "--output", default="output.txt") |
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28 parser.add_argument("--filtered_file", default="filtered_output.txt") |
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29 parser.add_argument("-s","--sort_col", help="") |
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30 |
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31 args = parser.parse_args() |
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32 filters(args) |
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33 |
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34 def str_to_bool(v): |
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35 if v.lower() in ('yes', 'true', 't', 'y', '1'): |
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36 return True |
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37 elif v.lower() in ('no', 'false', 'f', 'n', '0'): |
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38 return False |
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39 else: |
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40 raise argparse.ArgumentTypeError('Boolean value expected.') |
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41 |
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42 #Check if a variable is a float or an integer |
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43 def is_number(number_format, n): |
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44 float_format = re.compile(r"^[-]?[0-9][0-9]*.?[0-9]+$") |
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45 int_format = re.compile(r"^[-]?[0-9][0-9]*$") |
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46 test = "" |
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47 if number_format == "int": |
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48 test = re.match(int_format, n) |
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49 elif number_format == "float": |
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50 test = re.match(float_format, n) |
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51 if test: |
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52 return True |
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53 |
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54 #Filter the document |
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55 def filters(args): |
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56 filename = args.input.split(",")[0] |
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57 header = str_to_bool(args.input.split(",")[1]) |
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58 csv_file = read_file(filename) |
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59 results_dict = {} |
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60 |
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61 if args.kw: |
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62 keywords = args.kw |
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63 for k in keywords: |
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64 results_dict=filter_keyword(csv_file, header, results_dict, k[0], k[1], k[2]) |
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65 |
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66 if args.kw_file: |
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67 key_files = args.kw_file |
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68 for kf in key_files: |
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69 keywords = read_option(kf[0]) |
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70 results_dict=filter_keyword(csv_file, header, results_dict, keywords, kf[1], kf[2]) |
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71 |
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72 if args.value: |
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73 for v in args.value: |
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74 if is_number("float", v[0]): |
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75 results_dict = filter_value(csv_file, header, results_dict, v[0], v[1], v[2]) |
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76 else: |
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77 raise ValueError("Please enter a number in filter by value") |
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78 |
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79 if args.values_range: |
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80 for vr in args.values_range: |
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81 if (is_number("float", vr[0]) or is_number("int", vr[0])) and (is_number("float",vr[1]) or is_number("int",vr[1])): |
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82 results_dict = filter_values_range(csv_file, header, results_dict, vr[0], vr[1], vr[2], vr[3]) |
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83 |
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84 remaining_lines=[] |
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85 filtered_lines=[] |
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86 |
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87 if header is True : |
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88 remaining_lines.append(csv_file[0]) |
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89 filtered_lines.append(csv_file[0]) |
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90 |
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91 for id_line,line in enumerate(csv_file) : |
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92 if id_line in results_dict : #skip header and empty lines |
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93 if args.operator == 'OR' : |
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94 if any(results_dict[id_line]) : |
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95 filtered_lines.append(line) |
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96 else : |
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97 remaining_lines.append(line) |
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98 |
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99 elif args.operator == "AND" : |
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100 if all(results_dict[id_line]) : |
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101 filtered_lines.append(line) |
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102 else : |
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103 remaining_lines.append(line) |
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104 |
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105 #sort of results by column |
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106 if args.sort_col : |
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107 sort_col=args.sort_col.split(",")[0] |
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108 sort_col=column_from_txt(sort_col) |
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109 reverse=str_to_bool(args.sort_col.split(",")[1]) |
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110 remaining_lines= sort_by_column(remaining_lines,sort_col,reverse,header) |
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111 filtered_lines = sort_by_column(filtered_lines,sort_col,reverse,header) |
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112 |
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113 # Write results to output |
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114 with open(args.output,"w") as output : |
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115 writer = csv.writer(output,delimiter="\t") |
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116 writer.writerows(remaining_lines) |
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117 |
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118 # Write filtered lines to filtered_output |
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119 with open(args.filtered_file,"w") as filtered_output : |
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120 writer = csv.writer(filtered_output,delimiter="\t") |
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121 writer.writerows(filtered_lines) |
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122 |
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123 #function to sort the csv_file by value in a specific column |
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124 def sort_by_column(tab,sort_col,reverse,header): |
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125 |
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126 if len(tab) > 1 : #if there's more than just a header or 1 row |
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127 if header is True : |
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128 head=tab[0] |
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129 tab=tab[1:] |
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130 |
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131 if is_number("int",tab[0][sort_col]) : |
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132 tab = sorted(tab, key=lambda row: int(row[sort_col]), reverse=reverse) |
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133 elif is_number("float",tab[0][sort_col]) : |
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134 tab = sorted(tab, key=lambda row: float(row[sort_col]), reverse=reverse) |
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135 else : |
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136 tab = sorted(tab, key=lambda row: row[sort_col], reverse=reverse) |
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137 |
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138 if header is True : tab = [head]+tab |
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139 |
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140 return tab |
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141 |
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142 #Read the keywords file to extract the list of keywords |
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143 def read_option(filename): |
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144 with open(filename, "r") as f: |
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145 filter_list=f.read().splitlines() |
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146 filter_list=[key for key in filter_list if len(key.replace(' ',''))!=0] |
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147 filters=";".join(filter_list) |
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148 |
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149 return filters |
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150 |
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151 # Read input file |
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152 def read_file(filename): |
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153 with open(filename,"r") as f : |
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154 reader=csv.reader(f,delimiter="\t") |
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155 tab=list(reader) |
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156 |
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157 # Remove empty lines (contain only space or new line or "") |
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158 #[tab.remove(blank) for blank in tab if blank.isspace() or blank == ""] |
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159 tab=[line for line in tab if len("".join(line).replace(" ","")) !=0 ] |
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160 |
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161 return tab |
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162 |
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163 #seek for keywords in rows of csvfile, return a dictionary of boolean (true if keyword found, false otherwise) |
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164 def filter_keyword(csv_file, header, results_dict, keywords, ncol, match): |
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165 match=str_to_bool(match) |
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166 ncol=column_from_txt(ncol) |
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167 |
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168 keywords = keywords.upper().split(";") # Split list of filter keyword |
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169 [keywords.remove(blank) for blank in keywords if blank.isspace() or blank == ""] # Remove blank keywords |
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170 keywords = [k.strip() for k in keywords] # Remove space from 2 heads of keywords |
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171 |
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172 for id_line,line in enumerate(csv_file): |
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173 if header is True and id_line == 0 : continue |
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174 #line = line.replace("\n", "") |
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175 keyword_inline = line[ncol].replace('"', "").split(";") |
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176 #line = line + "\n" |
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177 |
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178 #Perfect match or not |
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179 if match is True : |
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180 found_in_line = any(pid.upper() in keywords for pid in keyword_inline) |
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181 else: |
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182 found_in_line = any(ft in pid.upper() for pid in keyword_inline for ft in keywords) |
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183 |
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184 #if the keyword is found in line |
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185 if id_line in results_dict : results_dict[id_line].append(found_in_line) |
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186 else : results_dict[id_line]=[found_in_line] |
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187 |
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188 return results_dict |
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189 |
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190 #filter ba determined value in rows of csvfile, return a dictionary of boolean (true if value filtered, false otherwise) |
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191 def filter_value(csv_file, header, results_dict, filter_value, ncol, opt): |
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192 |
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193 filter_value = float(filter_value) |
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194 ncol=column_from_txt(ncol) |
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195 |
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196 for id_line,line in enumerate(csv_file): |
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197 if header is True and id_line == 0 : continue |
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198 value = line[ncol].replace('"', "").strip() |
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199 if value.replace(".", "", 1).isdigit(): |
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200 to_filter=value_compare(value,filter_value,opt) |
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201 |
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202 #adding the result to the dictionary |
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203 if id_line in results_dict : results_dict[id_line].append(to_filter) |
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204 else : results_dict[id_line]=[to_filter] |
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205 |
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206 return results_dict |
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207 |
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208 #filter ba determined value in rows of csvfile, return a dictionary of boolean (true if value filtered, false otherwise) |
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209 def filter_values_range(csv_file, header, results_dict, bottom_value, top_value, ncol, inclusive): |
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210 inclusive=str_to_bool(inclusive) |
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211 bottom_value = float(bottom_value) |
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212 top_value=float(top_value) |
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213 ncol=column_from_txt(ncol) |
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214 |
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215 for id_line, line in enumerate(csv_file): |
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216 if header is True and id_line == 0 : continue |
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217 value = line[ncol].replace('"', "").strip() |
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218 if value.replace(".", "", 1).isdigit(): |
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219 value=float(value) |
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220 if inclusive is True: |
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221 in_range = not (bottom_value <= value <= top_value) |
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222 else : |
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223 in_range = not (bottom_value < value < top_value) |
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224 |
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225 #adding the result to the dictionary |
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226 if id_line in results_dict : results_dict[id_line].append(in_range) |
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227 else : results_dict[id_line]=[in_range] |
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228 |
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229 return results_dict |
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230 |
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231 def column_from_txt(ncol): |
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232 if is_number("int", ncol.replace("c", "")): |
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233 ncol = int(ncol.replace("c", "")) - 1 |
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234 else: |
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235 raise ValueError("Please specify the column where " |
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236 "you would like to apply the filter " |
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237 "with valid format") |
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238 return ncol |
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239 |
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240 #return True if value is in the determined values, false otherwise |
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241 def value_compare(value,filter_value,opt): |
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242 test_value=False |
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243 |
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244 if opt == "<": |
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245 if float(value) < filter_value: |
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246 test_value = True |
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247 elif opt == "<=": |
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248 if float(value) <= filter_value: |
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249 test_value = True |
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250 elif opt == ">": |
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251 if float(value) > filter_value: |
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252 test_value = True |
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253 elif opt == ">=": |
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254 if float(value) >= filter_value: |
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255 test_value = True |
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256 elif opt == "=": |
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257 if float(value) == filter_value: |
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258 test_value = True |
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259 elif opt == "!=": |
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260 if float(value) != filter_value: |
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261 test_value = True |
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262 |
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263 return test_value |
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264 |
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265 if __name__ == "__main__": |
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266 options() |