Mercurial > repos > proteore > filter_keywords_values

annotate filter_kw_val.py @ 6:c6ba1e6f6869 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 74b6a02a2e64d02551c05b52d571b888ac73cac9
author proteore
date Fri, 20 Apr 2018 09:07:23 -0400
parents 1e9911190142
children 6f32c1e12572
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1 import argparse
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2 import re
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5 def options():
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6 """
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7 Parse options:
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8 -i, --input Input filename and boolean value if the file contains header ["filename,true/false"]
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9 -m, --match if the keywords should be filtered in exact
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10 --kw Keyword to be filtered, the column number where this filter applies,
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11 boolean value if the keyword should be filtered in exact ["keyword,ncol,true/false"].
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12 This option can be repeated: --kw "kw1,c1,true" --kw "kw2,c1,false" --kw "kw3,c2,true"
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13 --kwfile A file that contains keywords to be filter, the column where this filter applies and
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14 boolean value if the keyword should be filtered in exact ["filename,ncol,true/false"]
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15 --value The value to be filtered, the column number where this filter applies and the
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16 operation symbol ["value,ncol,=/>/>=/</<="]
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17 --o --output The output filename
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18 --trash_file The file contains removed lines
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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("-o", "--output", default="output.txt")
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26 parser.add_argument("--trash_file", default="trash_MQfilter.txt")
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27
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28 args = parser.parse_args()
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29
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30 filters(args)
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31
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32 def isnumber(number_format, n):
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33 """
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34 Check if a variable is a float or an integer
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35 """
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36 float_format = re.compile(r"^[-]?[0-9][0-9]*.?[0-9]+$")
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37 int_format = re.compile(r"^[-]?[0-9][0-9]*$")
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38 test = ""
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39 if number_format == "int":
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40 test = re.match(int_format, n)
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41 elif number_format == "float":
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42 test = re.match(float_format, n)
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43 if test:
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44 return True
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45
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46 def filters(args):
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47 """
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48 Filter the document
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49 """
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50 MQfilename = args.input.split(",")[0]
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51 header = args.input.split(",")[1]
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52 MQfile = readMQ(MQfilename)
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53 results = [MQfile, None]
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54
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55 if args.kw:
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56 keywords = args.kw
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57 for k in keywords:
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58 results = filter_keyword(results[0], header, results[1], k[0], k[1], k[2])
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59 if args.kw_file:
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60 key_files = args.kw_file
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61 for kf in key_files:
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62 ids = readOption(kf[0])
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63 results = filter_keyword(results[0], header, results[1], ids, kf[1], kf[2])
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64 if args.value:
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65 for v in args.value:
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66 if isnumber("float", v[0]):
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67 results = filter_value(results[0], header, results[1], v[0], v[1], v[2])
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68 else:
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69 raise ValueError("Please enter a number in filter by value")
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70
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71 # Write results to output
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72 output = open(args.output, "w")
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73 output.write("".join(results[0]))
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74 output.close()
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75
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76 # Write deleted lines to trash_file
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77 trash = open(args.trash_file, "w")
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78 trash.write("".join(results[1]))
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79 trash.close()
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80
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81 def readOption(filename):
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82 # Read the keywords file to extract the list of keywords
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83 f = open(filename, "r")
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84 file_content = f.read()
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85 filter_list = file_content.split("\n")
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86 filters = ""
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87 for i in filter_list:
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88 filters += i + ";"
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89 filters = filters[:-1]
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90 return filters
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91
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92 def readMQ(MQfilename):
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93 # Read input file
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94 mqfile = open(MQfilename, "r")
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95 mq = mqfile.readlines()
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96 # Remove empty lines (contain only space or new line or "")
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97 [mq.remove(blank) for blank in mq if blank.isspace() or blank == ""]
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98 return mq
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99
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100 def filter_keyword(MQfile, header, filtered_lines, ids, ncol, match):
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101 mq = MQfile
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102 if isnumber("int", ncol.replace("c", "")):
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103 id_index = int(ncol.replace("c", "")) - 1
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104 else:
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105 raise ValueError("Please specify the column where "
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106 "you would like to apply the filter "
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107 "with valid format")
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108
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109 # Split list of filter IDs
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110 ids = ids.upper().split(";")
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111 # Remove blank IDs
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112 [ids.remove(blank) for blank in ids if blank.isspace() or blank == ""]
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113 # Remove space from 2 heads of IDs
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114 ids = [id.strip() for id in ids]
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115
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116
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117 if header == "true":
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118 header = mq[0]
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119 content = mq[1:]
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120 else:
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121 header = ""
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122 content = mq[:]
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123
0
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124 if not filtered_lines: # In case there is already some filtered lines from other filters
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125 filtered_lines = []
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126 if header != "":
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127 filtered_lines.append(header)
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128
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129 for line in content:
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130 line = line.replace("\n", "")
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131 id_inline = line.split("\t")[id_index].replace('"', "").split(";")
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132 # Take only first IDs
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133 #one_id_line = line.replace(line.split("\t")[id_index], id_inline[0])
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134 line = line + "\n"
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135
0
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136 if match != "false":
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137 # Filter protein IDs
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138 if any(pid.upper() in ids for pid in id_inline):
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139 filtered_lines.append(line)
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140 mq.remove(line)
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141 #else:
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142 # mq[mq.index(line)] = one_id_line
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143 else:
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144 if any(ft in pid.upper() for pid in id_inline for ft in ids):
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145 filtered_lines.append(line)
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146 mq.remove(line)
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147 #else:
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148 # mq[mq.index(line)] = one_id_line
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149 return mq, filtered_lines
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150
0
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151 def filter_value(MQfile, header, filtered_prots, filter_value, ncol, opt):
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152 mq = MQfile
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153 if ncol and isnumber("int", ncol.replace("c", "")):
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154 index = int(ncol.replace("c", "")) - 1
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155 else:
1
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156 raise ValueError("Please specify the column where "
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157 "you would like to apply the filter "
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158 "with valid format")
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159 if header == "true":
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160 header = mq[0]
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161 content = mq[1:]
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162 else:
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163 header = ""
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164 content = mq[:]
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165 if not filtered_prots: # In case there is already some filtered lines from other filters
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166 filtered_prots = []
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167 if header != "":
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168 filtered_prots.append(header)
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169
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170 for line in content:
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171 prot = line.replace("\n","")
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172 filter_value = float(filter_value)
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173 pep = prot.split("\t")[index].replace('"', "")
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174 if pep.replace(".", "", 1).isdigit():
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175 if opt == "<":
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176 if float(pep) >= filter_value:
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177 filtered_prots.append(line)
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178 mq.remove(line)
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179 elif opt == "<=":
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180 if float(pep) > filter_value:
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181 filtered_prots.append(line)
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182 mq.remove(line)
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183 elif opt == ">":
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184 #print(prot.number_of_prots, filter_value, int(prot.number_of_prots) > filter_value)
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185 if float(pep) <= filter_value:
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186 filtered_prots.append(line)
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187 mq.remove(line)
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188 elif opt == ">=":
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189 if float(pep) < filter_value:
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190 filtered_prots.append(line)
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191 mq.remove(line)
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192 else:
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193 if float(pep) != filter_value:
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194 filtered_prots.append(line)
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195 mq.remove(line)
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196 return mq, filtered_prots
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197
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198 if __name__ == "__main__":
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199 options()