Mercurial > repos > jay > pdaug_peptide_sequence_analysis

annotate PDAUG_Basic_Plots/PDAUG_Basic_Plots.py @ 9:90e3b1968ae6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author jay
date Wed, 12 Jan 2022 19:36:54 +0000
parents d11a54691a2f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
parents:
diff changeset
1 from wordcloud import WordCloud, STOPWORDS
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2 import matplotlib.pyplot as plt
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3 import glob, os, sys
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4 import pandas as pd
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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5 import plotly.express as px
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6 ###################################
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7 from wordcloud import WordCloud, STOPWORDS
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8 import matplotlib.pyplot as plt
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11 def ReturnPeptide(Infile):
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13 file = open(Infile)
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14 lines = file.readlines()
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16 Index = []
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17 Pep = []
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19 for line in lines:
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20 if '>' in line:
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21 line = line.strip('\n')
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22 line = line.strip('\r')
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23 Index.append(line.strip('\n'))
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24 else:
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25 line = line.strip('\n')
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26 line = line.strip('\r')
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27 Pep.append(line)
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28 return Pep, Index
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31 def FragReturn(Seq, d):
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32
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33 tokens = []
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34 for seq in Seq:
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35
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36 for l in range(d):
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37 if l < d:
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38 for x in range(int(len(seq)/d)):
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39 s = (x*d)+l
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40 e = s+d
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41 if len(seq[s:e]) == d:
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42 tokens.append(seq[s:e])
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43
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44 else:
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45 pass
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46 else:
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47 pass
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48 return tokens
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50 def PlotWordCloud(TokenList, OutFile):
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52 comment_words = ''
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53 stopwords = set(STOPWORDS)
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54 comment_words += " ".join(TokenList)+" "
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56 wordcloud = WordCloud(width = 800, height = 800,
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57 background_color ='white',
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58 stopwords = stopwords,
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59 min_font_size = 10).generate(comment_words)
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60
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61 plt.figure(figsize = (8, 8), facecolor = None)
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62 plt.imshow(wordcloud)
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63 plt.axis("off")
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64 plt.tight_layout(pad = 0)
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65 plt.savefig(OutFile,dpi=600)
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68 def HeatMapPlot(Infile, IndexColumn, x_label, y_label, Workdirpath, htmlOutDir, htmlFname):
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70 if not os.path.exists(htmlOutDir):
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71 os.makedirs(htmlOutDir)
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73 df = pd.read_csv(Infile, sep="\t")
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74 y_ticks = list(df[IndexColumn])
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76 fig = px.imshow(df[df.columns.tolist()[1:]], labels=dict(x=x_label, y=y_label), y=y_ticks)
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77 fig.update_xaxes(side="top")
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79 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
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82 def BoxPlot(InFile, Feature, label, Workdirpath, htmlOutDir, htmlFname):
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83
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84 Workdirpath = os.path.join(os.getcwd(),'report_dir')
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85
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86 if not os.path.exists(htmlOutDir):
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87 os.makedirs(htmlOutDir)
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88
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89 df = pd.read_csv(InFile, sep="\t")
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90 fig = px.box(df, y=Feature, color=label, notched=True, title="Box plot of "+Feature )
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91 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
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93
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94 def ScatterPlot(InFile, Feature1, Feature2, Feature3, Label, PlotType, Workdirpath, htmlOutDir, htmlFname):
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95
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96 Workdirpath = os.path.join(os.getcwd(),'report_dir')
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97
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98 if not os.path.exists(htmlOutDir):
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99 os.makedirs(htmlOutDir)
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101 df = pd.read_csv(InFile, sep="\t")
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103
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104 if PlotType == "3D":
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105 fig = px.scatter_3d(df, x=Feature1, y=Feature2, z=Feature3, color=Label)
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106 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
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107
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108 elif PlotType == "2D":
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109 fig = px.scatter(df, x=Feature1, y=Feature2, color=Label)
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110 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
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111
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112
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113 def WordCloudPlot(InFile, d, Workdirpath, htmlOutDir, htmlFname):
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114
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115 Workdirpath = os.path.join(os.getcwd(),'report_dir')
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116 if not os.path.exists(htmlOutDir):
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117 os.makedirs(htmlOutDir)
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118
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119 Peps,_ = ReturnPeptide(InFile)
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120 Frags = FragReturn(Peps, int(d))
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121
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122 PlotWordCloud(Frags, "out.png")
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123 #HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname))
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124
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125
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126 if __name__=="__main__":
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127
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128
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129 import argparse
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130
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131 parser = argparse.ArgumentParser(description='Deployment tool')
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132 subparsers = parser.add_subparsers()
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133
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134 HM = subparsers.add_parser('HeatMap')
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135 HM.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file")
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136 HM.add_argument("-C", "--IndexColumn", required=True, help="")
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137 HM.add_argument("-x", "--x_label", required=True, help="")
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138 HM.add_argument("-y","--y_label", required=True, help="")
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139 HM.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html directory")
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140 HM.add_argument("--htmlFname", required=False, help="HTML out file", default="report.html")
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141 HM.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Path to working directory")
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142
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143 BP = subparsers.add_parser('BoxPlot')
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144 BP.add_argument("-I", "--InFile", required=True, default=None, help="Input file")
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145 BP.add_argument("-F", "--Feature", required=True, default=None, help="Feature list")
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146 BP.add_argument("-O", "--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html dir")
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147 BP.add_argument("-Hf", "--htmlFname", required=False, help="HTML out file", default="report.html")
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148 BP.add_argument("-Wp", "--Workdirpath", required=False, default=os.getcwd(), help="Path to Working Directory")
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149 BP.add_argument("-L", "--Label", required=False, default=False, help="Working Directory Path")
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150
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151 SP = subparsers.add_parser('ScatterPlot')
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152 SP.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file")
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153 SP.add_argument("-F1", "--Feature1", required=True, default=True, help="Path to target tsv file")
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154 SP.add_argument("-F2", "--Feature2", required=True, default=True, help="Roatate ticks")
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155 SP.add_argument("-F3", "--Feature3", required=False, help="Roatate ticks")
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156 SP.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
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157 SP.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="jai.html")
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158 SP.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
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159 SP.add_argument("-T", "--PlotType", required=True, help="")
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160 SP.add_argument("-L","--Label", required=False, default=False, help="Working Directory Path")
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161
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162 WC = subparsers.add_parser('WordCloud')
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163 WC.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file")
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164 WC.add_argument("-D", "--FragSize", required=True, default=None, help="Path to target tsv file")
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165 WC.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
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166 WC.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="report.html")
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167 WC.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
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168
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169
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170 args = parser.parse_args()
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171
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172 if sys.argv[1] == "HeatMap":
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173 HeatMapPlot(args.InFile, args.IndexColumn, args.x_label, args.y_label, args.Workdirpath, args.htmlOutDir, args.htmlFname)
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174
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175 elif sys.argv[1] == "ScatterPlot":
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176 ScatterPlot(args.InFile, args.Feature1, args.Feature2, args.Feature3, args.Label, args.PlotType, args.Workdirpath, args.htmlOutDir, args.htmlFname)
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177
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178 elif sys.argv[1] == "BoxPlot":
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179 BoxPlot(args.InFile, args.Feature, args.Label, args.Workdirpath, args.htmlOutDir, args.htmlFname)
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180
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181 elif sys.argv[1] == "WordCloud":
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182 WordCloudPlot(args.InFile, args.FragSize, args.Workdirpath, args.htmlOutDir, args.htmlFname)
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183
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184 else:
5
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185 print("Incorrect option provided: %s" % (sys.argv[1]))