Mercurial > repos > jay > pdaug_peptide_length_distribution
annotate PDAUG_Basic_Plots/PDAUG_Basic_Plots.py @ 3:b5545b41ab70 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit edb37634e419f75dd66292e712de51278746d883"
author | jay |
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date | Wed, 30 Dec 2020 02:58:14 +0000 |
parents | 3f9bdcf83244 |
children | af016c0e2f16 |
rev | line source |
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3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 from wordcloud import WordCloud, STOPWORDS |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import matplotlib.pyplot as plt |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import glob, os, sys |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 import pandas as pd |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 import plotly.express as px |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 ################################### |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7 from wordcloud import WordCloud, STOPWORDS |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 import matplotlib.pyplot as plt |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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9 |
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10 |
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11 def ReturnPeptide(Infile): |
3f9bdcf83244
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12 |
3f9bdcf83244
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13 file = open(Infile) |
3f9bdcf83244
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14 lines = file.readlines() |
3f9bdcf83244
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15 |
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16 Index = [] |
3f9bdcf83244
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17 Pep = [] |
3f9bdcf83244
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18 |
3f9bdcf83244
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19 for line in lines: |
3f9bdcf83244
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20 if '>' in line: |
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21 line = line.strip('\n') |
3f9bdcf83244
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22 line = line.strip('\r') |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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23 Index.append(line.strip('\n')) |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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24 else: |
3f9bdcf83244
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25 line = line.strip('\n') |
3f9bdcf83244
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26 line = line.strip('\r') |
3f9bdcf83244
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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27 Pep.append(line) |
3f9bdcf83244
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28 return Pep, Index |
3f9bdcf83244
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29 |
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30 |
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31 def FragReturn(Seq, d): |
3f9bdcf83244
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32 |
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33 tokens = [] |
3f9bdcf83244
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34 for seq in Seq: |
3f9bdcf83244
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35 |
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36 for l in range(d): |
3f9bdcf83244
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37 if l < d: |
3f9bdcf83244
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38 for x in range(int(len(seq)/d)): |
3f9bdcf83244
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39 s = (x*d)+l |
3f9bdcf83244
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40 e = s+d |
3f9bdcf83244
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41 if len(seq[s:e]) == d: |
3f9bdcf83244
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42 tokens.append(seq[s:e]) |
3f9bdcf83244
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43 |
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44 else: |
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45 pass |
3f9bdcf83244
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46 else: |
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47 pass |
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48 return tokens |
3f9bdcf83244
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49 |
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50 def PlotWordCloud(TokenList, OutFile): |
3f9bdcf83244
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51 |
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52 comment_words = '' |
3f9bdcf83244
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53 stopwords = set(STOPWORDS) |
3f9bdcf83244
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54 comment_words += " ".join(TokenList)+" " |
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55 |
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56 wordcloud = WordCloud(width = 800, height = 800, |
3f9bdcf83244
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57 background_color ='white', |
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58 stopwords = stopwords, |
3f9bdcf83244
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59 min_font_size = 10).generate(comment_words) |
3f9bdcf83244
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60 |
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61 plt.figure(figsize = (8, 8), facecolor = None) |
3f9bdcf83244
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62 plt.imshow(wordcloud) |
3f9bdcf83244
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63 plt.axis("off") |
3f9bdcf83244
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64 plt.tight_layout(pad = 0) |
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65 plt.savefig(OutFile,dpi=600) |
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66 |
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67 |
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68 def HeatMapPlot(Infile, IndexColumn, x_label, y_label, Workdirpath, htmlOutDir, htmlFname): |
3f9bdcf83244
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69 |
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70 if not os.path.exists(htmlOutDir): |
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71 os.makedirs(htmlOutDir) |
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72 |
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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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75 |
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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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78 |
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79 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) |
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80 |
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81 |
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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 ) |
3f9bdcf83244
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91 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) |
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92 |
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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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100 |
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101 df = pd.read_csv(InFile, sep="\t") |
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102 |
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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: |
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185 print("In Correct Option:") |