Mercurial > repos > workflow4metabolomics > kmd_hmdb_data_plot

annotate kmd_hmdb_plot_generator.py @ 0:59c8bad5f6bc draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
author workflow4metabolomics
date Tue, 29 Aug 2023 09:45:16 +0000
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0
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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1 #!/usr/bin/env python3
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2
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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3 import csv
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4 import itertools
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5 import os
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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6
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7 import click
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8
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9 import plotly.express
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10 import plotly.graph_objects
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11
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12 __version__ = "1.0.0"
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13
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14
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15 @click.group()
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16 def cli():
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17 pass
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18
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19
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20 @cli.command(help="")
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21 @click.option(
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22 "--version",
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23 is_flag=True,
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24 default=False,
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25 )
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26 @click.option(
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27 "--input",
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28 default="./test.tsv",
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29 help="Provide the mz-ratio."
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30 )
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31 @click.option(
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32 "--output",
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33 default="./test.html",
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34 help="Provide the database."
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35 )
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36 @click.option(
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37 "--x-column",
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38 default=["nominal_mass"],
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39 multiple=True,
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40 help="Provide the column names for the X axis.",
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41 )
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42 @click.option(
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43 "--y-column",
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44 default=["kendricks_mass_defect"],
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45 multiple=True,
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46 help="Provide the column names for the Y axis.",
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47 )
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48 @click.option(
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49 "--annotation-column",
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50 multiple=True,
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51 default=[
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52 "metabolite_name",
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53 "chemical_formula",
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54 ],
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55 help="Provide the columns name for the annotation."
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56 )
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57 def plot(*args, **kwargs):
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58
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59 if kwargs.pop("version"):
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60 print(__version__)
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61 exit(0)
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62
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63 input_path = kwargs.pop("input")
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64 data = read_input(input_path, kwargs)
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65 fig = build_fig(*data)
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66 build_html_plot(fig, kwargs.get("output"))
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67
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68
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69 def read_input(path: str, kwargs: {}):
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70 if not os.path.exists(path):
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71 raise ValueError(f"The path '{path}' does not exist.")
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72 sep = detect_sep(path)
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73 with open(path) as csv_file:
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74 line_generator = csv.reader(csv_file, delimiter=sep)
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75 first_line = next(line_generator)
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76 all_lines = list(line_generator)
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77 hover_names = (
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78 "metabolite_name",
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79 "chemical_formula",
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80 )
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81 annotation_indexes = get_index_of(first_line, hover_names)
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82 (
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83 x_index,
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84 y_index,
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85 x_column,
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86 y_column,
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87 ) = get_indexes_names(
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88 first_line,
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89 list(kwargs.get("x_column")),
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90 list(kwargs.get("y_column")),
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91 )
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92 x_lists = [[] for i in range(len(x_index))]
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93 y_lists = [[] for i in range(len(y_index))]
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94 x_column = list(map(first_line.__getitem__, x_index))
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95 y_column = list(map(first_line.__getitem__, y_index))
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96 trace_names = [
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97 f"f({x_column[i]}) = {y_column[i]}"
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98 for i in range(len(x_index))
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99 ]
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100 hover_names = kwargs["annotation_column"]
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101 annotation_indexes = [
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102 get_index_of(first_line, column)[0]
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103 for column in hover_names
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104 ]
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105 hover_names = list(map(first_line.__getitem__, annotation_indexes))
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106 annotations = list()
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107 for line in all_lines:
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108 for i in range(len(x_index)):
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109 x_lists[i].append(float(line[x_index[i]]))
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110 y_lists[i].append(float(line[y_index[i]]))
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111 annotations.append("<br>".join(
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112 f"{hover_names[hover_index]}: {line[index]}"
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113 for hover_index, index in enumerate(annotation_indexes)
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114 ))
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115 return x_lists, y_lists, annotations, trace_names
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116
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117
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118 def get_indexes_names(first_line, x_column, y_column):
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119 x_column, y_column = map(list, zip(*itertools.product(x_column, y_column)))
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120 x_index = get_index_of(first_line, x_column)
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121 y_index = get_index_of(first_line, y_column)
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122 for i in range(len(x_index))[::-1]:
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123 if x_index[i] == y_index[i]:
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124 del x_index[i], x_column[i], y_index[i], y_column[i],
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125 return (
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126 x_index,
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127 y_index,
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128 x_column,
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129 y_column,
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130 )
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131
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132
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133 def get_index_of(first_line, column):
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134 if isinstance(column, (tuple, list)):
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135 return [get_index_of(first_line, x)[0] for x in list(column)]
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136 try:
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137 return [int(column) - 1]
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138 except ValueError:
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139 return [first_line.index(column)]
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140
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141
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142 def build_fig(x_lists, y_lists, annotations, trace_names):
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143 fig = plotly.express.scatter()
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144 for i in range(len(x_lists)):
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145 fig.add_trace(
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146 plotly.graph_objects.Scatter(
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147 name=trace_names[i],
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148 x=x_lists[i],
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149 y=y_lists[i],
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150 hovertext=annotations,
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151 mode="markers",
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152 )
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153 )
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154 return fig
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155
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157 def detect_sep(tabular_file: str) -> str:
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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158 with open(tabular_file, "r") as file:
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159 first_line = file.readline()
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160 if len(first_line.split(',')) > len(first_line.split('\t')):
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161 return ','
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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162 return '\t'
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163
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164
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165 def build_html_plot(fig, output: str):
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166 return plotly.offline.plot(
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167 fig,
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168 filename=output,
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169 auto_open=False,
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170 )
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171
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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172
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173 if __name__ == "__main__":
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174 cli()