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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 from textwrap import dedent
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6
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7 import yaml
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8
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9
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10 def main():
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11 """
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12 Takes a tab-delimited text file with a mandatory header
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13 column and generates an HTML table.
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14 """
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15
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16 args = sys.argv
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17 if len(args) < 2 or len(args) >= 4:
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18 print(
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19 f"\nAt least one argument specifying the *.tblsum file is required.\n"
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20 + "No more than 2 command-line arguments should be passed.\n"
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21 )
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22 exit(1)
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23
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24 table_sum_on = str(args[1]).lower()
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25 table_sum_on_file = table_sum_on + ".tblsum.txt"
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26 cell_colors = f"{table_sum_on}.cellcolors.yml"
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27
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28 if len(args) == 3:
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29 description = str(args[2])
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30 else:
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31 description = "The results table shown here is a collection from all samples."
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32
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33 if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
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34 with open(cell_colors, "r") as cc_yml:
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35 cell_colors = yaml.safe_load(cc_yml)
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36 else:
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37 cell_colors = dict()
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38
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39 if not (os.path.exists(table_sum_on_file) and os.path.getsize(table_sum_on_file) > 0):
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40 exit(0)
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41
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42 with open(table_sum_on_file, "r") as tbl:
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43 header = tbl.readline()
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44 header_cols = header.strip().split("\t")
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45
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46 html = [
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47 dedent(
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48 f"""<script type="text/javascript">
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49 $(document).ready(function () {{
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50 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
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51 scrollX: true,
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52 fixedColumns: true, dom: 'Bfrtip',
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53 buttons: [
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54 'copy',
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55 {{
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56 extend: 'print',
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57 title: 'CPIPES: MultiQC Report: {table_sum_on}'
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58 }},
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59 {{
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60 extend: 'excel',
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61 filename: '{table_sum_on}_results',
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62 }},
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63 {{
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64 extend: 'csv',
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65 filename: '{table_sum_on}_results',
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66 }}
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67 ]
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68 }});
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69 }});
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70 </script>
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71 <div class="table-responsive">
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72 <style>
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73 #cpipes-process-custom-res tr:nth-child(even) {{
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74 background-color: #f2f2f2;
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75 }}
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76 </style>
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77 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
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78 <thead>
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79 <tr>"""
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80 )
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81 ]
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82
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83 for header_col in header_cols:
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84 html.append(
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85 dedent(
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86 f"""
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87 <th> {header_col} </th>"""
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88 )
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89 )
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90
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91 html.append(
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92 dedent(
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93 """
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94 </tr>
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95 </thead>
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96 <tbody>"""
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97 )
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98 )
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99
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100 for row in tbl:
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101 html.append("<tr>\n")
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102 data_cols = row.strip().split("\t")
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103 if len(header_cols) != len(data_cols):
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104 print(
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105 f"\nWARN: Number of header columns ({len(header_cols)}) and data "
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106 + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
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107 )
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108 if len(header_cols) > len(data_cols):
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109 data_cols += (len(header_cols) - len(data_cols)) * " "
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110 print(len(data_cols))
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111 else:
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112 header_cols += (len(data_cols) - len(header_cols)) * " "
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113
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114 html.append(
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115 dedent(
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116 f"""
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117 <td><samp>{data_cols[0]}</samp></td>
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118 """
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119 )
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120 )
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121
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122 for data_col in data_cols[1:]:
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123 data_col_w_color = f"""<td>{data_col}</td>
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124 """
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125 if (
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126 table_sum_on in cell_colors.keys()
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127 and data_col in cell_colors[table_sum_on].keys()
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128 ):
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129 data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
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130 """
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131 html.append(dedent(data_col_w_color))
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132 html.append("</tr>\n")
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133 html.append("</tbody>\n")
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134 html.append("</table>\n")
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135 html.append("</div>\n")
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136
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137 mqc_yaml = {
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138 "id": f"{table_sum_on.upper()}_collated_table",
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139 "section_name": f"{table_sum_on.upper()}",
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140 "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
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141 "plot_type": "html",
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142 "description": f"{description}",
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143 "data": ("").join(html),
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144 }
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145
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146 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
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147 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
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148
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149
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150 if __name__ == "__main__":
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151 main()
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