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1 #!/usr/bin/env python
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2
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3 import sys
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4 import yaml
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5 from textwrap import dedent
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6
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7 def main() :
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8 """
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kkonganti@0
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9 Takes a tab-delimited text file with a mandatory header
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10 column and generates an HTML table.
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11 """
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12
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13 args = sys.argv
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14 if (len(args) < 2 or len(args) > 3):
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15 print(f"\nTwo CL arguments are required!\n")
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16 exit(1)
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17
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18 table_sum_on = args[1].lower()
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19 workflow_name = args[2].lower()
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20
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21 with open(f"{table_sum_on}.tblsum.txt", "r") as tbl:
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22 header = tbl.readline()
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23 header_cols = header.strip().split('\t')
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24
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25 html = [
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26 dedent(
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27 f"""<script type="text/javascript">
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28 $(document).ready(function () {{
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29 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
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30 scrollX: true,
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31 fixedColumns: true, dom: 'Bfrtip',
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32 buttons: [
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33 'copy',
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34 {{
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35 extend: 'print',
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36 title: 'CPIPES: MultiQC Report: {table_sum_on}'
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37 }},
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38 {{
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39 extend: 'excel',
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40 filename: '{table_sum_on}_results',
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41 }},
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42 {{
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43 extend: 'csv',
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44 filename: '{table_sum_on}_results',
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45 }}
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46 ]
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47 }});
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48 }});
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49 </script>
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50 <div class="table-responsive">
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51 <style>
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52 #cpipes-process-custom-res tr:nth-child(even) {{
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53 background-color: #f2f2f2;
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54 }}
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55 </style>
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56 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
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57 <thead>
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58 <tr>"""
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59 )
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60 ]
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61
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62 for header_col in header_cols:
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63 html.append(
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64 dedent(
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65 f"""
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66 <th> {header_col} </th>"""
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67 )
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68 )
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69
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70 html.append(
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71 dedent(
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72 """
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73 </tr>
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74 </thead>
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75 <tbody>"""
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76 )
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77 )
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78
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79 for row in tbl:
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80 html.append("<tr>\n")
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81 data_cols = row.strip().split('\t')
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82 if ( len(header_cols) != len(data_cols) ):
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83 print(f"\nWARN: Number of header columns ({len(header_cols)}) and data " +
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84 f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n")
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85 if ( len(header_cols) > len(data_cols) ):
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86 data_cols += (( len(header_cols) - len(data_cols) ) * ' ' )
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87 print(len(data_cols))
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88 else:
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89 header_cols += (( len(data_cols) - len(header_cols) ) * ' ')
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90
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91 html.append(
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92 dedent(
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93 f"""
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94 <td><samp>{data_cols[0]}</samp></td>
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95 """
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96 )
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97 )
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98
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99 for data_col in data_cols[1:]:
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100 html.append(
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101 dedent(
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102 f"""<td>{data_col}</td>
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103 """
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104 )
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105 )
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106 html.append("</tr>\n")
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107 html.append("</tbody>\n")
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108 html.append("</table>\n")
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109 html.append("</div>\n")
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110
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111 mqc_yaml = {
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112 "id": f"{table_sum_on.upper()}_collated_table",
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113 "section_name": f"{table_sum_on.upper()}",
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114 "section_href": f"https://cfsan-git.fda.gov/Kranti.Konganti/{workflow_name}",
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115 "plot_type": "html",
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116 "description": "The results table shown here is a collection from all samples.",
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117 "data": ('').join(html),
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118 }
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119
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120 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
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121 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
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122
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123 if __name__ == "__main__":
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124 main() |
