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