Mercurial > repos > galaxytrakr > hfp_nowayout_awsbatch

comparison 0.5.0/bin/create_mqc_data_table.py @ 0:3c767f9cfd88 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:37:56 +0000
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-1:000000000000 0:3c767f9cfd88
1 #!/usr/bin/env python
2
3 import os
4 import sys
5 from textwrap import dedent
6
7 import yaml
8
9
10 def main():
11 """
12 Takes a tab-delimited text file with a mandatory header
13 column and generates an HTML table.
14 """
15
16 args = sys.argv
17 if len(args) < 2 or len(args) >= 4:
18 print(
19 f"\nAt least one argument specifying the *.tblsum file is required.\n"
20 + "No more than 2 command-line arguments should be passed.\n"
21 )
22 exit(1)
23
24 table_sum_on = str(args[1]).lower()
25 table_sum_on_file = table_sum_on + ".tblsum.txt"
26 cell_colors = f"{table_sum_on}.cellcolors.yml"
27
28 if len(args) == 3:
29 description = str(args[2])
30 else:
31 description = "The results table shown here is a collection from all samples."
32
33 if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
34 with open(cell_colors, "r") as cc_yml:
35 cell_colors = yaml.safe_load(cc_yml)
36 else:
37 cell_colors = dict()
38
39 if not (
40 os.path.exists(table_sum_on_file) and os.path.getsize(table_sum_on_file) > 0
41 ):
42 exit(0)
43
44 with open(table_sum_on_file, "r") as tbl:
45 header = tbl.readline()
46 header_cols = header.strip().split("\t")
47
48 html = [
49 dedent(
50 f"""<script type="text/javascript">
51 $(document).ready(function () {{
52 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
53 scrollX: true,
54 fixedColumns: true, dom: 'Bfrtip',
55 buttons: [
56 'copy',
57 {{
58 extend: 'print',
59 title: 'CPIPES: MultiQC Report: {table_sum_on}'
60 }},
61 {{
62 extend: 'excel',
63 filename: '{table_sum_on}_results',
64 }},
65 {{
66 extend: 'csv',
67 filename: '{table_sum_on}_results',
68 }}
69 ]
70 }});
71 }});
72 </script>
73 <div class="table-responsive">
74 <style>
75 #cpipes-process-custom-res tr:nth-child(even) {{
76 background-color: #f2f2f2;
77 }}
78 </style>
79 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
80 <thead>
81 <tr>"""
82 )
83 ]
84
85 for header_col in header_cols:
86 html.append(
87 dedent(
88 f"""
89 <th> {header_col} </th>"""
90 )
91 )
92
93 html.append(
94 dedent(
95 """
96 </tr>
97 </thead>
98 <tbody>"""
99 )
100 )
101
102 for row in tbl:
103 html.append("<tr>\n")
104 data_cols = row.strip().split("\t")
105 if len(header_cols) != len(data_cols):
106 print(
107 f"\nWARN: Number of header columns ({len(header_cols)}) and data "
108 + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
109 )
110 if len(header_cols) > len(data_cols):
111 data_cols += (len(header_cols) - len(data_cols)) * " "
112 print(len(data_cols))
113 else:
114 header_cols += (len(data_cols) - len(header_cols)) * " "
115
116 html.append(
117 dedent(
118 f"""
119 <td><samp>{data_cols[0]}</samp></td>
120 """
121 )
122 )
123
124 for data_col in data_cols[1:]:
125 data_col_w_color = f"""<td>{data_col}</td>
126 """
127 if (
128 table_sum_on in cell_colors.keys()
129 and data_col in cell_colors[table_sum_on].keys()
130 ):
131 data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
132 """
133 html.append(dedent(data_col_w_color))
134 html.append("</tr>\n")
135 html.append("</tbody>\n")
136 html.append("</table>\n")
137 html.append("</div>\n")
138
139 mqc_yaml = {
140 "id": f"{table_sum_on.upper()}_collated_table",
141 "section_name": f"{table_sum_on.upper()}",
142 "section_href": f"https://github.com/CFSAN-Biostatistics/nowayout",
143 "plot_type": "html",
144 "description": f"{description}",
145 "data": ("").join(html),
146 }
147
148 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
149 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
150
151
152 if __name__ == "__main__":
153 main()