Mercurial > repos > kkonganti > cfsan_cronology

annotate 0.1.0/bin/create_mqc_data_table.py @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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kkonganti@0 1 #!/usr/bin/env python
kkonganti@0 2
kkonganti@0 3 import os
kkonganti@0 4 import sys
kkonganti@0 5 from textwrap import dedent
kkonganti@0 6
kkonganti@0 7 import yaml
kkonganti@0 8
kkonganti@0 9
kkonganti@0 10 def main():
kkonganti@0 11 """
kkonganti@0 12 Takes a tab-delimited text file with a mandatory header
kkonganti@0 13 column and generates an HTML table.
kkonganti@0 14 """
kkonganti@0 15
kkonganti@0 16 args = sys.argv
kkonganti@0 17 if len(args) < 2 or len(args) >= 4:
kkonganti@0 18 print(
kkonganti@0 19 f"\nAt least one argument specifying the *.tblsum file is required.\n"
kkonganti@0 20 + "No more than 2 command-line arguments should be passed.\n"
kkonganti@0 21 )
kkonganti@0 22 exit(1)
kkonganti@0 23
kkonganti@0 24 table_sum_on = str(args[1]).lower()
kkonganti@0 25 table_sum_on_file = table_sum_on + ".tblsum.txt"
kkonganti@0 26 cell_colors = f"{table_sum_on}.cellcolors.yml"
kkonganti@0 27
kkonganti@0 28 if len(args) == 3:
kkonganti@0 29 description = str(args[2])
kkonganti@0 30 else:
kkonganti@0 31 description = "The results table shown here is a collection from all samples."
kkonganti@0 32
kkonganti@0 33 if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
kkonganti@0 34 with open(cell_colors, "r") as cc_yml:
kkonganti@0 35 cell_colors = yaml.safe_load(cc_yml)
kkonganti@0 36 else:
kkonganti@0 37 cell_colors = dict()
kkonganti@0 38
kkonganti@0 39 if not (os.path.exists(table_sum_on_file) and os.path.getsize(table_sum_on_file) > 0):
kkonganti@0 40 exit(0)
kkonganti@0 41
kkonganti@0 42 with open(table_sum_on_file, "r") as tbl:
kkonganti@0 43 header = tbl.readline()
kkonganti@0 44 header_cols = header.strip().split("\t")
kkonganti@0 45
kkonganti@0 46 html = [
kkonganti@0 47 dedent(
kkonganti@0 48 f"""<script type="text/javascript">
kkonganti@0 49 $(document).ready(function () {{
kkonganti@0 50 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@0 51 scrollX: true,
kkonganti@0 52 fixedColumns: true, dom: 'Bfrtip',
kkonganti@0 53 buttons: [
kkonganti@0 54 'copy',
kkonganti@0 55 {{
kkonganti@0 56 extend: 'print',
kkonganti@0 57 title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@0 58 }},
kkonganti@0 59 {{
kkonganti@0 60 extend: 'excel',
kkonganti@0 61 filename: '{table_sum_on}_results',
kkonganti@0 62 }},
kkonganti@0 63 {{
kkonganti@0 64 extend: 'csv',
kkonganti@0 65 filename: '{table_sum_on}_results',
kkonganti@0 66 }}
kkonganti@0 67 ]
kkonganti@0 68 }});
kkonganti@0 69 }});
kkonganti@0 70 </script>
kkonganti@0 71 <div class="table-responsive">
kkonganti@0 72 <style>
kkonganti@0 73 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@0 74 background-color: #f2f2f2;
kkonganti@0 75 }}
kkonganti@0 76 </style>
kkonganti@0 77 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@0 78 <thead>
kkonganti@0 79 <tr>"""
kkonganti@0 80 )
kkonganti@0 81 ]
kkonganti@0 82
kkonganti@0 83 for header_col in header_cols:
kkonganti@0 84 html.append(
kkonganti@0 85 dedent(
kkonganti@0 86 f"""
kkonganti@0 87 <th> {header_col} </th>"""
kkonganti@0 88 )
kkonganti@0 89 )
kkonganti@0 90
kkonganti@0 91 html.append(
kkonganti@0 92 dedent(
kkonganti@0 93 """
kkonganti@0 94 </tr>
kkonganti@0 95 </thead>
kkonganti@0 96 <tbody>"""
kkonganti@0 97 )
kkonganti@0 98 )
kkonganti@0 99
kkonganti@0 100 for row in tbl:
kkonganti@0 101 html.append("<tr>\n")
kkonganti@0 102 data_cols = row.strip().split("\t")
kkonganti@0 103 if len(header_cols) != len(data_cols):
kkonganti@0 104 print(
kkonganti@0 105 f"\nWARN: Number of header columns ({len(header_cols)}) and data "
kkonganti@0 106 + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
kkonganti@0 107 )
kkonganti@0 108 if len(header_cols) > len(data_cols):
kkonganti@0 109 data_cols += (len(header_cols) - len(data_cols)) * " "
kkonganti@0 110 print(len(data_cols))
kkonganti@0 111 else:
kkonganti@0 112 header_cols += (len(data_cols) - len(header_cols)) * " "
kkonganti@0 113
kkonganti@0 114 html.append(
kkonganti@0 115 dedent(
kkonganti@0 116 f"""
kkonganti@0 117 <td><samp>{data_cols[0]}</samp></td>
kkonganti@0 118 """
kkonganti@0 119 )
kkonganti@0 120 )
kkonganti@0 121
kkonganti@0 122 for data_col in data_cols[1:]:
kkonganti@0 123 data_col_w_color = f"""<td>{data_col}</td>
kkonganti@0 124 """
kkonganti@0 125 if (
kkonganti@0 126 table_sum_on in cell_colors.keys()
kkonganti@0 127 and data_col in cell_colors[table_sum_on].keys()
kkonganti@0 128 ):
kkonganti@0 129 data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
kkonganti@0 130 """
kkonganti@0 131 html.append(dedent(data_col_w_color))
kkonganti@0 132 html.append("</tr>\n")
kkonganti@0 133 html.append("</tbody>\n")
kkonganti@0 134 html.append("</table>\n")
kkonganti@0 135 html.append("</div>\n")
kkonganti@0 136
kkonganti@0 137 mqc_yaml = {
kkonganti@0 138 "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@0 139 "section_name": f"{table_sum_on.upper()}",
kkonganti@0 140 "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
kkonganti@0 141 "plot_type": "html",
kkonganti@0 142 "description": f"{description}",
kkonganti@0 143 "data": ("").join(html),
kkonganti@0 144 }
kkonganti@0 145
kkonganti@0 146 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@0 147 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@0 148
kkonganti@0 149
kkonganti@0 150 if __name__ == "__main__":
kkonganti@0 151 main()