Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.7.0/bin/create_mqc_data_table.py @ 19:4b304d77bbfb

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 11:20:22 -0400
parents 0e7a0053e4a6
children
rev   line source
kkonganti@17 1 #!/usr/bin/env python
kkonganti@17 2
kkonganti@17 3 import os
kkonganti@17 4 import sys
kkonganti@17 5 from textwrap import dedent
kkonganti@17 6
kkonganti@17 7 import yaml
kkonganti@17 8
kkonganti@17 9
kkonganti@17 10 def main():
kkonganti@17 11 """
kkonganti@17 12 Takes a tab-delimited text file with a mandatory header
kkonganti@17 13 column and generates an HTML table.
kkonganti@17 14 """
kkonganti@17 15
kkonganti@17 16 args = sys.argv
kkonganti@17 17 if len(args) < 2 or len(args) >= 4:
kkonganti@17 18 print(
kkonganti@17 19 f"\nAt least one argument specifying the *.tblsum file is required.\n"
kkonganti@17 20 + "No more than 2 command-line arguments should be passed.\n"
kkonganti@17 21 )
kkonganti@17 22 exit(1)
kkonganti@17 23
kkonganti@17 24 table_sum_on = str(args[1]).lower()
kkonganti@17 25 table_sum_on_file = table_sum_on + ".tblsum.txt"
kkonganti@17 26 cell_colors = f"{table_sum_on}.cellcolors.yml"
kkonganti@17 27
kkonganti@17 28 if len(args) == 3:
kkonganti@17 29 description = str(args[2])
kkonganti@17 30 else:
kkonganti@17 31 description = "The results table shown here is a collection from all samples."
kkonganti@17 32
kkonganti@17 33 if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
kkonganti@17 34 with open(cell_colors, "r") as cc_yml:
kkonganti@17 35 cell_colors = yaml.safe_load(cc_yml)
kkonganti@17 36 else:
kkonganti@17 37 cell_colors = dict()
kkonganti@17 38
kkonganti@17 39 if not (os.path.exists(table_sum_on_file) and os.path.getsize(table_sum_on_file) > 0):
kkonganti@17 40 exit(0)
kkonganti@17 41
kkonganti@17 42 with open(table_sum_on_file, "r") as tbl:
kkonganti@17 43 header = tbl.readline()
kkonganti@17 44 header_cols = header.strip().split("\t")
kkonganti@17 45
kkonganti@17 46 html = [
kkonganti@17 47 dedent(
kkonganti@17 48 f"""<script type="text/javascript">
kkonganti@17 49 $(document).ready(function () {{
kkonganti@17 50 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@17 51 scrollX: true,
kkonganti@17 52 fixedColumns: true, dom: 'Bfrtip',
kkonganti@17 53 buttons: [
kkonganti@17 54 'copy',
kkonganti@17 55 {{
kkonganti@17 56 extend: 'print',
kkonganti@17 57 title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@17 58 }},
kkonganti@17 59 {{
kkonganti@17 60 extend: 'excel',
kkonganti@17 61 filename: '{table_sum_on}_results',
kkonganti@17 62 }},
kkonganti@17 63 {{
kkonganti@17 64 extend: 'csv',
kkonganti@17 65 filename: '{table_sum_on}_results',
kkonganti@17 66 }}
kkonganti@17 67 ]
kkonganti@17 68 }});
kkonganti@17 69 }});
kkonganti@17 70 </script>
kkonganti@17 71 <div class="table-responsive">
kkonganti@17 72 <style>
kkonganti@17 73 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@17 74 background-color: #f2f2f2;
kkonganti@17 75 }}
kkonganti@17 76 </style>
kkonganti@17 77 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@17 78 <thead>
kkonganti@17 79 <tr>"""
kkonganti@17 80 )
kkonganti@17 81 ]
kkonganti@17 82
kkonganti@17 83 for header_col in header_cols:
kkonganti@17 84 html.append(
kkonganti@17 85 dedent(
kkonganti@17 86 f"""
kkonganti@17 87 <th> {header_col} </th>"""
kkonganti@17 88 )
kkonganti@17 89 )
kkonganti@17 90
kkonganti@17 91 html.append(
kkonganti@17 92 dedent(
kkonganti@17 93 """
kkonganti@17 94 </tr>
kkonganti@17 95 </thead>
kkonganti@17 96 <tbody>"""
kkonganti@17 97 )
kkonganti@17 98 )
kkonganti@17 99
kkonganti@17 100 for row in tbl:
kkonganti@17 101 html.append("<tr>\n")
kkonganti@17 102 data_cols = row.strip().split("\t")
kkonganti@17 103 if len(header_cols) != len(data_cols):
kkonganti@17 104 print(
kkonganti@17 105 f"\nWARN: Number of header columns ({len(header_cols)}) and data "
kkonganti@17 106 + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
kkonganti@17 107 )
kkonganti@17 108 if len(header_cols) > len(data_cols):
kkonganti@17 109 data_cols += (len(header_cols) - len(data_cols)) * " "
kkonganti@17 110 print(len(data_cols))
kkonganti@17 111 else:
kkonganti@17 112 header_cols += (len(data_cols) - len(header_cols)) * " "
kkonganti@17 113
kkonganti@17 114 html.append(
kkonganti@17 115 dedent(
kkonganti@17 116 f"""
kkonganti@17 117 <td><samp>{data_cols[0]}</samp></td>
kkonganti@17 118 """
kkonganti@17 119 )
kkonganti@17 120 )
kkonganti@17 121
kkonganti@17 122 for data_col in data_cols[1:]:
kkonganti@17 123 data_col_w_color = f"""<td>{data_col}</td>
kkonganti@17 124 """
kkonganti@17 125 if (
kkonganti@17 126 table_sum_on in cell_colors.keys()
kkonganti@17 127 and data_col in cell_colors[table_sum_on].keys()
kkonganti@17 128 ):
kkonganti@17 129 data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
kkonganti@17 130 """
kkonganti@17 131 html.append(dedent(data_col_w_color))
kkonganti@17 132 html.append("</tr>\n")
kkonganti@17 133 html.append("</tbody>\n")
kkonganti@17 134 html.append("</table>\n")
kkonganti@17 135 html.append("</div>\n")
kkonganti@17 136
kkonganti@17 137 mqc_yaml = {
kkonganti@17 138 "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@17 139 "section_name": f"{table_sum_on.upper()}",
kkonganti@17 140 "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
kkonganti@17 141 "plot_type": "html",
kkonganti@17 142 "description": f"{description}",
kkonganti@17 143 "data": ("").join(html),
kkonganti@17 144 }
kkonganti@17 145
kkonganti@17 146 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@17 147 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@17 148
kkonganti@17 149
kkonganti@17 150 if __name__ == "__main__":
kkonganti@17 151 main()