Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.6.1/bin/create_mqc_data_table.py @ 12:c5faadb3386f

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:57:15 -0400
parents 749faef1caa9
children
rev   line source
kkonganti@11 1 #!/usr/bin/env python
kkonganti@11 2
kkonganti@11 3 import os
kkonganti@11 4 import sys
kkonganti@11 5 from textwrap import dedent
kkonganti@11 6
kkonganti@11 7 import yaml
kkonganti@11 8
kkonganti@11 9
kkonganti@11 10 def main():
kkonganti@11 11 """
kkonganti@11 12 Takes a tab-delimited text file with a mandatory header
kkonganti@11 13 column and generates an HTML table.
kkonganti@11 14 """
kkonganti@11 15
kkonganti@11 16 args = sys.argv
kkonganti@11 17 if len(args) < 2 or len(args) >= 4:
kkonganti@11 18 print(
kkonganti@11 19 f"\nAt least one argument specifying the *.tblsum file is required.\n"
kkonganti@11 20 + "No more than 2 command-line arguments should be passed.\n"
kkonganti@11 21 )
kkonganti@11 22 exit(1)
kkonganti@11 23
kkonganti@11 24 table_sum_on = str(args[1]).lower()
kkonganti@11 25 table_sum_on_file = table_sum_on + ".tblsum.txt"
kkonganti@11 26 cell_colors = f"{table_sum_on}.cellcolors.yml"
kkonganti@11 27
kkonganti@11 28 if len(args) == 3:
kkonganti@11 29 description = str(args[2])
kkonganti@11 30 else:
kkonganti@11 31 description = "The results table shown here is a collection from all samples."
kkonganti@11 32
kkonganti@11 33 if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
kkonganti@11 34 with open(cell_colors, "r") as cc_yml:
kkonganti@11 35 cell_colors = yaml.safe_load(cc_yml)
kkonganti@11 36 else:
kkonganti@11 37 cell_colors = dict()
kkonganti@11 38
kkonganti@11 39 if not (os.path.exists(table_sum_on_file) and os.path.getsize(table_sum_on_file) > 0):
kkonganti@11 40 exit(0)
kkonganti@11 41
kkonganti@11 42 with open(table_sum_on_file, "r") as tbl:
kkonganti@11 43 header = tbl.readline()
kkonganti@11 44 header_cols = header.strip().split("\t")
kkonganti@11 45
kkonganti@11 46 html = [
kkonganti@11 47 dedent(
kkonganti@11 48 f"""<script type="text/javascript">
kkonganti@11 49 $(document).ready(function () {{
kkonganti@11 50 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@11 51 scrollX: true,
kkonganti@11 52 fixedColumns: true, dom: 'Bfrtip',
kkonganti@11 53 buttons: [
kkonganti@11 54 'copy',
kkonganti@11 55 {{
kkonganti@11 56 extend: 'print',
kkonganti@11 57 title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@11 58 }},
kkonganti@11 59 {{
kkonganti@11 60 extend: 'excel',
kkonganti@11 61 filename: '{table_sum_on}_results',
kkonganti@11 62 }},
kkonganti@11 63 {{
kkonganti@11 64 extend: 'csv',
kkonganti@11 65 filename: '{table_sum_on}_results',
kkonganti@11 66 }}
kkonganti@11 67 ]
kkonganti@11 68 }});
kkonganti@11 69 }});
kkonganti@11 70 </script>
kkonganti@11 71 <div class="table-responsive">
kkonganti@11 72 <style>
kkonganti@11 73 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@11 74 background-color: #f2f2f2;
kkonganti@11 75 }}
kkonganti@11 76 </style>
kkonganti@11 77 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@11 78 <thead>
kkonganti@11 79 <tr>"""
kkonganti@11 80 )
kkonganti@11 81 ]
kkonganti@11 82
kkonganti@11 83 for header_col in header_cols:
kkonganti@11 84 html.append(
kkonganti@11 85 dedent(
kkonganti@11 86 f"""
kkonganti@11 87 <th> {header_col} </th>"""
kkonganti@11 88 )
kkonganti@11 89 )
kkonganti@11 90
kkonganti@11 91 html.append(
kkonganti@11 92 dedent(
kkonganti@11 93 """
kkonganti@11 94 </tr>
kkonganti@11 95 </thead>
kkonganti@11 96 <tbody>"""
kkonganti@11 97 )
kkonganti@11 98 )
kkonganti@11 99
kkonganti@11 100 for row in tbl:
kkonganti@11 101 html.append("<tr>\n")
kkonganti@11 102 data_cols = row.strip().split("\t")
kkonganti@11 103 if len(header_cols) != len(data_cols):
kkonganti@11 104 print(
kkonganti@11 105 f"\nWARN: Number of header columns ({len(header_cols)}) and data "
kkonganti@11 106 + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
kkonganti@11 107 )
kkonganti@11 108 if len(header_cols) > len(data_cols):
kkonganti@11 109 data_cols += (len(header_cols) - len(data_cols)) * " "
kkonganti@11 110 print(len(data_cols))
kkonganti@11 111 else:
kkonganti@11 112 header_cols += (len(data_cols) - len(header_cols)) * " "
kkonganti@11 113
kkonganti@11 114 html.append(
kkonganti@11 115 dedent(
kkonganti@11 116 f"""
kkonganti@11 117 <td><samp>{data_cols[0]}</samp></td>
kkonganti@11 118 """
kkonganti@11 119 )
kkonganti@11 120 )
kkonganti@11 121
kkonganti@11 122 for data_col in data_cols[1:]:
kkonganti@11 123 data_col_w_color = f"""<td>{data_col}</td>
kkonganti@11 124 """
kkonganti@11 125 if (
kkonganti@11 126 table_sum_on in cell_colors.keys()
kkonganti@11 127 and data_col in cell_colors[table_sum_on].keys()
kkonganti@11 128 ):
kkonganti@11 129 data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
kkonganti@11 130 """
kkonganti@11 131 html.append(dedent(data_col_w_color))
kkonganti@11 132 html.append("</tr>\n")
kkonganti@11 133 html.append("</tbody>\n")
kkonganti@11 134 html.append("</table>\n")
kkonganti@11 135 html.append("</div>\n")
kkonganti@11 136
kkonganti@11 137 mqc_yaml = {
kkonganti@11 138 "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@11 139 "section_name": f"{table_sum_on.upper()}",
kkonganti@11 140 "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
kkonganti@11 141 "plot_type": "html",
kkonganti@11 142 "description": f"{description}",
kkonganti@11 143 "data": ("").join(html),
kkonganti@11 144 }
kkonganti@11 145
kkonganti@11 146 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@11 147 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@11 148
kkonganti@11 149
kkonganti@11 150 if __name__ == "__main__":
kkonganti@11 151 main()