Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.5.0/bin/create_mqc_data_table.py @ 10:1b9de878b04a

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"planemo upload"
author kkonganti
date Thu, 15 Jun 2023 11:16:45 -0400
parents 365849f031fd
children
rev   line source
kkonganti@1 1 #!/usr/bin/env python
kkonganti@1 2
kkonganti@1 3 import os
kkonganti@1 4 import sys
kkonganti@1 5 from textwrap import dedent
kkonganti@1 6
kkonganti@1 7 import yaml
kkonganti@1 8
kkonganti@1 9
kkonganti@1 10 def main():
kkonganti@1 11 """
kkonganti@1 12 Takes a tab-delimited text file with a mandatory header
kkonganti@1 13 column and generates an HTML table.
kkonganti@1 14 """
kkonganti@1 15
kkonganti@1 16 args = sys.argv
kkonganti@1 17 if len(args) < 2 or len(args) >= 4:
kkonganti@1 18 print(
kkonganti@1 19 f"\nAt least one argument specifying the *.tblsum file is required.\n"
kkonganti@1 20 + "No more than 2 command-line arguments should be passed.\n"
kkonganti@1 21 )
kkonganti@1 22 exit(1)
kkonganti@1 23
kkonganti@1 24 table_sum_on = str(args[1]).lower()
kkonganti@1 25 cell_colors = f"{table_sum_on}.cellcolors.yml"
kkonganti@1 26
kkonganti@1 27 if len(args) == 3:
kkonganti@1 28 description = str(args[2])
kkonganti@1 29 else:
kkonganti@1 30 description = "The results table shown here is a collection from all samples."
kkonganti@1 31
kkonganti@1 32 if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
kkonganti@1 33 with open(cell_colors, "r") as cc_yml:
kkonganti@1 34 cell_colors = yaml.safe_load(cc_yml)
kkonganti@1 35 else:
kkonganti@1 36 cell_colors = dict()
kkonganti@1 37
kkonganti@1 38 with open(f"{table_sum_on}.tblsum.txt", "r") as tbl:
kkonganti@1 39 header = tbl.readline()
kkonganti@1 40 header_cols = header.strip().split("\t")
kkonganti@1 41
kkonganti@1 42 html = [
kkonganti@1 43 dedent(
kkonganti@1 44 f"""<script type="text/javascript">
kkonganti@1 45 $(document).ready(function () {{
kkonganti@1 46 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@1 47 scrollX: true,
kkonganti@1 48 fixedColumns: true, dom: 'Bfrtip',
kkonganti@1 49 buttons: [
kkonganti@1 50 'copy',
kkonganti@1 51 {{
kkonganti@1 52 extend: 'print',
kkonganti@1 53 title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@1 54 }},
kkonganti@1 55 {{
kkonganti@1 56 extend: 'excel',
kkonganti@1 57 filename: '{table_sum_on}_results',
kkonganti@1 58 }},
kkonganti@1 59 {{
kkonganti@1 60 extend: 'csv',
kkonganti@1 61 filename: '{table_sum_on}_results',
kkonganti@1 62 }}
kkonganti@1 63 ]
kkonganti@1 64 }});
kkonganti@1 65 }});
kkonganti@1 66 </script>
kkonganti@1 67 <div class="table-responsive">
kkonganti@1 68 <style>
kkonganti@1 69 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@1 70 background-color: #f2f2f2;
kkonganti@1 71 }}
kkonganti@1 72 </style>
kkonganti@1 73 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@1 74 <thead>
kkonganti@1 75 <tr>"""
kkonganti@1 76 )
kkonganti@1 77 ]
kkonganti@1 78
kkonganti@1 79 for header_col in header_cols:
kkonganti@1 80 html.append(
kkonganti@1 81 dedent(
kkonganti@1 82 f"""
kkonganti@1 83 <th> {header_col} </th>"""
kkonganti@1 84 )
kkonganti@1 85 )
kkonganti@1 86
kkonganti@1 87 html.append(
kkonganti@1 88 dedent(
kkonganti@1 89 """
kkonganti@1 90 </tr>
kkonganti@1 91 </thead>
kkonganti@1 92 <tbody>"""
kkonganti@1 93 )
kkonganti@1 94 )
kkonganti@1 95
kkonganti@1 96 for row in tbl:
kkonganti@1 97 html.append("<tr>\n")
kkonganti@1 98 data_cols = row.strip().split("\t")
kkonganti@1 99 if len(header_cols) != len(data_cols):
kkonganti@1 100 print(
kkonganti@1 101 f"\nWARN: Number of header columns ({len(header_cols)}) and data "
kkonganti@1 102 + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
kkonganti@1 103 )
kkonganti@1 104 if len(header_cols) > len(data_cols):
kkonganti@1 105 data_cols += (len(header_cols) - len(data_cols)) * " "
kkonganti@1 106 print(len(data_cols))
kkonganti@1 107 else:
kkonganti@1 108 header_cols += (len(data_cols) - len(header_cols)) * " "
kkonganti@1 109
kkonganti@1 110 html.append(
kkonganti@1 111 dedent(
kkonganti@1 112 f"""
kkonganti@1 113 <td><samp>{data_cols[0]}</samp></td>
kkonganti@1 114 """
kkonganti@1 115 )
kkonganti@1 116 )
kkonganti@1 117
kkonganti@1 118 for data_col in data_cols[1:]:
kkonganti@1 119 data_col_w_color = f"""<td>{data_col}</td>
kkonganti@1 120 """
kkonganti@1 121 if (
kkonganti@1 122 table_sum_on in cell_colors.keys()
kkonganti@1 123 and data_col in cell_colors[table_sum_on].keys()
kkonganti@1 124 ):
kkonganti@1 125 data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
kkonganti@1 126 """
kkonganti@1 127 html.append(dedent(data_col_w_color))
kkonganti@1 128 html.append("</tr>\n")
kkonganti@1 129 html.append("</tbody>\n")
kkonganti@1 130 html.append("</table>\n")
kkonganti@1 131 html.append("</div>\n")
kkonganti@1 132
kkonganti@1 133 mqc_yaml = {
kkonganti@1 134 "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@1 135 "section_name": f"{table_sum_on.upper()}",
kkonganti@1 136 "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
kkonganti@1 137 "plot_type": "html",
kkonganti@1 138 "description": f"{description}",
kkonganti@1 139 "data": ("").join(html),
kkonganti@1 140 }
kkonganti@1 141
kkonganti@1 142 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@1 143 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@1 144
kkonganti@1 145
kkonganti@1 146 if __name__ == "__main__":
kkonganti@1 147 main()