kkonganti@17: #!/usr/bin/env python
kkonganti@17: 
kkonganti@17: import os
kkonganti@17: import sys
kkonganti@17: from textwrap import dedent
kkonganti@17: 
kkonganti@17: import yaml
kkonganti@17: 
kkonganti@17: 
kkonganti@17: def main():
kkonganti@17:     """
kkonganti@17:     Takes a tab-delimited text file with a mandatory header
kkonganti@17:     column and generates an HTML table.
kkonganti@17:     """
kkonganti@17: 
kkonganti@17:     args = sys.argv
kkonganti@17:     if len(args) < 2 or len(args) >= 4:
kkonganti@17:         print(
kkonganti@17:             f"\nAt least one argument specifying the *.tblsum file is required.\n"
kkonganti@17:             + "No more than 2 command-line arguments should be passed.\n"
kkonganti@17:         )
kkonganti@17:         exit(1)
kkonganti@17: 
kkonganti@17:     table_sum_on = str(args[1]).lower()
kkonganti@17:     table_sum_on_file = table_sum_on + ".tblsum.txt"
kkonganti@17:     cell_colors = f"{table_sum_on}.cellcolors.yml"
kkonganti@17: 
kkonganti@17:     if len(args) == 3:
kkonganti@17:         description = str(args[2])
kkonganti@17:     else:
kkonganti@17:         description = "The results table shown here is a collection from all samples."
kkonganti@17: 
kkonganti@17:     if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
kkonganti@17:         with open(cell_colors, "r") as cc_yml:
kkonganti@17:             cell_colors = yaml.safe_load(cc_yml)
kkonganti@17:     else:
kkonganti@17:         cell_colors = dict()
kkonganti@17: 
kkonganti@17:     if not (os.path.exists(table_sum_on_file) and os.path.getsize(table_sum_on_file) > 0):
kkonganti@17:         exit(0)
kkonganti@17: 
kkonganti@17:     with open(table_sum_on_file, "r") as tbl:
kkonganti@17:         header = tbl.readline()
kkonganti@17:         header_cols = header.strip().split("\t")
kkonganti@17: 
kkonganti@17:         html = [
kkonganti@17:             dedent(
kkonganti@17:                 f"""<script type="text/javascript">
kkonganti@17:                     $(document).ready(function () {{
kkonganti@17:                         $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@17:                             scrollX: true,
kkonganti@17:                             fixedColumns: true, dom: 'Bfrtip',
kkonganti@17:                             buttons: [
kkonganti@17:                                 'copy',
kkonganti@17:                                 {{
kkonganti@17:                                     extend: 'print',
kkonganti@17:                                     title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@17:                                 }},
kkonganti@17:                                 {{
kkonganti@17:                                     extend: 'excel',
kkonganti@17:                                     filename: '{table_sum_on}_results',
kkonganti@17:                                 }},
kkonganti@17:                                 {{
kkonganti@17:                                     extend: 'csv',
kkonganti@17:                                     filename: '{table_sum_on}_results',
kkonganti@17:                                 }}
kkonganti@17:                             ]
kkonganti@17:                         }});
kkonganti@17:                     }});
kkonganti@17:                 </script>
kkonganti@17:                 <div class="table-responsive">
kkonganti@17:                 <style>
kkonganti@17:                 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@17:                     background-color: #f2f2f2;
kkonganti@17:                 }}
kkonganti@17:                 </style>
kkonganti@17:                 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@17:                 <thead>
kkonganti@17:                 <tr>"""
kkonganti@17:             )
kkonganti@17:         ]
kkonganti@17: 
kkonganti@17:         for header_col in header_cols:
kkonganti@17:             html.append(
kkonganti@17:                 dedent(
kkonganti@17:                     f"""
kkonganti@17:                         <th> {header_col} </th>"""
kkonganti@17:                 )
kkonganti@17:             )
kkonganti@17: 
kkonganti@17:         html.append(
kkonganti@17:             dedent(
kkonganti@17:                 """
kkonganti@17:                 </tr>
kkonganti@17:                 </thead>
kkonganti@17:                 <tbody>"""
kkonganti@17:             )
kkonganti@17:         )
kkonganti@17: 
kkonganti@17:         for row in tbl:
kkonganti@17:             html.append("<tr>\n")
kkonganti@17:             data_cols = row.strip().split("\t")
kkonganti@17:             if len(header_cols) != len(data_cols):
kkonganti@17:                 print(
kkonganti@17:                     f"\nWARN: Number of header columns ({len(header_cols)}) and data "
kkonganti@17:                     + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
kkonganti@17:                 )
kkonganti@17:                 if len(header_cols) > len(data_cols):
kkonganti@17:                     data_cols += (len(header_cols) - len(data_cols)) * " "
kkonganti@17:                     print(len(data_cols))
kkonganti@17:                 else:
kkonganti@17:                     header_cols += (len(data_cols) - len(header_cols)) * " "
kkonganti@17: 
kkonganti@17:             html.append(
kkonganti@17:                 dedent(
kkonganti@17:                     f"""
kkonganti@17:                         <td><samp>{data_cols[0]}</samp></td>
kkonganti@17:                     """
kkonganti@17:                 )
kkonganti@17:             )
kkonganti@17: 
kkonganti@17:             for data_col in data_cols[1:]:
kkonganti@17:                 data_col_w_color = f"""<td>{data_col}</td>
kkonganti@17:                 """
kkonganti@17:                 if (
kkonganti@17:                     table_sum_on in cell_colors.keys()
kkonganti@17:                     and data_col in cell_colors[table_sum_on].keys()
kkonganti@17:                 ):
kkonganti@17:                     data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
kkonganti@17:                     """
kkonganti@17:                 html.append(dedent(data_col_w_color))
kkonganti@17:             html.append("</tr>\n")
kkonganti@17:         html.append("</tbody>\n")
kkonganti@17:         html.append("</table>\n")
kkonganti@17:         html.append("</div>\n")
kkonganti@17: 
kkonganti@17:         mqc_yaml = {
kkonganti@17:             "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@17:             "section_name": f"{table_sum_on.upper()}",
kkonganti@17:             "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
kkonganti@17:             "plot_type": "html",
kkonganti@17:             "description": f"{description}",
kkonganti@17:             "data": ("").join(html),
kkonganti@17:         }
kkonganti@17: 
kkonganti@17:         with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@17:             yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@17: 
kkonganti@17: 
kkonganti@17: if __name__ == "__main__":
kkonganti@17:     main()