--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/bin/create_mqc_data_table.py	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,147 @@
+#!/usr/bin/env python
+
+import os
+import sys
+from textwrap import dedent
+
+import yaml
+
+
+def main():
+    """
+    Takes a tab-delimited text file with a mandatory header
+    column and generates an HTML table.
+    """
+
+    args = sys.argv
+    if len(args) < 2 or len(args) >= 4:
+        print(
+            f"\nAt least one argument specifying the *.tblsum file is required.\n"
+            + "No more than 2 command-line arguments should be passed.\n"
+        )
+        exit(1)
+
+    table_sum_on = str(args[1]).lower()
+    cell_colors = f"{table_sum_on}.cellcolors.yml"
+
+    if len(args) == 3:
+        description = str(args[2])
+    else:
+        description = "The results table shown here is a collection from all samples."
+
+    if os.path.exists(cell_colors) and os.path.getsize(cell_colors) > 0:
+        with open(cell_colors, "r") as cc_yml:
+            cell_colors = yaml.safe_load(cc_yml)
+    else:
+        cell_colors = dict()
+
+    with open(f"{table_sum_on}.tblsum.txt", "r") as tbl:
+        header = tbl.readline()
+        header_cols = header.strip().split("\t")
+
+        html = [
+            dedent(
+                f"""<script type="text/javascript">
+                    $(document).ready(function () {{
+                        $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
+                            scrollX: true,
+                            fixedColumns: true, dom: 'Bfrtip',
+                            buttons: [
+                                'copy',
+                                {{
+                                    extend: 'print',
+                                    title: 'CPIPES: MultiQC Report: {table_sum_on}'
+                                }},
+                                {{
+                                    extend: 'excel',
+                                    filename: '{table_sum_on}_results',
+                                }},
+                                {{
+                                    extend: 'csv',
+                                    filename: '{table_sum_on}_results',
+                                }}
+                            ]
+                        }});
+                    }});
+                </script>
+                <div class="table-responsive">
+                <style>
+                #cpipes-process-custom-res tr:nth-child(even) {{
+                    background-color: #f2f2f2;
+                }}
+                </style>
+                <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
+                <thead>
+                <tr>"""
+            )
+        ]
+
+        for header_col in header_cols:
+            html.append(
+                dedent(
+                    f"""
+                        <th> {header_col} </th>"""
+                )
+            )
+
+        html.append(
+            dedent(
+                """
+                </tr>
+                </thead>
+                <tbody>"""
+            )
+        )
+
+        for row in tbl:
+            html.append("<tr>\n")
+            data_cols = row.strip().split("\t")
+            if len(header_cols) != len(data_cols):
+                print(
+                    f"\nWARN: Number of header columns ({len(header_cols)}) and data "
+                    + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n"
+                )
+                if len(header_cols) > len(data_cols):
+                    data_cols += (len(header_cols) - len(data_cols)) * " "
+                    print(len(data_cols))
+                else:
+                    header_cols += (len(data_cols) - len(header_cols)) * " "
+
+            html.append(
+                dedent(
+                    f"""
+                        <td><samp>{data_cols[0]}</samp></td>
+                    """
+                )
+            )
+
+            for data_col in data_cols[1:]:
+                data_col_w_color = f"""<td>{data_col}</td>
+                """
+                if (
+                    table_sum_on in cell_colors.keys()
+                    and data_col in cell_colors[table_sum_on].keys()
+                ):
+                    data_col_w_color = f"""<td style="background-color: {cell_colors[table_sum_on][data_col]}">{data_col}</td>
+                    """
+                html.append(dedent(data_col_w_color))
+            html.append("</tr>\n")
+        html.append("</tbody>\n")
+        html.append("</table>\n")
+        html.append("</div>\n")
+
+        mqc_yaml = {
+            "id": f"{table_sum_on.upper()}_collated_table",
+            "section_name": f"{table_sum_on.upper()}",
+            "section_href": f"https://github.com/CFSAN-Biostatistics/bettercallsal",
+            "plot_type": "html",
+            "description": f"{description}",
+            "data": ("").join(html),
+        }
+
+        with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
+            yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()