--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/bin/gen_sim_abn_table.py	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,191 @@
+#!/usr/bin/env python3
+
+# Kranti Konganti
+
+import argparse
+import glob
+import inspect
+import logging
+import os
+import pprint
+import re
+from collections import defaultdict
+
+
+# Multiple inheritence for pretty printing of help text.
+class MultiArgFormatClasses(
+    argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter
+):
+    pass
+
+
+# Main
+def main() -> None:
+    """
+    This script will take the final taxonomic classification files and create a
+    global relative abundance type file in the current working directory. The
+    relative abundance type files should be in CSV or TSV format and should have
+    the lineage or taxonomy in first column and samples in the subsequent columns.
+    """
+    # Set logging.
+    logging.basicConfig(
+        format="\n"
+        + "=" * 55
+        + "\n%(asctime)s - %(levelname)s\n"
+        + "=" * 55
+        + "\n%(message)s\n\n",
+        level=logging.DEBUG,
+    )
+
+    # Debug print.
+    ppp = pprint.PrettyPrinter(width=55)
+    prog_name = inspect.stack()[0].filename
+
+    parser = argparse.ArgumentParser(
+        prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
+    )
+
+    required = parser.add_argument_group("required arguments")
+
+    required.add_argument(
+        "-abn",
+        dest="rel_abn_dir",
+        default=False,
+        required=True,
+        help="Absolute UNIX path to the parent directory that contains the\n"
+        + "abundance type files.",
+    )
+    parser.add_argument(
+        "-op",
+        dest="out_prefix",
+        default="nowayout.tblsum",
+        required=False,
+        help="Set the output file(s) prefix for output(s) generated\nby this program.",
+    )
+    parser.add_argument(
+        "-header",
+        dest="header",
+        action="store_true",
+        default=True,
+        required=False,
+        help="Do the relative abundance files have a header.",
+    )
+    parser.add_argument(
+        "-filepat",
+        dest="file_pat",
+        default="*.lineage_summary.tsv",
+        required=False,
+        help="Files will be searched by this suffix for merged output generation\nby this program.",
+    )
+    parser.add_argument(
+        "-failedfilepat",
+        dest="failed_file_pat",
+        default="*FAILED.txt",
+        required=False,
+        help="Files will be searched by this suffix for merged output generation\nby this program.",
+    )
+    parser.add_argument(
+        "-delim",
+        dest="delim",
+        default="\t",
+        required=False,
+        help="The delimitor by which the fields are separated in the file.",
+    )
+
+    args = parser.parse_args()
+    rel_abn_dir = args.rel_abn_dir
+    is_header = args.header
+    out_prefix = args.out_prefix
+    file_pat = args.file_pat
+    failed_file_pat = args.failed_file_pat
+    delim = args.delim
+    suffix = re.sub(r"^\*", "", file_pat)
+    rel_abn_comb = os.path.join(os.getcwd(), out_prefix + ".txt")
+    rel_abn_files = glob.glob(os.path.join(rel_abn_dir, file_pat))
+    failed_rel_abn_files = glob.glob(os.path.join(rel_abn_dir, failed_file_pat))
+    empty_results = "Relative abundance results did not pass thresholds"
+    sample2lineage, seen_lineage = (defaultdict(defaultdict), defaultdict(int))
+
+    if len(rel_abn_files) == 0:
+        logging.info(
+            "Unable to find any files with .tsv extentsion.\nNow trying .csv extension."
+        )
+        rel_abn_files = glob.glob(os.path.join(rel_abn_dir, "*.csv"))
+        delim = ","
+
+    if len(failed_rel_abn_files) == 0:
+        logging.info(
+            f"Unable to find any files with patttern {failed_file_pat}.\n"
+            + "The failed samples will not appear in the final aggregate file."
+        )
+
+    if rel_abn_dir:
+        if not os.path.isdir(rel_abn_dir):
+            logging.error("UNIX path\n" + f"{rel_abn_dir}\n" + "does not exist!")
+            exit(1)
+        if len(rel_abn_files) <= 0:
+            with open(rel_abn_comb, "w") as rel_abn_comb_fh:
+                rel_abn_comb_fh.write(f"Sample\n{empty_results} in any samples\n")
+            rel_abn_comb_fh.close()
+            exit(0)
+
+        for failed_rel_abn in failed_rel_abn_files:
+            with open(failed_rel_abn, "r") as failed_fh:
+                sample2lineage[failed_fh.readline().strip()].setdefault(
+                    "unclassified", []
+                ).append(float("1.0"))
+            failed_fh.close()
+
+        for rel_abn_file in rel_abn_files:
+            sample_name = re.match(r"(^.+?)\..*$", os.path.basename(rel_abn_file))[1]
+
+            with open(rel_abn_file, "r") as rel_abn_fh:
+                if is_header:
+                    sample_names = rel_abn_fh.readline().strip().split(delim)[1:]
+                    if len(sample_names) > 2:
+                        logging.error(
+                            "The individual relative abundance file has more "
+                            + "\nthan 1 sample. This is rare in the context of running the "
+                            + "\n nowayout Nextflow workflow."
+                        )
+                        exit(1)
+                    elif len(sample_names) < 2:
+                        sample_name = re.sub(suffix, "", os.path.basename(rel_abn_file))
+                        logging.info(
+                            "Seems like there is no sample name in the lineage summary file."
+                            + f"\nTherefore, sample name has been extracted from file name: {sample_name}."
+                        )
+                    else:
+                        sample_name = sample_names[0]
+
+                for line in rel_abn_fh.readlines():
+                    cols = line.strip().split(delim)
+                    lineage = cols[0]
+                    abn = cols[1]
+                    sample2lineage[sample_name].setdefault(lineage, []).append(
+                        float(abn)
+                    )
+                    seen_lineage[lineage] = 1
+
+        with open(rel_abn_comb, "w") as rel_abn_comb_fh:
+            samples = sorted(sample2lineage.keys())
+            rel_abn_comb_fh.write(f"Lineage{delim}" + delim.join(samples) + "\n")
+
+            for lineage in sorted(seen_lineage.keys()):
+                rel_abn_comb_fh.write(lineage)
+                for sample in samples:
+                    if lineage in sample2lineage[sample].keys():
+                        rel_abn_comb_fh.write(
+                            delim
+                            + "".join(
+                                [str(abn) for abn in sample2lineage[sample][lineage]]
+                            )
+                        )
+                    else:
+                        rel_abn_comb_fh.write(f"{delim}0.0")
+                rel_abn_comb_fh.write("\n")
+        rel_abn_comb_fh.close()
+
+
+if __name__ == "__main__":
+    main()