Updating new features

ProtPeptigram/DataProcessor.py

@@ -7,7 +7,6 @@
 from typing import List, Dict, Union, Optional, Tuple, Set
 from Bio import SeqIO
 
-
 class PeptideDataProcessor:
     """
     Process peptide data from PEAKS Online output for visualization with ImmunoViz.
@@ -24,7 +23,7 @@ def __init__(self,
                  peaks_file: str = None, 
                  fasta_file: str = None,
                  contaminant_keywords: List[str] = None,
-                 sample_prefix: str = "Intensity_"):
+                 sample_prefix:str = "Intensity"): #sample_prefix: str = "Intensity_"):
         """
         Initialize the PeptideDataProcessor.
 
@@ -37,7 +36,7 @@ def __init__(self,
         contaminant_keywords : List[str], optional
             List of keywords to identify contaminant proteins
         sample_prefix : str, optional
-            Prefix for sample intensity columns (default: "Intensity_")
+            Prefix for sample intensity columns (default: "Intensity")
         """
         # Set default contaminant keywords if not provided
         if contaminant_keywords is None:

ProtPeptigram/main.py

@@ -0,0 +1,209 @@
+""" Peptigram: mapping peptide to source protein"""
+
+import argparse
+import sys
+from multiprocessing import Pool
+from rich.text import Text
+from rich_argparse import RichHelpFormatter
+from ProtPeptigram.logger import CONSOLE as console
+from ProtPeptigram import __author__, __version__
+from ProtPeptigram.runner import run_pipeline
+
+
+def _welcome():
+    """Display application banner."""
+
+    tool_icon = r"""
+    ____             __        ____             __  _                          
+   / __ \_________  / /_      / __ \___  ____  / /_(_)___ __________ _____ ___ 
+  / /_/ / ___/ __ \/ __/_____/ /_/ / _ \/ __ \/ __/ / __ `/ ___/ __ `/ __ `__ \
+ / ____/ /  / /_/ / /_/_____/ ____/  __/ /_/ / /_/ / /_/ / /  / /_/ / / / / / /
+/_/   /_/   \____/\__/     /_/    \___/ .___/\__/_/\__, /_/   \__,_/_/ /_/ /_/ 
+                                     /_/          /____/                                                                                                                                
+    """
+
+    console.print(tool_icon, style="blue")
+
+
+
+def _print_credits(credits=False):
+    """Print software credits to terminal."""
+    text = Text()
+    text.append("\n")
+    if credits:
+        text.append("Please cite: \n", style="bold")
+        text.append(
+            "GibbsCluster - 2.0 (Simultaneous alignment and clustering of peptide data)\n",
+            style="bold link https://services.healthtech.dtu.dk/services/GibbsCluster-2.0/",
+        )
+        text.append(
+            "Seq2Logo - 2.0 (Visualization of amino acid binding motifs)\n",
+            style="bold link https://services.healthtech.dtu.dk/services/Seq2Logo-2.0/",
+        )
+        text.append(
+            "MHC Motif Atlas (MHC motif PSM matrics are genrated using mhcmotifatlas please cite [link])\n\n",
+            style="bold link http://mhcmotifatlas.org/home",
+        )
+    else:
+        text.append(
+            "Prot-Petigram", style="bold link https://www.monash.edu/research/compomics/"
+        )
+        text.append(f" (v{__version__})\n", style="bold")
+    if credits:
+        text.append(
+            "HLA motif finder pipeline for identifying peptide motif immunopeptididomic data.\n",
+            style="italic",
+        )
+    text.append("Developed at Li Lab / Purcell Lab, Monash University, Australia.\n")
+    text.append("Please cite: ")
+    if credits:
+        text.append(
+            "Sanjay Krishna, Nathon Craft & Chen Li et al. bioRxiv (2024)",
+            style="link https://www.monash.edu/research/compomics/",
+        )
+    else:
+        text.append(
+            "Sanjay Krishna & Chen Li et al. bioRxiv (2024)",
+            style="ttps://www.monash.edu/research/compomics/",
+        )
+    text.append("\n")
+    if credits:
+        text.stylize("#006cb5")
+    console.print(text)
+
+
+def main():
+    """Main function to parse CLI arguments and execute the pipeline."""
+    _welcome()
+    _print_credits()
+    parser = argparse.ArgumentParser(
+        description="Prot-Petigram: Mapping peptides to source protein 🧬🧬🧬.",
+        formatter_class=lambda prog: RichHelpFormatter(prog, max_help_position=42),
+    )
+
+    parser.add_argument(
+        "-i",
+        "--input",
+        type=str,
+        help="input path csv file from peaks output"
+    )
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=str,
+        help="output dir path to save the processed data"
+    )
+    parser.add_argument(
+        "-f",
+        "--fasta",
+        type=str,
+        help="fasta file containing protein sequences"
+    )
+    parser.add_argument(
+        "-r",
+        "--regex",
+        type=str,
+        help=r"regex pattern to filter protein names. e.g., '(\W+\d+)\|' to extract protein names from Uniprot IDs"
+    )
+
+    parser.add_argument(
+        "-th",
+        "--threshold",
+        type=float,
+        default=0.0,
+        help="intensity threshold for filtering peptides"
+    )
+
+    parser.add_argument(
+        "-ms",
+        "--min-samples",
+        type=int,
+        default=1,
+        help="minimum number of samples a peptide must be present in"
+    )
+
+    parser.add_argument(
+        "-pl",
+        "--protein_list",
+        type=str,
+        help="path to a text file containing a list of protein IDs to filter"
+    )
+
+    parser.add_argument(
+        "-tp",
+        "--top",
+        type=str,
+        default=5,
+        help="fasta file containing protein sequences"
+    )
+
+    parser.add_argument(
+        "-t",
+        "--threads",
+        type=int,
+        default=1,
+        help="Number of threads to use for processing (default: 1)"
+    )
+
+    parser.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        version=f"Prot-Petigram v{__version__}"
+    )
+
+    parser.add_argument(
+        "-c",
+        "--credits",
+        action="store_true",
+        help="Print software credits"
+    )
+
+    args = parser.parse_args()
+    if args.credits:
+        _print_credits(credits=True)
+        sys.exit(0)
+
+    if args.input and args.fasta:
+        if args.threads > 1:
+            console.log(
+                f"Using {args.threads} threads for processing.",
+                style="bold green"
+            )
+            with Pool(processes=args.threads) as pool:
+                pool.apply_async(
+                    run_pipeline,
+                    args=(
+                        args.input,
+                        args.fasta,
+                        args.output,
+                        args.top,
+                        args.protein_list,
+                        args.regex,
+                        args.threshold,
+                        args.min_samples
+                    )
+                )
+                pool.close()
+                pool.join()
+        else:
+            console.log("Running in single-threaded mode.", style="bold yellow")
+            run_pipeline(
+                args.input,
+                args.fasta,
+                args.output,
+                args.top,
+                args.protein_list,
+                args.regex,
+                args.threshold,
+                args.min_samples
+            )
+    else:
+        parser.error("Both input CSV file (-i/--input) and FASTA file (-f/--fasta) are required.")
+
+
+
+
+if __name__ == "__main__":
+    main()