Delete Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts.py

Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts.py

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-'''
-Author & Date: Adri K. Grow + ChatGPT, Nov 11th 2024
-Motivation: assess and rename assembled transcript files for PTL6p1 (or EPv1p1)
-Intention: warn if any 'transcripts.fasta' files are missing or empty for an LKH, otherwise rename and copy them with their newly assigned 10-digit code by LKH
-Input:
-    - a base directory containing subdirectories for each LKH assembled transcriptome, named 'WTA_LKH<xxxx>', each containing a 'transcripts.fasta' file
-    - a mapping .txt file with LKH#s tab-separated with corresponding 10-digit codes
-Output: 
-    - a folder named 'renamed_transcripts' with 'transcripts.fasta' files now named by 10-digit codes; e.g. "Sr_rh_Ro04_assembledTranscripts.fasta"
-Dependencies: python3
-Usage: python3 ProcessAndRenamePlateTranscripts.py <assembled transcriptomes directory> <mapping_file.txt>
-'''
-
-import os
-import shutil
-import sys
-
-def read_lkh_mapping(mapping_file):
-    """Reads the LKH number to 10-digit code mapping from a file."""
-    mapping = {}
-    with open(mapping_file, 'r') as file:
-        for line in file:
-            lkh_number, code = line.strip().split('\t')
-            mapping[lkh_number] = code
-    return mapping
-
-def process_directory(base_dir, mapping, output_dir):
-    """Iterates over all subdirectories in base_dir, processes transcripts.fasta files."""
-    if not os.path.exists(output_dir):
-        os.makedirs(output_dir)  # Create output directory if it doesn't exist
-    
-    # Iterate over subdirectories in base_dir
-    for folder_name in os.listdir(base_dir):
-        folder_path = os.path.join(base_dir, folder_name)
-
-        if os.path.isdir(folder_path) and folder_name.startswith("WTA_LKH"):
-            lkh_number = folder_name.split('_')[1]  # Extract LKH number from folder name
-            transcripts_file = os.path.join(folder_path, 'transcripts.fasta')
-            
-            # Check if the file exists and is not empty
-            if not os.path.isfile(transcripts_file):
-                print(f"    WARNING: file 'transcripts.fasta' is missing in folder {folder_name}.")
-                continue  # Skip to the next folder
-            
-            if os.path.getsize(transcripts_file) == 0:
-                print(f"    WARNING: file 'transcripts.fasta' is empty in folder {folder_name}.")
-                continue  # Skip to the next folder
-            
-            # If file exists and is not empty, proceed with renaming and copying
-            if lkh_number in mapping:
-                new_name = f"{mapping[lkh_number]}_assembledTranscripts.fasta"
-                output_path = os.path.join(output_dir, new_name)
-                
-                # Copy the file with the new name
-                shutil.copy(transcripts_file, output_path)
-                #print(f"Copied and renamed {transcripts_file} to {output_path}.")
-            else:
-                print(f"Notification: No 10-digit code found for LKH number {lkh_number} in folder {folder_name}.")
-
-def main():
-    # Check if the user provided the correct number of command-line arguments
-    if len(sys.argv) != 3:
-        print("Usage: python script.py <base_dir> <mapping_file>")
-        sys.exit(1)
-    
-    # Get the base directory and mapping file from command line arguments
-    base_dir = sys.argv[1]
-    mapping_file = sys.argv[2]
-    
-    # Check if the directories/files exist
-    if not os.path.isdir(base_dir):
-        print(f"Error: The directory '{base_dir}' does not exist.")
-        sys.exit(1)
-
-    if not os.path.isfile(mapping_file):
-        print(f"Error: The file '{mapping_file}' does not exist.")
-        sys.exit(1)
-    
-    # Output directory will be created in the current working directory
-    output_dir = os.path.join(os.getcwd(), "renamed_transcripts")
-    
-    # Read the LKH to code mapping
-    mapping = read_lkh_mapping(mapping_file)
-    
-    # Process the directories
-    process_directory(base_dir, mapping, output_dir)
-
-if __name__ == "__main__":
-    main()