From 2ad02897c801c5dd47da284903a0538406146848 Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Wed, 15 Jan 2025 11:22:39 -0500
Subject: [PATCH] Add files via upload

---
 .../ProcessAndRenamePlateTranscripts_AKG.py   | 89 +++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts_AKG.py

diff --git a/Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts_AKG.py b/Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts_AKG.py
new file mode 100644
index 0000000..34cbba9
--- /dev/null
+++ b/Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts_AKG.py
@@ -0,0 +1,89 @@
+'''
+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_AKG.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()