From dfd826ee94f6a5ba91bc775d14f58df5055689fc Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Thu, 13 Feb 2025 16:29:13 -0500
Subject: [PATCH] Add files via upload

---
 .../ProcessAndRenameAssembledData.py          | 85 +++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 Utilities/For_Assemblies/ProcessAndRenameAssembledData.py

diff --git a/Utilities/For_Assemblies/ProcessAndRenameAssembledData.py b/Utilities/For_Assemblies/ProcessAndRenameAssembledData.py
new file mode 100644
index 0000000..97395eb
--- /dev/null
+++ b/Utilities/For_Assemblies/ProcessAndRenameAssembledData.py
@@ -0,0 +1,85 @@
+'''
+Author & Date: Adri K. Grow + ChatGPT, Nov 11th 2024
+    - Updated 02/13/25 to accept either transcriptome and genome assembled data in command line
+Motivation: assess and rename assembled transcript or genome files for PTL6p1 (or EPv1p1)
+Intention: warn if any 'transcripts.fasta' or 'contigs.fasta' files are missing or empty for an LKH, otherwise rename and copy them with their assigned 10-digit code by LKH
+Input:
+    - a base directory containing subdirectories for each LKH assembled file, named 'WTA_LKH<xxxx>' or 'WGA_LKH<xxxx>', each containing a 'transcripts.fasta' or 'contigs.fasta' file
+    - a mapping .txt file with LKH#s tab-separated with corresponding 10-digit codes
+Output: 
+    - a folder named 'renamed_transcripts|contigs' with assembled files now named by 10-digit codes; e.g. "Sr_rh_Ro04_assembledTranscripts.fasta"
+Dependencies: python3
+Usage: 
+    - for transcriptomes: python3 ProcessAndRenameAssembledData.py <assembled transcriptomes directory> <mapping_file.txt> transcriptomes
+    - for genomes: python3 ProcessAndRenameAssembledData.py <assembled genomes directory> <mapping_file.txt> genomes
+'''
+
+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, data_type):
+    """Iterates over all subdirectories in base_dir, processes relevant fasta files."""
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)  # Create output directory if it doesn't exist
+    
+    # Set file naming patterns based on data type
+    folder_prefix = "WTA_LKH" if data_type == "transcriptomes" else "WGA_LKH"
+    fasta_filename = "transcripts.fasta" if data_type == "transcriptomes" else "contigs.fasta"
+    output_suffix = "_assembledTranscripts.fasta" if data_type == "transcriptomes" else "_assembledContigs.fasta"
+    
+    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(folder_prefix):
+            lkh_number = folder_name.split('_')[1]  # Extract LKH number from folder name
+            fasta_file = os.path.join(folder_path, fasta_filename)
+            
+            if not os.path.isfile(fasta_file):
+                print(f"    WARNING: file '{fasta_filename}' is missing in folder {folder_name}.")
+                continue
+            
+            if os.path.getsize(fasta_file) == 0:
+                print(f"    WARNING: file '{fasta_filename}' is empty in folder {folder_name}.")
+                continue
+            
+            if lkh_number in mapping:
+                new_name = f"{mapping[lkh_number]}{output_suffix}"
+                output_path = os.path.join(output_dir, new_name)
+                shutil.copy(fasta_file, output_path)
+            else:
+                print(f"Notification: No 10-digit code found for LKH number {lkh_number} in folder {folder_name}.")
+
+def main():
+    if len(sys.argv) != 4 or sys.argv[3] not in ["transcriptomes", "genomes"]:
+        print("Usage: python script.py <base_dir> <mapping_file> <transcriptomes|genomes>")
+        sys.exit(1)
+    
+    base_dir = sys.argv[1]
+    mapping_file = sys.argv[2]
+    data_type = sys.argv[3]
+    
+    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_dir = os.path.join(os.getcwd(), "renamed_transcripts" if data_type == "transcriptomes" else "renamed_contigs")
+    
+    mapping = read_lkh_mapping(mapping_file)
+    process_directory(base_dir, mapping, output_dir, data_type)
+
+if __name__ == "__main__":
+    main()