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99.scripts/miscs/rename_trinity_fasta.py

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+#!/usr/bin/env python3
+"""
+Trinity FASTA Sequence Renaming Script
+Function: Rename sequences in FASTA file to format: [prefix@sequence_number]
+"""
+
+import sys
+import os
+
+def rename_fasta_sequences(input_file, prefix, output_file=None):
+    """
+    Rename sequence headers in a FASTA file
+    
+    Parameters:
+        input_file: Input FASTA filename
+        prefix: Prefix for sequence names
+        output_file: Output filename (optional, defaults to input_file_renamed.fasta)
+    """
+    
+    # Set output filename
+    if output_file is None:
+        file_base, file_ext = os.path.splitext(input_file)
+        output_file = f"{file_base}_renamed{file_ext}"
+    
+    # Counter for sequences
+    seq_count = 0
+    
+    try:
+        with open(input_file, 'r') as fin, open(output_file, 'w') as fout:
+            for line in fin:
+                if line.startswith('>'):
+                    # Sequence header line: rename it
+                    seq_count += 1
+                    new_name = f">{prefix}@mrna_{seq_count}\n"
+                    fout.write(new_name)
+                else:
+                    # Sequence data line: write as-is
+                    fout.write(line)
+        
+        print(f"Successfully renamed {seq_count} sequences")
+        print(f"Input file: {input_file}")
+        print(f"Output file: {output_file}")
+        print(f"Naming format: {prefix}@mrna_number")
+        
+    except FileNotFoundError:
+        print(f"Error: Input file '{input_file}' not found")
+        sys.exit(1)
+    except Exception as e:
+        print(f"Error processing file: {e}")
+        sys.exit(1)
+
+def main():
+    """Main function"""
+    if len(sys.argv) < 3:
+        print("Usage: python script.py <fasta_file> <prefix> [output_file]")
+        print("Example: python script.py sequences.fasta Gene new_sequences.fasta")
+        sys.exit(1)
+    
+    input_file = sys.argv[1]
+    prefix = sys.argv[2]
+    output_file = sys.argv[3] if len(sys.argv) > 3 else None
+    
+    # Verify input file exists
+    if not os.path.isfile(input_file):
+        print(f"Error: File '{input_file}' does not exist")
+        sys.exit(1)
+    
+    rename_fasta_sequences(input_file, prefix, output_file)
+
+if __name__ == "__main__":
+    main()