Add Vercel configuration for rewrites and build settings

99.scripts/miscs/rename_trinity_fasta.py

@@ -7,41 +7,53 @@ 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}"
-    
+
+    match_tsv = f"{output_file}.tsv"
+    print(f"Input file: {input_file}")
+    print(f"Output file: {output_file}")
+    print(f"Naming format: {prefix}@mrna_<number>")
+    print(f"Match TSV file: {match_tsv}")
+
     # Counter for sequences
     seq_count = 0
-    
+
     try:
-        with open(input_file, 'r') as fin, open(output_file, 'w') as fout:
+        with (
+            open(input_file, "r") as fin,
+            open(output_file, "w") as fout,
+            open(match_tsv, "w") as tsvout,
+        ):
+            tsvout.write("Original_Name\tNew_Name\n")
             for line in fin:
-                if line.startswith('>'):
+                if line.startswith(">"):
                     # Sequence header line: rename it
                     seq_count += 1
-                    new_name = f">{prefix}@mrna_{seq_count}\n"
-                    fout.write(new_name)
+                    original_name = line[1:].strip().split()[0]
+                    new_name = f"{prefix}@mrna_{seq_count}\n"
+                    fout.write(f">{new_name}")
+                    tsvout.write(f"{original_name}\t{new_name}\n")
                 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)
@@ -49,23 +61,25 @@ def rename_fasta_sequences(input_file, prefix, output_file=None):
         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()