Add Vercel configuration for rewrites and build settings

99.scripts/workflow/phylogeny_reconstruction/04.concatenate_ogs.py

@@ -94,11 +94,18 @@ def concatenate_fasta_files(fasta_files, output_file):
     print(f"Total output sequence length: {len(concatenated_sequences[0].seq)}.")
 
 
-def get_fasta_files_from_directory(directory, extensions):
+def get_fasta_files_from_directory(directory, extensions, list_file=None):
     """
     get all FASTA files from a directory with specified extensions
     """
     fasta_files = []
+    if list_file:
+        with open(list_file, "r") as lf:
+            for line in lf:
+                filepath = os.path.join(directory, line.strip())
+                if os.path.isfile(filepath):
+                    fasta_files.append(filepath)
+        return sorted(fasta_files)
     for filename in os.listdir(directory):
         if any(filename.endswith(ext) for ext in extensions):
             fasta_files.append(os.path.join(directory, filename))
@@ -119,12 +126,15 @@ def main():
         default=[".fasta", ".fa", ".fna"],
         help="FASTA file extensions to look for in directory",
     )
+    parser.add_argument("-l", "--list", help="List of input FASTA files", default=None)
 
     args = parser.parse_args()
 
     # 获取输入文件
     if args.directory:
-        fasta_files = get_fasta_files_from_directory(args.directory, args.extensions)
+        fasta_files = get_fasta_files_from_directory(
+            args.directory, args.extensions, args.list
+        )
         if not fasta_files:
             print(
                 f"Cannot find FASTA files in {args.directory} with extensions {args.extensions}"
@@ -137,7 +147,7 @@ def main():
         return
 
     print(f"Found {len(fasta_files)} FASTA files:")
-    
+
     # Perform concatenation
     concatenate_fasta_files(fasta_files, args.output)