Modif func fasta and example

app.py

@@ -12,36 +12,39 @@ from modal_app import app, chai1_inference, download_inference_dependencies, her
 # Definition of the tools for the MCP server 
 
 # Function to return a fasta file
-def return_fasta_file() -> str:
-    """Create a FASTA file from a protein sequence string.
+def create_fasta_file(sequence: str, name: Optional[str] = None) -> str:
+    """Create a FASTA file from a protein sequence string with a unique name.
     
     Args:
-        sequence (str): The protein sequence string
+        sequence (str): The protein sequence string with optional line breaks
         name (str, optional): The name/identifier for the sequence. Defaults to "PROTEIN"
-        output_file (str, optional): Path to save the FASTA file. If None, saves to default location.
     
     Returns:
-        str: Path to the created FASTA file
+        str: Name of the created FASTA file
     """
-    # Clean the sequence by removing whitespace and newlines
-    sequence = ''.join(sequence.split())
+    # Remove any trailing/leading whitespace but preserve line breaks
+    lines = sequence.strip().split('\n')
     
-    # Set default name if none provided
-    if name is None:
-        name = "PROTEIN"
+    # Check if the first line is a FASTA header
+    if not lines[0].startswith('>'):
+        # If no header provided, add one
+        if name is None:
+            name = "PROTEIN"
+        sequence = f">{name}\n{sequence}"
     
-    # Create FASTA content
-    fasta_content = f">{name}\n{sequence}\n"
+    # Create FASTA content (preserving line breaks)
+    fasta_content = sequence
     
-    # Set default output path if none provided
-    if output_file is None:
-        output_file = here / "inputs" / "chai1_custom_input.fasta"
+    # Generate a unique file name
+    unique_id = hashlib.sha256(uuid4().bytes).hexdigest()[:8]
+    file_name = f"chai1_{unique_id}_input.fasta"
+    file_path = here / "inputs" / file_name
     
     # Write the FASTA file
-    with open(output_file, "w") as f:
+    with open(file_path, "w") as f:
         f.write(fasta_content)
     
-    return str(output_file)
+    return file_name
 
 # Function to create a custom JSON config file
 def create_custom_config(
@@ -105,7 +108,7 @@ def compute_Chai1(
         if not fasta_file:
             fasta_file = here / "inputs" / "chai1_default_input.fasta"   
         print(f"🧬 running Chai inference on {fasta_file}")
-        print("titi")
+        fasta_file = here / "inputs" / fasta_file
         print(fasta_file)
         fasta_content = Path(fasta_file).read_text()
 
@@ -151,10 +154,10 @@ with gr.Blocks() as demo:
     """) 
     
     with gr.Tab("Configuration 📦"):
-        text_input = gr.Textbox()
-        text_output = gr.Textbox()
-        text_button = gr.Button("Generate Configuration")
-        text_button.click(fn=create_custom_config, inputs=[text_input], outputs=[text_output])
+        text_input = gr.Textbox(placeholder="Fasta format sequences", label="Fasta content", lines=10)
+        text_output = gr.Textbox(placeholder="Fasta file name", label="Fasta file name")
+        text_button = gr.Button("Create Fasta file")
+        text_button.click(fn=create_fasta_file, inputs=[text_input], outputs=[text_output])
         
         gr.Markdown(
         """
@@ -176,8 +179,8 @@ with gr.Blocks() as demo:
         For any issues or questions, please contact the developer or refer to the documentation.
         ## Example Fasta File
         ```
-        >sp|P12345|EXAMPLE_HUMAN Example protein
-        MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVQKLLLQGQGQGQGQGQGQGQGQGQGQ       
+        >protein|name=example-protein
+        AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFD      
         """) 
        
     with gr.Tab("Run folding simulation 🚀"):