first

app.py

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+import gradio as gr
+from utils import run_clinker
+
+
+with gr.Blocks(title="Clinker Gene Cluster Comparison") as demo:
+    gr.Markdown("## Clinker Gene Cluster Comparison\nEnter one NCBI nucleotide accession per line.")
+    accessions_input = gr.Textbox(
+        lines=6,
+        placeholder="e.g.\nMH816969\nMH816970",
+        label="Accessions",
+    )
+    run_btn = gr.Button("Run", variant="primary")
+    status = gr.Textbox(label="Status", interactive=False)
+    html_output = gr.HTML(label="Clinker Output")
+
+    run_btn.click(
+        fn=run_clinker,
+        inputs=accessions_input,
+        outputs=[html_output, status],
+    )
+
+demo.launch()

requirements.txt

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+gradio
+biopython
+clinker-bio

utils.py

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+import os
+import shutil
+import tempfile
+import subprocess
+from Bio import Entrez, SeqIO
+
+Entrez.email = "user@example.com"
+
+
+def fetch_genbank(accession, out_dir):
+    handle = Entrez.efetch(db="nuccore", id=accession, rettype="gbwithparts", retmode="text")
+    record = SeqIO.read(handle, "genbank")
+    handle.close()
+    path = os.path.join(out_dir, f"{accession}.gbk")
+    SeqIO.write(record, path, "genbank")
+    return path
+
+
+def run_clinker(accessions_text):
+    accessions = [a.strip() for a in accessions_text.strip().splitlines() if a.strip()]
+    if not accessions:
+        return None, "Please enter at least one accession."
+
+    work_dir = tempfile.mkdtemp()
+    gbk_files = []
+    errors = []
+
+    for acc in accessions:
+        try:
+            gbk_files.append(fetch_genbank(acc, work_dir))
+        except Exception as e:
+            errors.append(f"{acc}: {e}")
+
+    if not gbk_files:
+        shutil.rmtree(work_dir)
+        return None, "Failed to download any records:\n" + "\n".join(errors)
+
+    html_out = os.path.join(work_dir, "output.html")
+    result = subprocess.run(["clinker"] + gbk_files + ["-p", html_out], capture_output=True, text=True)
+
+    if not os.path.exists(html_out):
+        shutil.rmtree(work_dir)
+        return None, f"clinker failed:\n{result.stderr}"
+
+    with open(html_out) as f:
+        html_content = f.read()
+
+    shutil.rmtree(work_dir)
+    msg = "Done." if not errors else "Done.\nSkipped:\n" + "\n".join(errors)
+    return html_content, msg