OpenCloning · manulera · Jun 12, 2026 · Jun 11, 2026 · Jun 11, 2026 · Jun 11, 2026
diff --git a/packages/opencloning/src/opencloning/batch_cloning/index.html b/packages/opencloning/src/opencloning/batch_cloning/index.html
@@ -41,8 +41,8 @@
 <body>
     <h1>Batch Cloning Methods</h1>
     <div class="method">
-        <a href="/batch_cloning/pombe">S. pombe Gene Cloning</a>
-        <p>Batch cloning of S. pombe genes using homologous recombination.</p>
+        <a href="/batch_cloning/yeast_primer_design">Yeast PCR-based Cloning primer design</a>
+        <p>Design PCR-based cloning strategies for yeast in batch (Bähler et al. 1998).</p>
     </div>
     <div class="method">
         <a href="/batch_cloning/ziqiang_et_al2024">CRISPR Guide RNA Cloning</a>

diff --git a/packages/opencloning/src/opencloning/batch_cloning/pombe/__init__.py b/packages/opencloning/src/opencloning/batch_cloning/pombe/__init__.py
@@ -1,79 +1,163 @@
 from fastapi import Form, File, UploadFile, HTTPException
 from typing import Annotated, Literal
-from tempfile import TemporaryDirectory
 import os
-from fastapi.responses import FileResponse
-from .pombe_get_primers import main as pombe_primers
+import tempfile
+from fastapi.responses import FileResponse, HTMLResponse
 from .pombe_clone import main as pombe_clone
 from .pombe_summary import main as pombe_summary
 from .pombe_gather import main as pombe_gather
+from .pombe_primer_table import build_primer_summary_df, primer_summary_to_html
 import shutil
-import traceback
 from ...get_router import get_router
 from fastapi import Request
+from opencloning.dna_functions import get_sequence_from_euroscarf_url, request_from_addgene, request_from_snapgene
+from pydna.primer import Primer
+from pydna.opencloning_models import UploadedFileSource
+from pydna.parsers import parse as pydna_parse
+from pydna.parsers import parse_snapgene
 
 router = get_router()
 
 
-@router.get('/batch_cloning/pombe')
+@router.get('/batch_cloning/yeast_primer_design')
 async def get_batch_cloning_page(request: Request):
     return FileResponse(os.path.join(os.path.dirname(__file__), 'index.html'))
 
 
-@router.post('/batch_cloning/pombe')
+DEFAULT_PLASMID_OPTIONS = {
+    'gene_deletion': {
+        'kanmx6': ('addgene', '39296', None),
+        'natmx6': ('snapgene', 'yeast_plasmids', 'pFA6a-natMX6'),
+        'hphmx6': ('snapgene', 'yeast_plasmids', 'pFA6a-hphMX6'),
+    },
+    'gene_cterm_tagging': {
+        'kanmx6': ('addgene', '87023', None),
+        'natmx6': ('addgene', '52693', None),
+        'hphmx6': ('addgene', '105156', None),
+    },
+    'promoter_not_tag': {
+        'kanmx6': ('addgene', '39280', None),  # pFA6a-kanMX6-P3nmt1
+        'natmx6': ('euroscarf', 'P30425', None),  # pFA6a-natMX6-P3nmt1
+        'hphmx6': ('addgene', '105162', None),  # pFA6a-hphMX6-3nmt1
+    },
+}
+
+
+def raise_plasmid_import_error(exception: Exception, mode) -> None:
+    raise HTTPException(status_code=503, detail=f'Failed to import plasmid from {mode}: {exception}') from exception
+
+
+@router.post('/batch_cloning/yeast_primer_design')
 async def post_batch_cloning(
+    cloning_type: Annotated[
+        Literal['gene_deletion', 'gene_cterm_tagging', 'promoter_not_tag', 'promoter_with_tag'], Form(...)
+    ],
+    desired_output: Annotated[Literal['simulate_cloning', 'primers_only'], Form(...)],
+    assembly_accession: str = Form(..., pattern=r'^GC[AF]_[0-9.]+$', min_length=1),
     gene_list: str = Form(...),
+    integration_binding_forward: str = Form(..., pattern=r'^[ACGTacgt]+$', min_length=1),
+    integration_binding_reverse: str = Form(..., pattern=r'^[ACGTacgt]+$', min_length=1),
     plasmid_file: UploadFile | None = File(None),
     addgene_id: str | None = Form(None),
-    plasmid_option: Annotated[Literal['addgene', 'file'], Form(...)] = None,
-    checking_primer_forward: str = Form(..., pattern=r'^[ACGTacgt]+$', min_length=1),
-    checking_primer_reverse: str = Form(..., pattern=r'^[ACGTacgt]+$', min_length=1),
+    plasmid_option: Annotated[Literal['addgene', 'file', 'default'], Form(...)] = None,
+    checking_primer_forward: str = Form('', pattern=r'^[ACGTacgt]*$'),
+    checking_primer_reverse: str = Form('', pattern=r'^[ACGTacgt]*$'),
+    resistance_marker: Annotated[Literal['kanmx6', 'natmx6', 'hphmx6', 'other'], Form(...)] = None,
 ):
-
-    plasmid = plasmid_file if plasmid_option == 'file' else addgene_id
-    if plasmid is None:
-        raise HTTPException(status_code=400, detail='No plasmid provided')
-
     genes = [gene.strip() for gene in gene_list.split() if gene.strip()]
 
     if not genes:
         raise HTTPException(status_code=400, detail='No valid genes provided')
 
-    with TemporaryDirectory() as temp_dir:
-        if plasmid_option == 'file':
-            # Write the plasmid to the temp dir
-            with open(os.path.join(temp_dir, plasmid_file.filename), 'wb') as f:
-                shutil.copyfileobj(plasmid_file.file, f)
-
-        # Write the checking primers
-        with open(os.path.join(temp_dir, 'checking_primers.fa'), 'w') as f:
-            f.write(f'>common_insert_fwd\n{checking_primer_forward}\n>common_insert_rvs\n{checking_primer_reverse}')
-
-        for gene in genes:
-            try:
-                await pombe_primers(gene, temp_dir)
-            except Exception:
-                raise HTTPException(status_code=404, detail=f'Primers for {gene} not found')
-            try:
-                if plasmid_option == 'file':
-                    with open(os.path.join(temp_dir, plasmid_file.filename), 'rb') as f:
-                        await pombe_clone(
-                            gene, 'GCF_000002945.2', temp_dir, UploadFile(file=f, filename=plasmid_file.filename)
-                        )
-                else:
-                    await pombe_clone(gene, 'GCF_000002945.2', temp_dir, addgene_id)
-            except Exception:
-                # Show the stack trace in console
-                print(f'Error occurred while cloning {gene}:')
-                traceback.print_exc()
-                raise HTTPException(status_code=400, detail=f'Clone for {gene} failed')
+    if desired_output == 'primers_only':
+        gene_primers = []
+        try:
+            for gene in genes:
+                primers = await pombe_clone(
+                    gene,
+                    assembly_accession,
+                    integration_binding_forward,
+                    integration_binding_reverse,
+                    cloning_type,
+                    primers_only=True,
+                )
+                gene_primers.append((gene, cloning_type, primers))
+        except ValueError as e:
+            raise HTTPException(status_code=400, detail=str(e))
+
+        primer_df = build_primer_summary_df(gene_primers)
+        return HTMLResponse(content=primer_summary_to_html(primer_df))
+
+    common_primer_forward = (
+        Primer(checking_primer_forward, name='common_insert_fwd') if checking_primer_forward else None
+    )
+    common_primer_reverse = (
+        Primer(checking_primer_reverse, name='common_insert_rvs') if checking_primer_reverse else None
+    )
+
+    if plasmid_option == 'default':
+        try:
+            mode, first, second = DEFAULT_PLASMID_OPTIONS[cloning_type][resistance_marker]
+            if mode == 'addgene':
+                plasmid = await request_from_addgene(first)
+            elif mode == 'euroscarf':
+                plasmid = await get_sequence_from_euroscarf_url(first)
+            else:
+                plasmid = await request_from_snapgene(first, second)
+        except KeyError:
+            raise HTTPException(
+                status_code=400, detail=f'Resistance marker {resistance_marker} is not supported for default plasmid'
+            )
+        except Exception as e:
+            raise_plasmid_import_error(e, mode)
+
+    elif plasmid_option == 'file':
+        try:
+            assert plasmid_file is not None
+            assert plasmid_file.filename is not None
+            file_content = await plasmid_file.read()
+            if plasmid_file.filename.endswith('.dna'):
+                plasmid = parse_snapgene(file_content)[0]
+            else:
+                plasmid = pydna_parse(file_content.decode('utf-8'))[0]
+                plasmid.source = UploadedFileSource(
+                    file_name=plasmid_file.filename,
+                    sequence_file_format=plasmid.annotations['pydna_parse_sequence_file_format'],
+                    index_in_file=0,
+                )
+        except Exception as e:
+            raise HTTPException(status_code=400, detail=f'Plasmid loading failed: {e}')
+
+    if plasmid_option == 'addgene':
+        assert addgene_id is not None
+        try:
+            plasmid = await request_from_addgene(addgene_id)
+        except Exception as e:
+            raise_plasmid_import_error(e, 'addgene')
+
+    with tempfile.TemporaryDirectory() as temp_dir:
+        try:
+            for gene in genes:
+                await pombe_clone(
+                    gene,
+                    assembly_accession,
+                    integration_binding_forward,
+                    integration_binding_reverse,
+                    cloning_type,
+                    output_dir=temp_dir,
+                    plasmid=plasmid,
+                    common_primer_forward=common_primer_forward,
+                    common_primer_reverse=common_primer_reverse,
+                )
+        except ValueError as e:
+            raise HTTPException(status_code=400, detail=f'Cloning failed: {e}')
+
         try:
             pombe_summary(temp_dir)
             pombe_gather(temp_dir)
         except Exception as e:
             raise HTTPException(status_code=400, detail=f'Summary failed: {e}')
 
-        # zip the temp dir and return it
         zip_filename = f'{temp_dir}_archive'
         shutil.make_archive(zip_filename, 'zip', temp_dir)
         zip_file = f'{zip_filename}.zip'