update ziqiang et al. with extra options and product names (#237)

Author: manulera

batch_cloning/ziqiang_et_al2024.html

@@ -59,6 +59,10 @@ <h1>Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis</h
 CCGTGTACTGTAGTTACAGT
 TGTGGTTCCCCGGCCGTCTT
 ATACTCTAGTCCTCAACGCC</textarea>
+        <div style="margin: 10px auto; text-align: center;">
+            <input type="checkbox" id="bpOnly" name="bpOnly">
+            <label for="bpOnly">Generate only entry clone (stop after BP)</label>
+        </div>
         <br>
         <div id="error" class="error">
         </div>
@@ -80,7 +84,10 @@ <h1>Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis</h
             if (valid) {
                 // Submit the form data via fetch
                 try {
-                    const response = await fetch(window.location.href, {
+                    const bpOnly = document.getElementById('bpOnly').checked;
+                    const url = new URL(window.location.href);
+                    url.searchParams.set('until_bp', bpOnly);
+                    const response = await fetch(url, {
                         method: 'POST',
                         headers: {
                             'Content-Type': 'application/json',

batch_cloning/ziqiang_et_al2024.json

@@ -54,15 +54,15 @@
       "sequence_file_format": "genbank",
       "overhang_crick_3prime": 0,
       "overhang_watson_3prime": 0,
-      "file_content": "LOCUS       name                     465 bp    DNA     linear   UNK 01-JAN-1980\nDEFINITION  description.\nACCESSION   id\nVERSION     id\nKEYWORDS    .\nSOURCE      .\n  ORGANISM  .\n            .\nFEATURES             Location/Qualifiers\nORIGIN\n        1 ggggacagct ttcttgtaca aagtggaacg acttgccttc cgcacaatac atcatttctt\n       61 cttagctttt tttcttcttc ttcgttcata cagttttttt ttgtttatca gcttacattt\n      121 tcttgaaccg tagctttcgt tttcttcttt ttaactttcc attcggagtt tttgtatctt\n      181 gtttcatagt ttgtcccagg attagaatga ttaggcatcg aaccttcaag aatttgattg\n      241 aataaaacat cttcattctt aagatatgaa gataatcttc aaaaggcccc tgggaatctg\n      301 aaagaagaga agcaggccca tttatatggg aaagaacaat agtatttctt atataggccc\n      361 atttaagttg aaaacaatct tcaaaagtcc cacatcgctt agataagaaa acgaagctga\n      421 gtttatatac agctagagtc gaagtagtga ttaacatgag accat\n//"
+      "file_content": "LOCUS       U6-26_promoter           465 bp    DNA     linear   UNK 01-JAN-1980\nDEFINITION  description.\nACCESSION   14\nVERSION     14\nKEYWORDS    .\nSOURCE      \n  ORGANISM  .\n            .\nFEATURES             Location/Qualifiers\nORIGIN\n        1 ggggacagct ttcttgtaca aagtggaacg acttgccttc cgcacaatac atcatttctt\n       61 cttagctttt tttcttcttc ttcgttcata cagttttttt ttgtttatca gcttacattt\n      121 tcttgaaccg tagctttcgt tttcttcttt ttaactttcc attcggagtt tttgtatctt\n      181 gtttcatagt ttgtcccagg attagaatga ttaggcatcg aaccttcaag aatttgattg\n      241 aataaaacat cttcattctt aagatatgaa gataatcttc aaaaggcccc tgggaatctg\n      301 aaagaagaga agcaggccca tttatatggg aaagaacaat agtatttctt atataggccc\n      361 atttaagttg aaaacaatct tcaaaagtcc cacatcgctt agataagaaa acgaagctga\n      421 gtttatatac agctagagtc gaagtagtga ttaacatgag accat\n//"
     },
     {
       "id": 16,
       "type": "TextFileSequence",
       "sequence_file_format": "genbank",
       "overhang_crick_3prime": 0,
       "overhang_watson_3prime": 0,
-      "file_content": "LOCUS       name                     230 bp    DNA     linear   UNK 01-JAN-1980\nDEFINITION  description.\nACCESSION   id\nVERSION     id\nKEYWORDS    .\nSOURCE      .\n  ORGANISM  .\n            .\nFEATURES             Location/Qualifiers\nORIGIN\n        1 taggtctccg cttttttttg caaaattttc cagatcgatt tcttcttcct ctgttcttcg\n       61 gcgttcaatt tctggggttt tctcttcgtt ttctgtaact gaaacctaaa atttgaccta\n      121 aaaaaaatct caaataatat gattcagtgg ttttgtactt ttcagttagt tgagttttgc\n      181 agttccgatg agataaacca atatcaactt tattatacaa agttgtcccc\n//"
+      "file_content": "LOCUS       U6-26_term               230 bp    DNA     linear   UNK 01-JAN-1980\nDEFINITION  description.\nACCESSION   16\nVERSION     16\nKEYWORDS    .\nSOURCE      \n  ORGANISM  .\n            .\nFEATURES             Location/Qualifiers\nORIGIN\n        1 taggtctccg cttttttttg caaaattttc cagatcgatt tcttcttcct ctgttcttcg\n       61 gcgttcaatt tctggggttt tctcttcgtt ttctgtaact gaaacctaaa atttgaccta\n      121 aaaaaaatct caaataatat gattcagtgg ttttgtactt ttcagttagt tgagttttgc\n      181 agttccgatg agataaacca atatcaactt tattatacaa agttgtcccc\n//"
     },
     {
       "id": 18,
@@ -145,7 +145,7 @@
       ],
       "output": 14,
       "type": "PCRSource",
-      "output_name": null,
+      "output_name": "U6-26_promoter",
       "circular": false,
       "assembly": [
         {
@@ -192,7 +192,7 @@
       ],
       "output": 16,
       "type": "PCRSource",
-      "output_name": null,
+      "output_name": "U6-26_term",
       "circular": false,
       "assembly": [
         {

main.py

@@ -1553,7 +1553,7 @@ async def get_other_frontend_files(name: str):
 
 
 @router.post('/batch_cloning/ziqiang_et_al2024', response_model=BaseCloningStrategy)
-async def ziqiang_et_al2024_post(protospacers: list[str]):
+async def ziqiang_et_al2024_post(protospacers: list[str], until_bp: bool = Query(False)):
     try:
         validate_protospacers(protospacers)
     except ValueError as e:
@@ -1577,7 +1577,14 @@ async def ziqiang_et_al2024_post(protospacers: list[str]):
 
     template_sequence = next(s for s in template.sequences if s.id == 18)
     for i, (fwd_primer_id, rvs_primer_id) in enumerate(zip(primer_ids_for_pcrs[::2], primer_ids_for_pcrs[1::2])):
-        pcr_source = PCRSource(id=next_node_id, output_name=f"pcr_protospacer_{i + 1}")
+        if i == 0:
+            name = 'start_ps1'
+        elif i == (len(primer_ids_for_pcrs) // 2) - 1:
+            name = f'end_ps{i}'
+        else:
+            name = f'end_ps{i}_start_ps{i + 1}'
+
+        pcr_source = PCRSource(id=next_node_id, output_name=name)
         fwd_primer = next(p for p in template.primers if p.id == fwd_primer_id)
         rvs_primer = next(p for p in template.primers if p.id == rvs_primer_id)
 
@@ -1629,6 +1636,13 @@ async def ziqiang_et_al2024_post(protospacers: list[str]):
     template.sequences.append(gateway_product)
     template.sources.append(gateway_source)
 
+    if until_bp:
+        # Delete sources and sequences left
+        ids2delete = list(range(5, 11))
+        template.sources = [s for s in template.sources if s.id not in ids2delete]
+        template.sequences = [s for s in template.sequences if s.id not in ids2delete]
+        return template
+
     # Now we want to do a Gateway with everything, so we need to find all sequences that are not input of anything
     all_input_ids = sum([s.input for s in template.sources], [])
     sequences_to_clone = [s for s in template.sequences if s.id not in all_input_ids]