opencloning 0.2.7.1__tar.gz → 0.2.7.3__tar.gz

{opencloning-0.2.7.1 → opencloning-0.2.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.7.1
+Version: 0.2.7.3
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
 Author: Manuel Lera-Ramirez

{opencloning-0.2.7.1 → opencloning-0.2.7.3}/pyproject.toml

@@ -3,7 +3,7 @@ authors = ["Manuel Lera-Ramirez <manulera14@gmail.com>"]
 description = "Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others."
 license = "MIT"
 name = "opencloning"
-version = "v0.2.7.1"
+version = "v0.2.7.3"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"

{opencloning-0.2.7.1 → opencloning-0.2.7.3}/src/opencloning/ncbi_requests.py

@@ -32,9 +32,11 @@ async def get_sequence_accessions_from_assembly_accession(assembly_accession: st
     resp = await async_get(url, headers=headers)
     data = resp.json()
     if 'reports' in data:
-        return [report['refseq_accession'] for report in data['reports']] + [
-            report['genbank_accession'] for report in data['reports']
+        refseq_accessions = [report['refseq_accession'] for report in data['reports'] if 'refseq_accession' in report]
+        genbank_accessions = [
+            report['genbank_accession'] for report in data['reports'] if 'genbank_accession' in report
         ]
+        return refseq_accessions + genbank_accessions
     elif 'total_count' in data:
         raise HTTPException(400, f'No sequence accessions linked, see {url}')
     else:

{opencloning-0.2.7.1 → opencloning-0.2.7.3}/src/opencloning/primer_design.py

@@ -32,11 +32,16 @@ def homologous_recombination_primers(
     target_tm: float,
     spacers: list[str] | None = None,
     tm_func: Callable[[str], float] = primer3_calc_tm,
+    estimate_function: Callable[[str], float] | None = None,
 ) -> tuple[str, str]:
 
     fragment2amplify = pcr_loc.extract(pcr_seq)
     amplicon = primer_design(
-        fragment2amplify, limit=minimal_hybridization_length, target_tm=target_tm, tm_func=tm_func
+        fragment2amplify,
+        limit=minimal_hybridization_length,
+        target_tm=target_tm,
+        tm_func=tm_func,
+        estimate_function=estimate_function,
     )
 
     if insert_forward:
@@ -87,10 +92,17 @@ def gibson_assembly_primers(
     circular: bool,
     spacers: list[str] | None = None,
     tm_func: Callable[[str], float] = primer3_calc_tm,
+    estimate_function: Callable[[str], float] | None = None,
 ) -> list[PrimerModel]:
 
     initial_amplicons = [
-        primer_design(template, limit=minimal_hybridization_length, target_tm=target_tm, tm_func=tm_func)
+        primer_design(
+            template,
+            limit=minimal_hybridization_length,
+            target_tm=target_tm,
+            tm_func=tm_func,
+            estimate_function=estimate_function,
+        )
         for template in templates
     ]
 
@@ -146,6 +158,7 @@ def simple_pair_primers(
     left_enzyme_inverted: bool = False,
     right_enzyme_inverted: bool = False,
     tm_func: Callable[[str], float] = primer3_calc_tm,
+    estimate_function: Callable[[str], float] | None = None,
 ) -> tuple[PrimerModel, PrimerModel]:
     """
     Design primers to amplify a DNA fragment, if left_enzyme or right_enzyme are set, the primers will be designed
@@ -158,7 +171,13 @@ def simple_pair_primers(
     if len(spacers) != 2:
         raise ValueError("The 'spacers' list must contain exactly two elements.")
 
-    amplicon = primer_design(template, limit=minimal_hybridization_length, target_tm=target_tm, tm_func=tm_func)
+    amplicon = primer_design(
+        template,
+        limit=minimal_hybridization_length,
+        target_tm=target_tm,
+        tm_func=tm_func,
+        estimate_function=estimate_function,
+    )
     fwd_primer, rvs_primer = amplicon.primers()
 
     if fwd_primer is None or rvs_primer is None: