pydna 5.4.0__py3-none-any.whl → 5.5.0__py3-none-any.whl

pydna/__init__.py

@@ -150,7 +150,7 @@ __license__ = "BSD"
 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "5.4.0"
+__version__ = "5.5.0"
 
 
 # create config directory

pydna/dseq.py

@@ -1479,11 +1479,6 @@ class Dseq(_Seq):
         enz = cutsite[1]
         watson, crick, ovhg = self.get_cut_parameters(cutsite, True)
 
-        # The cut positions fall within the sequence
-        # This could go into Biopython
-        if not self.circular and crick < 0 or crick > len(self):
-            return False
-
         # The overhang is double stranded
         overhang_dseq = self[watson:crick] if ovhg < 0 else self[crick:watson]
         if overhang_dseq.ovhg != 0 or overhang_dseq.watson_ovhg() != 0:

pydna/dseqrecord.py

@@ -788,9 +788,10 @@ class Dseqrecord(_SeqRecord):
         if self.circular:
             raise TypeError("TypeError: can't multiply circular Dseqrecord.")
         if number > 0:
-            new = _copy.copy(self)
+            new = _copy.deepcopy(self)
             for i in range(1, number):
                 new += self
+            new._per_letter_annotations = self._per_letter_annotations
             return new
         else:
             return self.__class__("")
@@ -1061,7 +1062,10 @@ class Dseqrecord(_SeqRecord):
         pydna.dseqrecord.Dseqrecord.lower"""
 
         upper = _copy.deepcopy(self)
+        # This is because the @seq.setter methods otherwise sets the _per_letter_annotations to an empty dict
+        prev_per_letter_annotation = upper._per_letter_annotations
         upper.seq = upper.seq.upper()
+        upper._per_letter_annotations = prev_per_letter_annotation
         return upper
 
     def lower(self):
@@ -1092,7 +1096,9 @@ class Dseqrecord(_SeqRecord):
 
         """
         lower = _copy.deepcopy(self)
+        prev_per_letter_annotation = lower._per_letter_annotations
         lower.seq = lower.seq.lower()
+        lower._per_letter_annotations = prev_per_letter_annotation
         return lower
 
     def orfs(self, minsize=300):

pydna/seqrecord.py

@@ -50,10 +50,29 @@ class SeqRecord(_SeqRecord):
     nicer output in the IPython shell.
     """
 
-    def __init__(self, seq, *args, id="id", name="name", description="description", **kwargs):
+    def __init__(
+        self,
+        seq,
+        id="id",
+        name="name",
+        description="description",
+        dbxrefs=None,
+        features=None,
+        annotations=None,
+        letter_annotations=None,
+    ):
         if isinstance(seq, str):
             seq = _Seq(seq)
-        super().__init__(seq, *args, id=id, name=name, description=description, **kwargs)
+        super().__init__(
+            seq,
+            id=id,
+            name=name,
+            description=description,
+            dbxrefs=dbxrefs,
+            features=features,
+            annotations=annotations,
+            letter_annotations=letter_annotations,
+        )
         self._fix_attributes()
 
     def _fix_attributes(self):
@@ -612,7 +631,7 @@ class SeqRecord(_SeqRecord):
 
         if format == "pydnafasta":
             return _pretty_str(
-                f">{self.id} {len(self)} bp {dict(((True,'circular'),(False,'linear')))[self.seq.circular]}\n{str(self.seq)}\n"
+                f">{self.id} {len(self)} bp {dict(((True, 'circular'), (False, 'linear')))[self.seq.circular]}\n{str(self.seq)}\n"
             )
         if format == "primer":
             return _pretty_str(

{pydna-5.4.0.dist-info → pydna-5.5.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.3
 Name: pydna
-Version: 5.4.0
+Version: 5.5.0
 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
 License: BSD
 Author: Björn F. Johansson
 Author-email: bjornjobb@gmail.com
-Requires-Python: >=3.8,<4.0
+Requires-Python: >=3.9,<4.0
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Education
@@ -13,7 +13,6 @@ Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -25,12 +24,11 @@ Provides-Extra: download
 Provides-Extra: express
 Provides-Extra: gel
 Requires-Dist: appdirs (>=1.4.4)
-Requires-Dist: biopython (>=1.80,<1.85)
+Requires-Dist: biopython (>=1.80)
 Requires-Dist: cai2 (>=1.0.5) ; extra == "express"
 Requires-Dist: matplotlib (>=3.4.3) ; extra == "gel"
 Requires-Dist: networkx (>=2.8.8)
-Requires-Dist: numpy (<1.24) ; python_version < "3.9"
-Requires-Dist: numpy (>1.26) ; python_version >= "3.9"
+Requires-Dist: numpy (>1.26)
 Requires-Dist: pillow (>=8.4.0) ; extra == "gel"
 Requires-Dist: prettytable (>=3.5.0)
 Requires-Dist: pydivsufsort (>=0.0.14)

{pydna-5.4.0.dist-info → pydna-5.5.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-pydna/__init__.py,sha256=uFnVyBghAdjtBuBA6ROIj0u0WH1jDY9AapdRLGDu2Yk,13391
+pydna/__init__.py,sha256=QmteIqgNg8sAeRrXfFOOewLYxuQy21oceQ2DeAggPig,13391
 pydna/_pretty.py,sha256=eMjYTy19AUTA-nntiYEql3FPVe4WzTLSZ4f0Jd6SLfo,1172
 pydna/_thermodynamic_data.py,sha256=9_w-97DpkbsWbJGHVijscMvUS_SFt7GxzrxspMRPZSg,10903
 pydna/all.py,sha256=i2dR9cAccr3AdtAMMeH4jazpVjxWjfvu8LB3LD9hwgY,2099
@@ -12,8 +12,8 @@ pydna/contig.py,sha256=aNKtXGaHY0c70tEEMHk_9lDMk9DQzjFRO6LK-GPtdwc,7991
 pydna/crispr.py,sha256=VbOe_nDVmdhlnYvnnmukJJhRMZr1gk1UK6qOJCCs988,3824
 pydna/design.py,sha256=IE04UXQqAkpX1leTZN8KPJjdd9gj1Es_4HNcTZML5Dw,28781
 pydna/download.py,sha256=uFoAvWYXr1C30071p9OweMdemvKO-1F2pB5CHo2k31U,1307
-pydna/dseq.py,sha256=OL1qwTuoutPHX1lSyJyoN_viJuWassVPPXv-Jk45tw4,53784
-pydna/dseqrecord.py,sha256=6w2MJF4b-6JJrmu4YV7-8lLPqWJAXcDWtJWzMlHG2A0,46785
+pydna/dseq.py,sha256=-iOK3uHplIgYfwbImHzJA2aZ8uXsBwXZbWwkO01-IMM,53601
+pydna/dseqrecord.py,sha256=qVWbAWT672TNYAx_R_TDqbTnlxbL2mN-c-I14PyetR0,47238
 pydna/editor.py,sha256=Au3kZ5DYqa6MYB3kXJePHOJOioSJ5w7jtlZ8kfHvKm8,3471
 pydna/fakeseq.py,sha256=eGeivoppQ8vSPQqggxFXARmUhU6oEBfdnIkGDR_v9UQ,1449
 pydna/fusionpcr.py,sha256=uRuHbwmZ2H5SThDUYW-KwxMB1DwqA2Khof7KXiMdxN8,2783
@@ -32,13 +32,13 @@ pydna/parsers.py,sha256=UlG5xh4EsNNPaPK4SoEE6KL52YxkQfLvKJiDm3DB5s4,6927
 pydna/primer.py,sha256=7AYWIhr1YbjG0Gak94bU6bTlsRUgWCIbKTndgsgWZ2M,2533
 pydna/readers.py,sha256=dsihpjRopxWeeab1bRAK4TRHMBLYK_SpK1j2llHrHk0,1850
 pydna/seq.py,sha256=Qwbx1uo-JIYXIuySXevNtxoDgohENHTTTCjPMnn4yjo,7703
-pydna/seqrecord.py,sha256=FLgdvr0zVDhSffxBguBs033SaSKmbNdRTGvA8bAj8ik,23203
+pydna/seqrecord.py,sha256=oz2YZR3_tkNj7YgdWmJr0MyREJZvCgvmq1g8hzuzNyQ,23530
 pydna/sequence_picker.py,sha256=jYbGUparKyIhDD30BzT2x-olnPpDjv-xvyaeIk6_V4E,1659
 pydna/threading_timer_decorator_exit.py,sha256=D91kqjKSavWDnXyc1Fo-CwPYtbmR2DjTXnBYSRXKmSA,2793
 pydna/tm.py,sha256=YVXgDMB_AxNyzPR9fYT1YWlfy80paKTl2r0bkLFNxU8,11330
 pydna/user_cloning.py,sha256=VSpYX1tdbcD_PzEt69Jz6Lud-yAkYMVXnzVd4v2usnE,692
 pydna/utils.py,sha256=7CQ8tkVcTcNY_k1eBbP242ax3X2MMZGZ1cPhHcDY8y4,22084
-pydna-5.4.0.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
-pydna-5.4.0.dist-info/METADATA,sha256=Qmeyd1KYYFxQvuE_ewAfwZwHswgo1azcjnx8DI8Mx74,24458
-pydna-5.4.0.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-pydna-5.4.0.dist-info/RECORD,,
+pydna-5.5.0.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
+pydna-5.5.0.dist-info/METADATA,sha256=c-uZramQdFTL6ceghaoWSt7aZNuJFoD8FeUhgAxmy9Y,24322
+pydna-5.5.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pydna-5.5.0.dist-info/RECORD,,

{pydna-5.4.0.dist-info → pydna-5.5.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.1
+Generator: poetry-core 2.1.1
 Root-Is-Purelib: true
 Tag: py3-none-any