pydna 5.5.6__py3-none-any.whl → 5.5.7__py3-none-any.whl

pydna/__init__.py

@@ -147,7 +147,7 @@ __license__ = "BSD"
 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "5.5.6"
+__version__ = "5.5.7"
 
 
 class _PydnaWarning(Warning):

pydna/assembly2.py

@@ -867,7 +867,7 @@ def assemble(
         f_u = fragments[u - 1] if u > 0 else fragments[-u - 1].reverse_complement()
         f_v = fragments[v - 1] if v > 0 else fragments[-v - 1].reverse_complement()
         seq_u = str(loc_u.extract(f_u).seq)
-        seq_v = str(loc_v.extract(f_v).seq.rc())
+        seq_v = str(loc_v.extract(f_v).seq.reverse_complement())
         # Test if seq_u and seq_v anneal
         if not anneal_strands(seq_u, seq_v):
             raise ValueError("Mismatch in assembly")
@@ -1946,7 +1946,7 @@ class PCRAssembly(Assembly):
         results = super().assemble_linear(only_adjacent_edges, max_assemblies)
         for result in results:
             rp = self.fragments[2]
-            result.seq = result.seq[: -len(rp)] + Dseq(str(rp.seq.rc()))
+            result.seq = result.seq[: -len(rp)] + Dseq(str(rp.seq.reverse_complement()))
         return results
 
 

pydna/dseq.py

@@ -785,7 +785,7 @@ class Dseq(Seq):
         >>> ssobj
         Dseq(-7)
         GATTACA
-        <BLANKLINE>
+        |||||||
         >>> round(ssobj.mw(), 1)
         2184.4
         >>> ds_lin_obj2 = Dseq("GATZFCA")
@@ -908,7 +908,8 @@ class Dseq(Seq):
         w, c = representation_tuple(
             self._data.decode("ascii"), length_limit_for_repr=length_limit_for_repr
         )
-
+        w = w or "|" * len(c)
+        c = c or "|" * len(w)
         return pretty_str(header + "\n" + w + "\n" + c)
 
     def reverse_complement(self) -> "Dseq":
@@ -1574,7 +1575,7 @@ class Dseq(Seq):
         ctag
         >>> ds.nibble_five_prime_left(4)
         Dseq(-4)
-        <BLANKLINE>
+        ||||
         ctag
         >>> ds = Dseq.from_representation(
         ... '''
@@ -1655,7 +1656,7 @@ class Dseq(Seq):
         >>> ds.nibble_five_prime_right(4)
         Dseq(-4)
         gatc
-        <BLANKLINE>
+        ||||
         >>> ds = Dseq.from_representation(
         ... '''
         ... gatc
@@ -1724,7 +1725,7 @@ class Dseq(Seq):
         >>> ds.nibble_three_prime_left(4)
         Dseq(-4)
         gatc
-        <BLANKLINE>
+        ||||
         >>> ds = Dseq.from_representation(
         ... '''
         ...   gatc
@@ -1792,7 +1793,7 @@ class Dseq(Seq):
         ctag
         >>> ds.nibble_three_prime_right(4)
         Dseq(-4)
-        <BLANKLINE>
+        ||||
         ctag
         >>> ds = Dseq.from_representation(
         ... '''
@@ -2583,7 +2584,7 @@ class Dseq(Seq):
         >>> strands[0]
         Dseq(-2)
         ta
-        <BLANKLINE>
+        ||
         >>> ds = Dseq("tagaaptapgtatg")
         >>> ds
         Dseq(-14)
@@ -2596,7 +2597,7 @@ class Dseq(Seq):
         atctt    catac
         >>> strands[0]
         Dseq(-2)
-        <BLANKLINE>
+        ||
         at
         """
 
@@ -2630,7 +2631,7 @@ class Dseq(Seq):
         >>> strands[0]
         Dseq(-2)
         ta
-        <BLANKLINE>
+        ||
         >>> new, strands = ds.shed_ss_dna([],[(6, 8)])
         >>> new
         Dseq(-14)
@@ -2638,7 +2639,7 @@ class Dseq(Seq):
         atcttc  ccatac
         >>> strands[0]
         Dseq(-2)
-        <BLANKLINE>
+        ||
         at
         >>> ds = Dseq("tagaagtaggtatg")
         >>> new, (strand1, strand2) = ds.shed_ss_dna([(6, 8), (9, 11)],[])
@@ -2649,11 +2650,11 @@ class Dseq(Seq):
         >>> strand1
         Dseq(-2)
         ta
-        <BLANKLINE>
+        ||
         >>> strand2
         Dseq(-2)
         gt
-        <BLANKLINE>
+        ||
         """
 
         watson_cutpairs = watson_cutpairs or list()
@@ -2872,14 +2873,14 @@ class Dseq(Seq):
         >>> Dseq(parts.sticky_left5)
         Dseq(-3)
         GGG
-        <BLANKLINE>
+        |||
         >>> Dseq(parts.middle)
         Dseq(-3)
         ATC
         TAG
         >>> Dseq(parts.sticky_right5)
         Dseq(-3)
-        <BLANKLINE>
+        |||
         TCA
 
         Parameters

pydna/seqrecord.py

@@ -21,7 +21,7 @@ from pydna.seq import ProteinSeq
 from pydna.common_sub_strings import common_sub_strings
 
 from Bio.Data.CodonTable import TranslationError
-from Bio.SeqRecord import SeqRecord
+from Bio.SeqRecord import SeqRecord as BioSeqRecordSeqRecord
 from Bio.SeqFeature import SimpleLocation
 from Bio.SeqFeature import CompoundLocation
 from pydna.seq import Seq
@@ -37,7 +37,7 @@ from warnings import warn
 import datetime
 
 
-class SeqRecord(SeqRecord):
+class SeqRecord(BioSeqRecordSeqRecord):
     """
     A subclass of the Biopython SeqRecord class.
 
@@ -86,7 +86,7 @@ class SeqRecord(SeqRecord):
         self.annotations = {ps(k): ps(v) for k, v in self.annotations.items()}
 
     @classmethod
-    def from_Bio_SeqRecord(clc, sr: SeqRecord):
+    def from_Bio_SeqRecord(clc, sr: BioSeqRecordSeqRecord):
         """Creates a pydnaSeqRecord from a Biopython SeqRecord."""
         # https://stackoverflow.com/questions/15404256/changing-the-\
         # class-of-a-python-object-casting

{pydna-5.5.6.dist-info → pydna-5.5.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pydna
-Version: 5.5.6
+Version: 5.5.7
 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
 License: BSD
 License-File: LICENSE.txt
@@ -39,7 +39,7 @@ Requires-Dist: pydivsufsort (>=0.0.14)
 Requires-Dist: pyfiglet (==0.8.post1)
 Requires-Dist: pyparsing (>=2.4.7) ; extra == "download"
 Requires-Dist: pyperclip (>=1.8.2) ; extra == "clipboard"
-Requires-Dist: regex (>=2024.11.6,<2025.0.0)
+Requires-Dist: regex (>=2024.11.6,<2027.0.0)
 Requires-Dist: requests (>=2.26.0) ; extra == "download"
 Requires-Dist: scipy (>=1.11.3) ; (python_version >= "3.12") and (extra == "gel")
 Requires-Dist: scipy (>=1.9.3) ; (python_version < "3.12") and (extra == "gel")

{pydna-5.5.6.dist-info → pydna-5.5.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-pydna/__init__.py,sha256=4u9wd3RbQkivNRKpEGXHT7Lrk7W7G5V64PJLOiSXKAk,7086
+pydna/__init__.py,sha256=qs2BcxGoPn7Bd9QWHXhpGaFHeKSI8UTjWHkNI1r5PN8,7086
 pydna/_pretty.py,sha256=S3J0z_czeP1HpR-lj5fXQo9OeZc3ONsvxEGAc-Oqvjo,885
 pydna/_thermodynamic_data.py,sha256=ctOCzI0SclCBQVk7tG01bDv76fMeOROrp_WdVG5jp20,10885
 pydna/all.py,sha256=jPeYTAPh5uNXnqsK-HfMFzlVXE6sSqsonHCgmt6lf2I,1502
@@ -6,14 +6,14 @@ pydna/alphabet.py,sha256=NOWIcsVjdPSR9aAZx5wzWD8061Pq2fOE1qAKfjqDzGg,29654
 pydna/amplicon.py,sha256=zql6MVqoKu9XEDlEmqxCQa5oZMDk3pyayP536k-yS38,5135
 pydna/amplify.py,sha256=DsMDJi6bRmP1CMku-jZ1_QXQ3-gbQ_P2M9kHR30zJ-Y,18738
 pydna/assembly.py,sha256=1bAaFZDAEAlz_LB31sjAPRtAkIFK_VIXpMIQpTf_8xU,19291
-pydna/assembly2.py,sha256=WmzygtYKLONRoccaqHM5O3xjbNzaSeOHR15EH-tVOmk,108764
+pydna/assembly2.py,sha256=csvva78OGg9gHKCMdQM-vCR2DW81tkkdCHUcBwYa0mA,108796
 pydna/codon.py,sha256=AZb8DjrS5lBAzNhL32GvE_P9V5DvSBbc7w9TaSeQHlc,2553
 pydna/common_sub_strings.py,sha256=pnSx3OAjwf2uclYxv-90XYZT3bMl_d8ZTDeoGtlgtWs,11467
 pydna/contig.py,sha256=yBF4TMq1pLL0Pe3tefl2sDzNFaeSddBpytN-z-xBeSw,14971
 pydna/cre_lox.py,sha256=sOj9R8_oFPGWs68vc4jf6LqWOXjMsVSwtJaeKl6ZF2M,4476
 pydna/crispr.py,sha256=iwu0Cjskzdb2r-In9633QIxQYKGmSNVOEM_dLK6lC54,3619
 pydna/design.py,sha256=GQTyH4fKsvd6fSel0uC8DNQIulq3HMg-jYHxqsQzoLw,31743
-pydna/dseq.py,sha256=cZN1Micwlgt8L73WjaIUlblb9KuQBxLzhM91cd5ijKo,83324
+pydna/dseq.py,sha256=5qWP7bhpE71OLrfbKRfpdMoSfUZNQRxrje62GbF14LQ,83281
 pydna/dseqrecord.py,sha256=jzo8jr6i4zZ6SdJJfbabdkGh_6U8PI0Ywa9LCdn91XE,49598
 pydna/fakeseq.py,sha256=uxyu1PXF-sVasEqhmyhMcsbpTy84uUtubDiZuxHNb9c,1174
 pydna/fusionpcr.py,sha256=tfIfGGkNoZjg_dodcEx9wTc12aLRnC7J3g-Vg3Jg1uA,2821
@@ -29,14 +29,14 @@ pydna/primer.py,sha256=s3CoPheB4PUuQJU_11VGEBZW62DesEiWmTC2HHzD7so,2248
 pydna/primer_screen.py,sha256=0CodBc9JThE-qkk5Z2DacSYIvSqhsFCGARzh-Bu236U,26418
 pydna/readers.py,sha256=9ZopQFW0CyYCmW4jy-6_w0_0BRUMLV2VAVDmHH4Ns5w,1731
 pydna/seq.py,sha256=H-MPWo2qQG6s5N0LKSziTKmb79ORCCNHofE2Gs0R5U8,10979
-pydna/seqrecord.py,sha256=aQtkx8Wjy_FbnD2_uVY--ULuWwLtxiVeQ0wlsZs2OXA,22816
+pydna/seqrecord.py,sha256=CXmUncUdZAgGD109m169cRyttoCdFk3sL4FptL-Sb5E,22865
 pydna/sequence_picker.py,sha256=wuRfQhuMgxrK6rrNykBFbRqErk-qXBPRvmEEIM0ji4o,1305
 pydna/sequence_regex.py,sha256=bp0JhUILRlXQ-zOjK6oz-cxjca46LBjA5wCuzga-Hmw,1238
 pydna/threading_timer_decorator_exit.py,sha256=D91kqjKSavWDnXyc1Fo-CwPYtbmR2DjTXnBYSRXKmSA,2793
 pydna/tm.py,sha256=kM31byeBog17xi-NnVL6yXPLyZrzpXRY9J6XfEAJa9I,11083
 pydna/types.py,sha256=W1qY6TSRv1nIj9dxEwTlc4XB3778arSeMg713fPnT9U,1337
 pydna/utils.py,sha256=vYJJnJlaSTVxmbusv-WDNid54nBUqs8pTFDcJG_I7tA,24989
-pydna-5.5.6.dist-info/METADATA,sha256=jUQ1ZJ5NYSJe71DHPnRWDYF1_pUeWqoMeOcLvYjitFE,24626
-pydna-5.5.6.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-pydna-5.5.6.dist-info/licenses/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
-pydna-5.5.6.dist-info/RECORD,,
+pydna-5.5.7.dist-info/METADATA,sha256=aPQuE7KoCUGX1roIMZ_Lxn8ZvWxPMGjujlpRhjuUAZw,24626
+pydna-5.5.7.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+pydna-5.5.7.dist-info/licenses/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
+pydna-5.5.7.dist-info/RECORD,,

{pydna-5.5.6.dist-info → pydna-5.5.7.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.3.0
+Generator: poetry-core 2.3.1
 Root-Is-Purelib: true
 Tag: py3-none-any