pydna 6.0.0a15__py3-none-any.whl → 6.0.0a25__py3-none-any.whl

pydna/__init__.py

@@ -149,7 +149,7 @@ __license__ = "BSD"
 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "6.0.0-a.15"
+__version__ = "6.0.0-a.25"
 
 # create config directory
 _os.environ["pydna_config_dir"] = _os.getenv("pydna_config_dir", _appdirs.user_config_dir("pydna"))

pydna/crispr.py

@@ -0,0 +1,128 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
+# This code is part of the Python-dna distribution and governed by its
+# license.  Please see the LICENSE.txt file that should have been included
+# as part of this package.
+"""Provides the Dseq class for handling double stranded DNA sequences.
+
+Dseq is a subclass of :class:`Bio.Seq.Seq`. The Dseq class
+is mostly useful as a part of the :class:`pydna.dseqrecord.Dseqrecord` class
+which can hold more meta data.
+
+The Dseq class support the notion of circular and linear DNA topology.
+"""
+
+from abc import ABC, abstractmethod
+import re
+from pydna.utils import rc
+
+
+class _cas(ABC):
+    scaffold = "ND"
+    pam = "ND"
+    size = 0
+    fst5 = 0
+    fst3 = 0
+
+    def __init__(self, protospacer):
+        self.protospacer = protospacer
+        self.compsite = re.compile(
+            f"(?=(?P<watson>{protospacer}{self.pam}))|(?=(?P<crick>{rc(self.pam)}{rc(protospacer)}))", re.UNICODE
+        )
+
+    @abstractmethod
+    def search(self, dna, linear=True):
+        """To override in subclass."""
+        pass
+
+    def __repr__(self):
+        return f"{type(self).__name__}({self.protospacer[:3]}..{self.protospacer[-3:]})"
+
+    @abstractmethod
+    def __str__(self):
+        """To override in subclass."""
+        pass
+
+
+class cas9(_cas):
+    """docstring.
+
+         |----size----------|
+
+         ---protospacer------
+                          -fst3
+         fst5             |-|
+         |--------------|
+                             PAM
+    5-NNGGAAGAGTAATACACTA-AAANGGNN-3
+      ||||||||||||||||||| ||||||||
+    3-NNCCTTCTCATTATGTGAT-TTTNCCNN-5
+        ||||||||||||||||| |||
+      5-GGAAGAGTAATACACTA-AAAg-u-a-a-g-g  Scaffold
+        ---gRNA spacer---    u-a
+                             u-a
+                             u-a
+                             u-a
+                             a-u
+                             g-u-g
+                            a    a
+                             g-c-a
+                             c-g
+                             u-a
+                             a-u
+                            g   a  tetraloop
+                             a-a
+    """
+
+    scaffold = "GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGG"
+    pam = ".GG"
+    size = 20
+    fst5 = 17
+    fst3 = -3
+    ovhg = fst5 - (size + fst3)
+
+    def search(self, dna, linear=True):
+        """docstring."""
+        dna = str(dna).upper()
+        if linear:
+            dna = dna
+        else:
+            dna = dna + dna[1 : self.size]
+        results = []
+        for mobj in self.compsite.finditer(dna):
+            w, c = mobj.groups()
+            if w:
+                results.append(mobj.start("watson") + 1 + self.fst5)
+            if c:
+                results.append(mobj.start("crick") + len(self.pam) + 1 - self.fst3)
+        return results
+
+    def __str__(self):
+        """docstring."""
+        return f">{type(self).__name__} protospacer scaffold\n{self.protospacer} {self.scaffold}"
+
+
+def protospacer(guide_construct, cas=cas9):
+    """docstring."""
+    in_watson = [
+        mobj.group("ps")
+        for mobj in re.finditer(f"(?P<ps>.{{{cas.size}}})(?:{cas.scaffold})", str(guide_construct.seq).upper())
+    ]
+    in_crick = [
+        rc(mobj.group("ps"))
+        for mobj in re.finditer(f"(?:{rc(cas.scaffold)})(?P<ps>.{{{cas.size}}})", str(guide_construct.seq).upper())
+    ]
+    return in_watson + in_crick
+
+
+if __name__ == "__main__":
+    import os as _os
+
+    cached = _os.getenv("pydna_cached_funcs", "")
+    _os.environ["pydna_cached_funcs"] = ""
+    import doctest
+
+    doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
+    _os.environ["pydna_cached_funcs"] = cached

pydna/ligate.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
+# This code is part of the Python-dna distribution and governed by its
+# license.  Please see the LICENSE.txt file that should have been included
+# as part of this package.
+"""docstring."""
+from operator import add
+from functools import reduce
+import networkx as _nx
+from itertools import permutations
+import logging as _logging
+
+_module_logger = _logging.getLogger("pydna." + __name__)
+
+
+def ligate(fragments: list):
+    """docstring."""
+    G = _nx.DiGraph()
+    G.add_nodes_from(["begin", "end"])
+    fragments = fragments[:]
+
+    fragments.extend(f.rc() for f in fragments[1:])
+
+    for node in fragments:
+        G.add_edge("begin", node)
+        G.add_edge(node, "end")
+
+    for seq1, seq2 in permutations(fragments, 2):
+        try:
+            seq1 + seq2
+        except TypeError as err:
+            if str(err) != "sticky ends not compatible!":
+                raise
+        else:
+            if seq1.seq.three_prime_end() != (
+                "blunt",
+                "",
+            ) and seq2.seq.five_prime_end() != ("blunt", ""):
+                G.add_edge(seq1, seq2)
+                try:
+                    G.remove_edge("begin", seq2)
+                except _nx.NetworkXError as err:
+                    if "not in graph" not in str(err):
+                        raise
+                try:
+                    G.remove_edge(seq1, "end")
+                except _nx.NetworkXError as err:
+                    if "not in graph" not in str(err):
+                        raise
+
+    cpaths = [p for p in sorted(_nx.simple_cycles(G), key=len) if len(p) > 1]
+    csequences = [reduce(add, x).looped() for x in cpaths]
+    lpaths = [p for p in sorted(_nx.all_simple_paths(G, "begin", "end"), key=len) if len(p) > 3]
+    lsequences = [reduce(add, lp[1:-1]) for lp in lpaths]
+
+    return csequences, lsequences
+
+
+if __name__ == "__main__":
+    import os as _os
+
+    cached = _os.getenv("pydna_cached_funcs", "")
+    _os.environ["pydna_cached_funcs"] = ""
+    import doctest
+
+    doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
+    _os.environ["pydna_cached_funcs"] = cached

pydna/myprimers.py

@@ -135,8 +135,9 @@ class PrimerList(_UserList):
                 i = oldstrs.index(str(p.seq).upper())
             except ValueError:
                 i = no + len(new)
-                suffix = p.id.split(str(i))[-1]
-                suffix.lstrip("_")
+                # suffix = p.id.removeprefix(f"{str(i)}_") # use this after removing python 3.8
+                suffix = p.id[len(f"{str(i)}_") :] if p.id.startswith(f"{str(i)}_") else p.id
+                # suffix.lstrip("_")
                 newprimer = _copy.copy(p)
                 newprimer.id = f"{i}_{suffix}"
                 new.append(newprimer)
@@ -144,7 +145,7 @@ class PrimerList(_UserList):
                 found.append(self[i])
         new = new[::-1]
         newold = new + found
-        return _pretty_str("\n".join([p.format("fasta") for p in newold]))
+        return _pretty_str("\n".join([p.format("primer") for p in newold]))
 
     def pydna_code_from_list(self, lst: list):
         """Pydna code for a list of primer objects."""
@@ -155,7 +156,7 @@ class PrimerList(_UserList):
             try:
                 prstrs.index(str(p.seq).upper())
             except ValueError as e:
-                print(f"{p.format('fasta')}")
+                print(f"{p.format('primer')}")
                 err = e
             else:
                 indices.append(self.data.index(p))
@@ -167,7 +168,7 @@ class PrimerList(_UserList):
         msg += f"{self.identifier} = {curly}\n\n"
         msg += ", ".join(f"{self.identifier}[{i}]" for i in indices)
         msg += " = parse_primers('''\n\n"
-        msg += "\n".join(self[i].format("fasta") for i in indices)
+        msg += "\n".join(self[i].format("primer") for i in indices)
         msg += "\n''')"
         return _pretty_str(msg)
 

pydna/seqrecord.py

@@ -615,6 +615,21 @@ class SeqRecord(_SeqRecord):
 
     def __format__(self, format):
         """docstring."""
+
+        def removeprefix(text, prefix):
+            """Until Python 3.8 is dropped, then use str.removeprefix."""
+            if text.startswith(prefix):
+                return text[len(prefix) :]
+            return text
+
+        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"
+            )
+        if format == "primer":
+            return _pretty_str(
+                f">{self.id} {len(self)}-mer{removeprefix(self.description, self.name).strip()}\n{str(self.seq)}\n"
+            )
         return _pretty_str(super().__format__(format))
 
     def __add__(self, other):

{pydna-6.0.0a15.dist-info → pydna-6.0.0a25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pydna
-Version: 6.0.0a15
+Version: 6.0.0a25
 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
 Home-page: https://github.com/BjornFJohansson/pydna#-pydna
 License: BSD

{pydna-6.0.0a15.dist-info → pydna-6.0.0a25.dist-info}/RECORD

@@ -1,4 +1,4 @@
-pydna/__init__.py,sha256=KGzllNGPhVhbJpaU-RElkF7czeeDt5c6cOz4GzV-5Q0,13035
+pydna/__init__.py,sha256=s_mxJrApNHS7MAajAxc28BJ3oun19_7GU7GcUFxLXzw,13035
 pydna/_pretty.py,sha256=8X-YttddmNO6vd536opcbNMAIJz5wK7savZhpssQ75A,1102
 pydna/_thermodynamic_data.py,sha256=9_w-97DpkbsWbJGHVijscMvUS_SFt7GxzrxspMRPZSg,10903
 pydna/all.py,sha256=i2dR9cAccr3AdtAMMeH4jazpVjxWjfvu8LB3LD9hwgY,2099
@@ -9,6 +9,7 @@ pydna/codon.py,sha256=7UMhxpcdKl4lwqA_ucHwD0CTz0l7ScGS7LbP6uAwr40,2408
 pydna/common_sub_strings.py,sha256=sRxqEaSmDFMCnEVD5Hu5veVvbOBZUrhxKcK6zWJXRpc,11157
 pydna/conftest.py,sha256=T5-WmHWLZH3U3ifxnbxd_oOiIFibIrkYpwNacCHlvsY,999
 pydna/contig.py,sha256=aNKtXGaHY0c70tEEMHk_9lDMk9DQzjFRO6LK-GPtdwc,7991
+pydna/crispr.py,sha256=n-QWU8aylK0oFEeHxsQWvketKeEfsER12L7EvDN4JHs,3697
 pydna/design.py,sha256=bmwT1v-h0pFEtzQ01ZLVhmgwl_OTUXLaVBaI5Q0bc2c,26442
 pydna/download.py,sha256=uFoAvWYXr1C30071p9OweMdemvKO-1F2pB5CHo2k31U,1307
 pydna/dseq.py,sha256=dhPDGbsnLq_W09WMucM5faexyQlns4djOHs5iDiTEwU,44975
@@ -23,18 +24,19 @@ pydna/genbankfixer.py,sha256=D2-I30fIPMndyefNzOaeAYbu6LGHC_SnOyjxJhhMfYw,20695
 pydna/genbankrecord.py,sha256=EWRQ9EB7xzIAVqk7ico0bL_JSjR92LXt0UTSQ0HztEI,5771
 pydna/goldengate.py,sha256=Fmkbb4kkau9h1o6I-MiQZ0rNHwmD4-1IK0BJaL1MblI,1774
 pydna/ladders.py,sha256=2SaTq7_Y8XLvEBK0UqgkB9aWePzG0g84cPiNtJfggx0,3574
+pydna/ligate.py,sha256=41YYBcZxGl1PzABZoi-zkRlRcR6sYCzT4rp5HE45A9Q,2205
 pydna/myenzymes.py,sha256=gnD9jP-G2ERTpR5vkeOD1LDvlhwW-rsolz0Zoo8IfMs,1797
-pydna/myprimers.py,sha256=i8IylT_aZ6tgq7wTrVTvttUfTX-g75IOrJEo7qDTCL0,7215
+pydna/myprimers.py,sha256=JtpdejRP6MkKplLv-p5NCMzxBTepYN0CVHSxxP3ms3Q,7362
 pydna/parsers.py,sha256=TUGRo-1Av3gRaHKHS4GM3Onou-X-Ai8IRICFvO8gDeo,7998
 pydna/primer.py,sha256=7AYWIhr1YbjG0Gak94bU6bTlsRUgWCIbKTndgsgWZ2M,2533
 pydna/readers.py,sha256=wgk4wBiCWZKqMIwof2YESGDzWOer6uAMgxUeJVOIQrM,1710
 pydna/seq.py,sha256=u_DX4awip98x0wBkFycEilpLY2wO8yqpcmVeCpVpDhA,4125
-pydna/seqrecord.py,sha256=zBO3kRIBd71ww8k_kRUKWEDJu3oiDrWlPJ7LujK0X9o,22129
+pydna/seqrecord.py,sha256=shQk8oH1Aw13vo03BUR-ER32mYT0PjjlILDBXc4QXyM,22754
 pydna/sequence_picker.py,sha256=KMyyXAidvHerRAf8oiOfnGwsMYnzMztTWulpxPiER7M,1645
 pydna/threading_timer_decorator_exit.py,sha256=D91kqjKSavWDnXyc1Fo-CwPYtbmR2DjTXnBYSRXKmSA,2793
 pydna/tm.py,sha256=moILUFi6W5vOfCp0uj5Cd0ADQFqgzluMJ6d-ABEUNL4,9753
 pydna/utils.py,sha256=glw3diUAYdrcgEaSSLwq6tno9upmBc8yzTCQOrPRI5I,23443
-pydna-6.0.0a15.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
-pydna-6.0.0a15.dist-info/METADATA,sha256=XzFvRaPpDoiv0ztDWlEpAsj-N491zZih4Y3MrJGpKzk,17702
-pydna-6.0.0a15.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-pydna-6.0.0a15.dist-info/RECORD,,
+pydna-6.0.0a25.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
+pydna-6.0.0a25.dist-info/METADATA,sha256=oxcA3Uj0ddBcQkPMnCdDkKPL2JGFOvI8DwinFj-eGDM,17702
+pydna-6.0.0a25.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+pydna-6.0.0a25.dist-info/RECORD,,