pydna 5.5.4__py3-none-any.whl → 5.5.6__py3-none-any.whl

pydna/conftest.py

@@ -1,42 +0,0 @@
-# -*- coding: utf-8 -*-
-"""conftest.py"""
-
-# import pathlib
-# import os
-
-# cwd = pathlib.Path(__file__).parent
-
-# def pytest_runtest_setup(item):
-#     # called for running each test in 'a' directory
-#     #os.chdir(cwd)
-#     pass
-
-
-# def pytest_configure(config):
-#    """
-#    Allows plugins and conftest files to perform initial configuration.
-#    This hook is called for every plugin and initial conftest
-#    file after command line options have been parsed.
-#    """
-#    os.chdir(cwd)
-#    print(f"cwd set to {cwd} in {__file__}")
-
-
-# def pytest_sessionstart(session):
-#     """
-#     Called after the Session object has been created and
-#     before performing collection and entering the run test loop.
-#     """
-
-
-# def pytest_sessionfinish(session, exitstatus):
-#     """
-#     Called after whole test run finished, right before
-#     returning the exit status to the system.
-#     """
-
-
-# def pytest_unconfigure(config):
-#     """
-#     called before test process is exited.
-#     """

pydna/download.py

@@ -1,32 +0,0 @@
-#!/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 a function for downloading online text files."""
-
-import textwrap as _textwrap
-
-# import os as _os
-from pydna._pretty import pretty_str as _pretty_str
-
-# from pydna.utils import memorize as _memorize
-# import logging as _logging
-
-# _module_logger = _logging.getLogger("pydna." + __name__)
-
-
-# @_memorize("pydna.download.download_text")
-def download_text(url):
-    """docstring."""
-    import requests
-
-    #    _module_logger.info("#### DOWNLOAD TEXT ####")
-    #    _module_logger.info("url = %s", url)
-    req = requests.get(url)
-    #    _module_logger.info("url = %s", str(req))
-    result = _textwrap.dedent(req.text).strip()
-    result = result.replace("\r\n", "\n").replace("\r", "\n")
-    #    _module_logger.info("result[:160] = %s", result[:160])
-    return _pretty_str(result)

pydna/genbankfile.py

@@ -1,42 +0,0 @@
-#!/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.
-from pydna.dseqrecord import Dseqrecord as _Dseqrecord
-
-
-class GenbankFile(_Dseqrecord):
-    def __init__(self, record, *args, path=None, **kwargs):
-        super().__init__(record, *args, **kwargs)
-        self.path = path
-
-    @classmethod
-    def from_SeqRecord(cls, record, *args, path=None, **kwargs):
-        obj = super().from_SeqRecord(record, *args, **kwargs)
-        obj.path = path
-        return obj
-
-    def __repr__(self):
-        """returns a short string representation of the object"""
-        return "File({})({}{})".format(
-            self.id, {True: "-", False: "o"}[not self.circular], len(self)
-        )
-
-    def _repr_pretty_(self, p, cycle):
-        """returns a short string representation of the object"""
-        p.text(
-            "File({})({}{})".format(
-                self.id, {True: "-", False: "o"}[not self.circular], len(self)
-            )
-        )
-
-    def _repr_html_(self):
-        return "<a href='{path}' target='_blank'>{path}</a><br>".format(path=self.path)
-
-    def reverse_complement(self):
-        answer = type(self)(super().reverse_complement(), path=self.path)
-        return answer
-
-    rc = reverse_complement

pydna/genbankrecord.py

@@ -1,168 +0,0 @@
-#!/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.
-
-from pydna.dseqrecord import Dseqrecord as _Dseqrecord
-from pydna._pretty import pretty_str as _ps
-import os as _os
-
-
-class GenbankRecord(_Dseqrecord):
-    def __init__(
-        self, record, *args, item="accession", start=None, stop=None, strand=1, **kwargs
-    ):
-        super().__init__(record, *args, **kwargs)
-        self.item = item
-        self.start = start
-        self.stop = stop
-        self.strand = strand
-        self._repr = item
-        if self.start is not None and self.stop is not None:
-            self._repr += " {}-{}".format(self.start, self.stop)
-        self._linktemplate = "<a href='https://www.ncbi.nlm.nih.gov/nuccore/{item}?from={start}&to={stop}&strand={strand}' target='_blank'>{text}</a>"
-        self.hyperlink = _ps(
-            self._linktemplate.format(
-                item=self.item,
-                start=self.start or "",
-                stop=self.stop or "",
-                strand=self.strand,
-                text=self._repr,
-            )
-        )
-
-    @classmethod
-    def from_string(
-        cls,
-        record: str = "",
-        *args,
-        item="accession",
-        start=None,
-        stop=None,
-        strand=1,
-        **kwargs,
-    ):
-        """docstring."""
-        obj = super().from_string(record, *args, **kwargs)
-        obj.item = item
-        obj.start = start
-        obj.stop = stop
-        obj.strand = strand
-        obj._repr = item
-        if obj.start is not None and obj.stop is not None:
-            obj._repr += " {}-{}".format(obj.start, obj.stop)
-        obj._linktemplate = "<a href='https://www.ncbi.nlm.nih.gov/nuccore/{item}?from={start}&to={stop}&strand={strand}' target='_blank'>{text}</a>"
-        obj.hyperlink = _ps(
-            obj._linktemplate.format(
-                item=obj.item,
-                start=obj.start or "",
-                stop=obj.stop or "",
-                strand=obj.strand,
-                text=obj._repr,
-            )
-        )
-        return obj
-
-    @classmethod
-    def from_SeqRecord(
-        cls, record, *args, item="accession", start=None, stop=None, strand=1, **kwargs
-    ):
-        obj = super().from_SeqRecord(record, *args, **kwargs)
-        obj.item = item
-        obj.start = start
-        obj.stop = stop
-        obj.strand = strand
-        obj._repr = item
-        if obj.start is not None and obj.stop is not None:
-            obj._repr += " {}-{}".format(obj.start, obj.stop)
-        obj._linktemplate = "<a href='https://www.ncbi.nlm.nih.gov/nuccore/{item}?from={start}&to={stop}&strand={strand}' target='_blank'>{text}</a>"
-        obj.hyperlink = _ps(
-            obj._linktemplate.format(
-                item=obj.item,
-                start=obj.start or "",
-                stop=obj.stop or "",
-                strand=obj.strand,
-                text=obj._repr,
-            )
-        )
-        return obj
-
-    def __getitem__(self, sl):
-        answer = super().__getitem__(sl)
-        answer.item = self.item
-        answer.start = (self.start or 0) + (sl.start or 0)
-        answer.stop = (self.start or 0) + (sl.stop or 0)
-        answer.strand = self.strand
-        return answer
-
-    def __repr__(self):
-        """returns a short string representation of the object"""
-        return "Gbnk({}{} {})".format(
-            {True: "-", False: "o"}[not self.circular], len(self), self._repr
-        )
-
-    def _repr_pretty_(self, p, cycle):
-        """returns a short string representation of the object"""
-        p.text(self.__repr__())
-
-    def _repr_html_(self):
-        return self.hyperlink
-
-    def reverse_complement(self):
-        answer = type(self)(
-            super().reverse_complement(),
-            item=self.item,
-            start=self.start,
-            stop=self.stop,
-            strand={1: 2, 2: 1}[self.strand],
-        )
-        return answer
-
-    rc = reverse_complement
-
-    def pydna_code(self):
-        """docstring."""  # FIXME
-
-        code = (
-            "from pydna.genbank import Genbank\n"
-            f"gb = Genbank('{_os.getenv('pydna_email')}')\n"
-            f"seq = gb.nucleotide('{self.item}'"
-        )
-        if self.start and self.start:
-            code += (
-                ",\n"
-                f"                    seq_start={self.start},\n"
-                f"                    seq_stop={self.stop},\n"
-                f"                    strand={self.strand})"
-            )
-        else:
-            code += ")"
-
-        return _ps(code)
-
-    def biopython_code(self):
-        """docstring."""  # FIXME
-
-        code = (
-            "from Bio import Entrez, SeqIO\n"
-            f"Entrez.email = '{_os.getenv('pydna_email')}'\n"
-            "handle = Entrez.efetch(db='nuccore',\n"
-            f"                       id='{self.item}',\n"
-            "                       rettype='gbwithparts',\n"
-            "                       retmode='text',"
-        )
-        if self.start and self.stop:
-            code += (
-                "\n"
-                f"                       seq_start={self.start},\n"
-                f"                       seq_stop={self.stop},\n"
-                f"                       strand={self.strand})\n"
-            )
-        else:
-            code += ")\n"
-
-        code += "record = SeqIO.read(handle, 'genbank')"
-
-        return _ps(code)

pydna/goldengate.py

@@ -1,45 +0,0 @@
-#!/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.
-
-#                                          ^^
-#     ^^      ..                                       ..
-#             []                                       []
-#           .:[]:_          ^^                       ,:[]:.
-#         .: :[]: :-.                             ,-: :[]: :.
-#       .: : :[]: : :`._                       ,.': : :[]: : :.
-#     .: : : :[]: : : : :-._               _,-: : : : :[]: : : :.
-# _..: : : : :[]: : : : : : :-._________.-: : : : : : :[]: : : : :-._
-# _:_:_:_:_:_:[]:_:_:_:_:_:_:_:_:_:_:_:_:_:_:_:_:_:_:_:[]:_:_:_:_:_:_
-# !!!!!!!!!!!![]!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!![]!!!!!!!!!!!!!
-# ^^^^^^^^^^^^[]^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^[]^^^^^^^^^^^^^
-#             []                                       []
-#             []                                       []
-#             []                                       []
-#  ~~^-~^_~^~/  \~^-~^~_~^-~_^~-^~_^~~-^~_~^~-~_~-^~_^/  \~^-~_~^-~~-
-# ~ _~~- ~^-^~-^~~- ^~_^-^~~_ -~^_ -~_-~~^- _~~_~-^_ ~^-^~~-_^-~ ~^
-
-"""Assembly of sequences by GoldenGate ligation assembly."""
-from Bio.Restriction import BsaI, BsmBI, BbsI, FokI
-from pydna.dseqrecord import Dseqrecord as _Dseqrecord
-
-# from copy import deepcopy as _deepcopy
-# import logging as _logging
-
-# _module_logger = _logging.getLogger("pydna." + __name__)
-
-BsaI, BsmBI, BbsI, FokI
-
-DNA = _Dseqrecord("gatcGAAGACtagagtctgattcg")
-
-a, b = DNA.cut(BbsI)
-
-assert a + b == DNA
-
-
-# MoClo
-
-# https://edinburgh-genome-foundry.github.io/GoldenHinges

pydna/ligate.py

@@ -1,62 +0,0 @@
-#!/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

pydna/user_cloning.py

@@ -1,29 +0,0 @@
-#!/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.
-
-
-# from abc import ABC, abstractmethod
-# import re
-# from pydna.utils import rc
-
-
-"""
-Nicking & USER cloning
-
-
-CGAuGTCGACTTAGATCTCACAGGCTTTTTTCAAGaCGGCCTTGAATTCAGTCATTTGGATCCGGCCGATC
-GCTACAGCTGAATCTAGAGTGTCCGAAAAAAGTTCTGCCGGAACTTAAGTCAGTAAACCTAGGCCGGCuAG
-
-1. Digest both strands
-2. Collect all linear ssDNA
-3. Anneal all combinations
-4. Keep ones present in original molecule
-5. Rank by stability
-6.
-
-"""

pydna-5.5.4.dist-info/RECORD

@@ -1,46 +0,0 @@
-pydna/__init__.py,sha256=Fb-8yiWHmQwChAGIXW38c0iWfPw4Cm3tQLHTiBOU9pc,12867
-pydna/_pretty.py,sha256=foRAxdL3Jiupuz7l38THBQZ7tu-5vQvLm1cKdDa7n6A,923
-pydna/_thermodynamic_data.py,sha256=9_w-97DpkbsWbJGHVijscMvUS_SFt7GxzrxspMRPZSg,10903
-pydna/all.py,sha256=xwkbR5Hn52xVfgLAXaEfIgtNwaBiGDbJFTQfa3Zi6HQ,1781
-pydna/amplicon.py,sha256=X4rCSanhlx1sPN0eAtcdAWg4Lw0WKrGQhv-cgZKtM3s,5343
-pydna/amplify.py,sha256=XRwmSMQ2d8Y379zcl56yU6rt1xWbSulWWHLqp-HRDc0,19260
-pydna/assembly.py,sha256=LM3-s3YysFvvkl1oooxoBjYLt0iMc3E1YLoqE05i8bs,19936
-pydna/assembly2.py,sha256=A_agqF57amqquwaYuEJmzhU8qn6XjGiNh1vHeDNcpC4,106017
-pydna/codon.py,sha256=Nxa_03n2wxXKACkzi55bUN1t5xUU_DBRRwh_ZLIb9_o,2568
-pydna/common_sub_strings.py,sha256=A-gJeA2cEyxKKGQSFoC0BKvcXUGJZcnTUU7x2xlAovc,11574
-pydna/conftest.py,sha256=T5-WmHWLZH3U3ifxnbxd_oOiIFibIrkYpwNacCHlvsY,999
-pydna/contig.py,sha256=m0XV0LO2AbArPZkjyNCf8c7_b1EkXFtYwXHJVG4eTY8,8168
-pydna/cre_lox.py,sha256=sOj9R8_oFPGWs68vc4jf6LqWOXjMsVSwtJaeKl6ZF2M,4476
-pydna/crispr.py,sha256=iwu0Cjskzdb2r-In9633QIxQYKGmSNVOEM_dLK6lC54,3619
-pydna/design.py,sha256=BAoPb4M47yMkF1p4gGmbomZPFyTl0WuXkv8sLSY_Tg0,29067
-pydna/download.py,sha256=7tT8LAEy2Vg05spGfbCea_sol6pUOOBVbxOtyk2mnlQ,1085
-pydna/dseq.py,sha256=2N_dXX36niJItQzN61PoVweee0xxP04_amJ3cSExAtU,54232
-pydna/dseqrecord.py,sha256=MMc6nWUqFfc8KmnDWKDeb2bze8qv9X2rSbZXSS-AXrU,49885
-pydna/fakeseq.py,sha256=uxyu1PXF-sVasEqhmyhMcsbpTy84uUtubDiZuxHNb9c,1174
-pydna/fusionpcr.py,sha256=tfIfGGkNoZjg_dodcEx9wTc12aLRnC7J3g-Vg3Jg1uA,2821
-pydna/gateway.py,sha256=iwNHrDIOqKl6_3Rdz7z7c8n_kcLQZuuu72oxNIjyyL8,8686
-pydna/gel.py,sha256=QE1uhnjWXLl2nXgbLs_1TWbPixgUa0-z_UR8jZaByS4,3371
-pydna/genbank.py,sha256=rH677VRklVKBpPoFRsl7Az8fZvrC8TD2lNrNoHO1wU8,8856
-pydna/genbankfile.py,sha256=ii0_RjNGnsfUThTN01c5PRLSZkQT3WlYDvoC6R6ozAA,1451
-pydna/genbankfixer.py,sha256=rJ7qMODx19aha6g8eHC28UfaCsRM983XbTMZXNRdE8w,20510
-pydna/genbankrecord.py,sha256=u9RNBifT0j8rrA2bSdWajodtwm42P52_VlXsxKeOvq0,5566
-pydna/goldengate.py,sha256=LvUWAzhG9OhN1wil7osJIkjfqwBLh355a18wCZO1TvI,1778
-pydna/ladders.py,sha256=fKfWwezxQpX4qon9YCMIwchMBkGVOu8-C02xXk90J-E,3310
-pydna/ligate.py,sha256=ap8xgS4aL9cH4w38e-kpw1Ixa7DtpYF_ipezrVXiHG0,1965
-pydna/opencloning_models.py,sha256=DOvoaG4eQSslguZQDWBsfYhKX1xxy4fYHQUqrdfMhmA,19535
-pydna/parsers.py,sha256=FW2RhZrxWX9wUYJcmt0qi1n7DZP0RfsNaXHhG0eVTWg,7319
-pydna/primer.py,sha256=k9Z_fHfBcY_rGnOtfys806rQBDtvyKwKl2ceSx3_w9A,2272
-pydna/readers.py,sha256=tKoonGlIB9ACeOMnzjhbCya1ooqhFMQIO_G36azN81E,1575
-pydna/seq.py,sha256=82gR1g2D8jfPy1So1pSJvlXYk4zkcKx_qmgvcydxth4,7579
-pydna/seqrecord.py,sha256=haLp1316KQkROkQ0HkJp-RfgWN-eDyLPzTGFLjgXwHk,23363
-pydna/sequence_picker.py,sha256=Pco9IrUwNSiS0wQ5hp5FMfE9kIN9XOwXasKLF9OA6DM,1402
-pydna/sequence_regex.py,sha256=DYuAJkWm_GqEGMpd0pE-Mad_B6POUP8gwjSCFR8RfXw,1259
-pydna/threading_timer_decorator_exit.py,sha256=D91kqjKSavWDnXyc1Fo-CwPYtbmR2DjTXnBYSRXKmSA,2793
-pydna/tm.py,sha256=0r4Aqjt_qanfqR8GNvqNh8us7AKM6JvaQKqHYsswAz4,11143
-pydna/types.py,sha256=Y9HxQ0wd-1AGuBzCSIU9JwZhGSrAIZBAFYjmEdOyL3M,1490
-pydna/user_cloning.py,sha256=VSpYX1tdbcD_PzEt69Jz6Lud-yAkYMVXnzVd4v2usnE,692
-pydna/utils.py,sha256=BwBOcr2HyLAPAVdpXEEDiwJ5MeWW096EOekvfyXxbDM,25227
-pydna-5.5.4.dist-info/METADATA,sha256=01RQRwIOoehyk7LNVpLSmQGgFynAyTZ97Di4juPnm0w,24379
-pydna-5.5.4.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pydna-5.5.4.dist-info/licenses/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
-pydna-5.5.4.dist-info/RECORD,,