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

pydna/__init__.py

@@ -5,6 +5,7 @@
 # license.  Please see the LICENSE.txt file that should have been included
 # as part of this package.
 
+
 """
 :copyright: Copyright 2013-2023 by Björn Johansson. All rights reserved.
 :license:   This code is part of the pydna package, governed by the
@@ -48,23 +49,27 @@ functions with a lowercase letter:
          ├── amplify
          │         ├── Anneal
          │         └── pcr
+         │
          ├── assembly
          │          └── Assembly
+         │
          ├── design
          │        ├── assembly_fragments
          │        └── primer_design
-         ├── download
-         │          └── download_text
+         │
          ├── dseqrecord
          │            └── Dseqrecord
          ├── gel
          │     └── Gel
+         │
          ├── genbank
          │         ├── genbank
          │         └── Genbank
+         │
          ├── parsers
          │         ├── parse
          │         └── parse_primers
+         │
          └── readers
                    ├── read
                    └── read_primers
@@ -131,18 +136,9 @@ See this repository for a collection of
 
 """
 
-
-# from pydna.utils import open_folder as _open_folder
-# from pathlib import Path as _Path
-import os as _os
-
-# import logging as _logging
-# import logging.handlers as _handlers
-# import appdirs as _appdirs
-# import configparser as _configparser
-# import tempfile as _tempfile
-from pydna._pretty import PrettyTable as _PrettyTable
-
+from pydna._pretty import PrettyTable
+from Bio.Restriction import FormattedSeq
+import os
 
 __author__ = "Björn Johansson"
 __copyright__ = "Copyright 2013 - 2023 Björn Johansson"
@@ -151,113 +147,7 @@ __license__ = "BSD"
 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "5.5.4"
-
-
-# obtain config directory from env or appdirs
-# _os.environ["pydna_config_dir"] = _os.getenv("pydna_config_dir", _appdirs.user_config_dir("pydna"))
-# config_dir = _Path(_os.environ["pydna_config_dir"])
-# config_dir.mkdir(parents=True, exist_ok=True)
-
-# set path for the pydna.ini file
-# _ini_path = config_dir / "pydna.ini"
-
-# define user_data_dir
-# user_data_dir = _Path(_appdirs.user_data_dir("pydna"))
-
-# default_ini = {
-#     "ape": "put/path/to/ape/here",
-#     "cached_funcs": "pydna.genbank.genbank.nucleotide",
-#     "data_dir": str(user_data_dir),
-#     "email": "someone@example.com",
-#     "enzymes": str(user_data_dir / "enzymes.md"),
-#     "log_dir": _appdirs.user_log_dir("pydna"),
-#     "loglevel": str(_logging.WARNING),
-#     "primers": str(user_data_dir / "primers.md"),
-#     "assembly_limit": str(10),
-# }
-
-# ini = default_ini.copy()
-
-# initiate a config parser instance
-# _parser = _configparser.ConfigParser()
-
-# if a pydna.ini exists, it is read
-# if _ini_path.exists():
-#     _parser.read(_ini_path)
-# pydna related environmental variables are set
-# from pydna.ini if they are not set already
-# _main = _parser["main"]
-# ini.update(_main)
-
-
-# for key, value in ini.items():
-#     _os.environ[f"pydna_{key}"] = _os.getenv(f"pydna_{key}", value)
-
-# logdir = _Path(_os.environ["pydna_log_dir"])
-
-# create log directory if not present
-# logdir.mkdir(parents=True, exist_ok=True)
-# _logmsg = "Log directory {}".format(logdir)
-
-# create logger
-# _logger = _logging.getLogger("pydna")
-# _logger.setLevel(int(_os.environ["pydna_loglevel"]))
-# _hdlr = _handlers.RotatingFileHandler(
-#     logdir / "pydna.log",
-#     mode="a",
-#     maxBytes=10 * 1024 * 1024,
-#     backupCount=10,
-#     encoding="utf-8",
-# )
-
-# _formatter = _logging.Formatter(("%(asctime)s %(levelname)s" " %(funcName)s %(message)s"))
-# _hdlr.setFormatter(_formatter)
-# _logger.addHandler(_hdlr)
-# _logger.info(_logmsg)
-# _logger.info("Environmental variable pydna_ape          = %s", _os.environ["pydna_ape"])
-# _logger.info("Environmental variable pydna_cached_funcs = %s", _os.environ["pydna_cached_funcs"])
-# _logger.info("Environmental variable pydna_data_dir     = %s", _os.environ["pydna_data_dir"])
-# _logger.info("Environmental variable pydna_email        = %s", _os.environ["pydna_email"])
-# _logger.info("Environmental variable pydna_log_dir      = %s", _os.environ["pydna_log_dir"])
-# _logger.info("Environmental variable pydna_loglevel     = %s", _os.environ["pydna_loglevel"])
-# _logger.info("Environmental variable pydna_primers      = %s", _os.environ["pydna_primers"])
-# _logger.info(
-#     "Environmental variable pydna_assembly_limit = %s",
-#     _os.environ["pydna_assembly_limit"],
-# )
-
-# create cache directory if not present
-
-# _Path(_os.environ["pydna_data_dir"]).mkdir(parents=True, exist_ok=True)
-
-# find out if optional dependecies for gel module are in place
-#
-#
-# def _missing_modules_for_gel():
-#    import importlib
-#    from importlib import util
-#
-#    _missing = []
-#    for _optm in ["scipy", "PIL", "numpy", "pyparsing", "requests"]:
-#        _missing.extend([_optm] if not util.find_spec(_optm) else [])
-#    del importlib
-#    del util
-#    return _missing
-#
-#
-# _missing = _missing_modules_for_gel()
-#
-# if _missing:
-#    _logger.warning(
-#        "gel simulation will NOT be available." " Missing modules: %s",
-#        ", ".join(_missing),
-#    )
-# else:
-#    _logger.info("gel simulation is available," " optional dependencies were found.")
-#
-
-# _logger.info("__version__ = %s", __version__)
+__version__ = "5.5.6"
 
 
 class _PydnaWarning(Warning):
@@ -297,87 +187,17 @@ class _PydnaDeprecationWarning(_PydnaWarning):
     pass
 
 
-# def open_current_folder():
-#     """Open the current working directory.
-
-#     Opens in the default file manager. The location for this folder is
-#     given by the :func:`os.getcwd` function
-#     """
-#     return _open_folder(_os.getcwd())
-
-
-# _logger.info("Current working directory = os.getcwd() = %s", _os.getcwd())
-
-
-# def open_cache_folder():
-#     """Open the pydna cache folder.
-
-#     Opens in the default file manager. The location for this folder is stored
-#     in the *pydna_data_dir* environmental variable.
-#     """
-#     return _open_folder(_os.environ["pydna_data_dir"])
-
-
-# def open_config_folder():
-#     """Open the pydna configuration folder.
-
-#     Opens in the default file manager. The location for this folder is stored
-#     in the *pydna_config_dir* environmental variable.
-
-#     The `pydna.ini` file can be edited to make pydna quicker to use.
-#     See the documentation of the :class:configparser.ConfigParser´ class.
-
-#     Below is the content of a typical `pydna.ini` file on a Linux
-#     system.
-
-#     ::
-
-#         [main]
-#         loglevel=30
-#         email=myemail@example.org
-#         data_dir=/home/user/.local/share/pydna
-#         log_dir=/home/user/.cache/pydna/log
-#         ape=tclsh /path/to/ape/AppMain.tcl
-#         cached_funcs=Genbank_nucleotide
-#         primers=/path/to/primers/PRIMERS.txt
-#         enzymes=/path/to/enzymes/RestrictionEnzymes.txt
-
-#     The email address is set to someone@example.com by default. If you change
-#     this to you own address, the :func:`pydna.genbank.genbank` function can be
-#     used to download sequences from Genbank directly without having to
-#     explicitly add the email address.
-
-#     Pydna can cache results from the following functions or methods:
-
-#     - :func:`pydna.genbank.Genbank.nucleotide`   Genbank_nucleotide
-#     - :func:`pydna.amplify.Anneal`               amplify_Anneal
-#     - :func:`pydna.assembly.Assembly`            assembly_Assembly
-#     - :func:`pydna.download.download_text`       download.download_text
-#     - :func:`pydna.dseqrecord.Dseqrecord.synced` Dseqrecord_synced
-
-#     These can be added separated by a comma to the cached_funcs entry
-#     in **pydna.ini** file or the pydna_cached_funcs environment variable.
-
-#     """
-#     return _open_folder(_os.environ["pydna_config_dir"])
-
-
-# def open_log_folder():
-#     """docstring."""
-#     return _open_folder(_os.environ["pydna_log_dir"])
-
-
 def get_env():
     """Print a an ascii table containing all environmental variables.
 
     Pydna related variables have names that starts with `pydna_`
     """
-    _table = _PrettyTable(["Variable", "Value"])
+    _table = PrettyTable(["Variable", "Value"])
     # _table.set_style(_prettytable.DEFAULT)
     _table.align["Variable"] = "l"  # Left align
     _table.align["Value"] = "l"  # Left align
     _table.padding_width = 1  # One space between column edges and contents
-    for k, v in sorted(_os.environ.items()):
+    for k, v in sorted(os.environ.items()):
         if k.lower().startswith("pydna"):
             _table.add_row([k, v])
     return _table
@@ -385,7 +205,7 @@ def get_env():
 
 def logo():
     """Ascii-art logotype of pydna."""
-    from pydna._pretty import pretty_str as _pretty_str
+    from pydna._pretty import pretty_str
 
     message = f"pydna {__version__}"
     try:
@@ -395,4 +215,19 @@ def logo():
     else:
         f = Figlet()
         message = f.renderText(message)
-    return _pretty_str(message)
+    return pretty_str(message)
+
+
+## Override Bio.Restriction.FormattedSeq._table
+
+
+def _make_FormattedSeq_table() -> bytes:
+    table = bytearray(256)
+    upper_to_lower = ord("A") - ord("a")
+    for c in b"ABCDEFGHIJKLMNOPQRSTUVWXYZ":  # Only allow IUPAC letters
+        table[c] = c  # map uppercase to uppercase
+        table[c - upper_to_lower] = c  # map lowercase to uppercase
+    return bytes(table)
+
+
+FormattedSeq._table = _make_FormattedSeq_table()

pydna/_pretty.py

@@ -6,10 +6,10 @@ The pretty_str class is similar to str but has a _repr_pretty_ method
 for for nicer string output in the IPython shell and Jupyter notebook.
 """
 
-from prettytable import PrettyTable as _Pt
-from prettytable import TableStyle as _TableStyle
-from copy import copy as _copy
-from typing import List as _List
+from prettytable import PrettyTable as Pt
+from prettytable import TableStyle
+from copy import copy
+from typing import List
 
 
 class pretty_str(str):
@@ -19,10 +19,10 @@ class pretty_str(str):
         p.text(self)
 
 
-class PrettyTable(_Pt):
+class PrettyTable(Pt):
     """docstring."""
 
-    def lol(self) -> _List[list]:
+    def lol(self) -> List[list]:
         """docstring."""
         return [self._field_names] + self._rows
 
@@ -31,6 +31,6 @@ class PrettyTable(_Pt):
         return self.get_string()
 
     def _repr_markdown_(self) -> pretty_str:
-        c = _copy(self)
-        c.set_style(_TableStyle.MARKDOWN)
+        c = copy(self)
+        c.set_style(TableStyle.MARKDOWN)
         return pretty_str(c.get_string())

pydna/_thermodynamic_data.py

@@ -5,10 +5,10 @@
 # license.  Please see the LICENSE.txt file that should have been included
 # as part of this package.
 
-import collections as _collections
+import collections
 
-dHBr = _collections.defaultdict(dict)
-dSBr = _collections.defaultdict(dict)
+dHBr = collections.defaultdict(dict)
+dSBr = collections.defaultdict(dict)
 
 dHBr[0][0] = -9100
 dSBr[0][0] = -24

pydna/all.py

@@ -18,7 +18,7 @@ ttt
 Dseqrecord(-3)
 >>> from pydna.all import __all__
 >>> __all__
-['Anneal', 'pcr', 'Assembly', 'genbank', 'Genbank', 'download_text', 'Dseqrecord',
+['Anneal', 'pcr', 'Assembly', 'genbank', 'Genbank', 'Dseqrecord',
 'Dseq', 'read', 'read_primer', 'parse', 'parse_primers', 'primer_design', 'assembly_fragments', 'eq', 'gbtext_clean']
 >>>
 """
@@ -30,20 +30,16 @@ __all__ = [
     "Assembly",
     "genbank",
     "Genbank",
-    "download_text",
     "Dseqrecord",
     "Dseq",
     "read",
     "read_primer",
     "parse",
     "parse_primers",
-    # "ape",
     "primer_design",
     "assembly_fragments",
-    # "circular_assembly_fragments",
     "eq",
     "gbtext_clean",
-    # "PrimerList",
 ]
 
 
@@ -52,20 +48,13 @@ from pydna.amplify import pcr
 from pydna.assembly import Assembly
 from pydna.genbank import genbank
 from pydna.genbank import Genbank
-from pydna.download import download_text
 from pydna.dseqrecord import Dseqrecord
 from pydna.dseq import Dseq
 from pydna.readers import read
 from pydna.readers import read_primer
 from pydna.parsers import parse
 from pydna.parsers import parse_primers
-
-# from pydna.editor import ape
 from pydna.design import primer_design
 from pydna.design import assembly_fragments
-
-# from pydna.design import circular_assembly_fragments
 from pydna.utils import eq
 from pydna.genbankfixer import gbtext_clean
-
-# from pydna.myprimers import PrimerList