pydna 5.5.1__py3-none-any.whl → 5.5.2__py3-none-any.whl

pydna/genbankfixer.py

@@ -33,7 +33,9 @@ GoodLocus = (
     + _pp.Word(_pp.nums).setResultsName("size")
     + _pp.Suppress(_pp.CaselessLiteral("bp"))
     + _pp.Word(_pp.alphas + "-").setResultsName("seqtype")
-    + (_pp.CaselessLiteral("linear") | _pp.CaselessLiteral("circular")).setResultsName("topology")
+    + (_pp.CaselessLiteral("linear") | _pp.CaselessLiteral("circular")).setResultsName(
+        "topology"
+    )
     + _pp.Optional(_pp.Word(_pp.alphas), default="   ").setResultsName("divcode")
     + _pp.Regex(r"(\d{2})-(\S{3})-(\d{4})").setResultsName("date")
 )
@@ -44,7 +46,9 @@ BrokenLocus1 = (
     + _pp.Word(_pp.nums).setResultsName("size")
     + _pp.Suppress(_pp.CaselessLiteral("bp"))
     + _pp.Word(_pp.alphas + "-").setResultsName("seqtype")
-    + (_pp.CaselessLiteral("linear") | _pp.CaselessLiteral("circular")).setResultsName("topology")
+    + (_pp.CaselessLiteral("linear") | _pp.CaselessLiteral("circular")).setResultsName(
+        "topology"
+    )
     + _pp.Optional(_pp.Word(_pp.alphas), default="   ").setResultsName("divcode")
     + _pp.Regex(r"(\d{2})-(\S{3})-(\d{4})").setResultsName("date")
 )
@@ -97,7 +101,8 @@ CapWord = _pp.Word("ABCDEFGHIJKLMNOPQRSTUVWXYZ")
 SpacedLine = _pp.White(min=1) + _pp.CharsNotIn("\n") + _pp.LineEnd()
 # HeaderLine = CapWord + CharsNotIn("\n") + LineEnd()
 GenericEntry = _pp.Group(
-    CapWord + _pp.Combine(_pp.CharsNotIn("\n") + _pp.LineEnd() + _pp.ZeroOrMore(SpacedLine))
+    CapWord
+    + _pp.Combine(_pp.CharsNotIn("\n") + _pp.LineEnd() + _pp.ZeroOrMore(SpacedLine))
 ).setResultsName("generics", listAllMatches=True)
 
 
@@ -135,7 +140,9 @@ RPAREN = _pp.Suppress(")")
 SEP = _pp.Suppress(_pp.Literal(".."))
 
 # recognize numbers w. < & > uncertainty specs, then strip the <> chars to make it fixed
-gbIndex = _pp.Word(_pp.nums + "<>").setParseAction(lambda s, l_, t: int(t[0].replace("<", "").replace(">", "")))
+gbIndex = _pp.Word(_pp.nums + "<>").setParseAction(
+    lambda s, l_, t: int(t[0].replace("<", "").replace(">", ""))
+)
 SimpleSlice = _pp.Group(gbIndex + SEP + gbIndex) | _pp.Group(gbIndex).setParseAction(
     lambda s, l_, t: [[t[0][0], t[0][0]]]
 )
@@ -194,12 +201,19 @@ QuoteFeaturekeyval = _pp.Group(
 
 # UnQuoted KeyVal: /key=value  (I'm assuming it doesn't do multilines this way? wrong! ApE does store long labels this way! sigh.)
 # NoQuoteFeaturekeyval = Group(Suppress('/') + Word(alphas+nums+"_-") + Suppress('=') + OneOrMore(CharsNotIn("\n")) )
-keyvalspacedline = _pp.White(exact=21) + _pp.CharsNotIn("/") + _pp.OneOrMore(_pp.CharsNotIn("\n")) + _pp.LineEnd()
+keyvalspacedline = (
+    _pp.White(exact=21)
+    + _pp.CharsNotIn("/")
+    + _pp.OneOrMore(_pp.CharsNotIn("\n"))
+    + _pp.LineEnd()
+)
 NoQuoteFeaturekeyval = _pp.Group(
     _pp.Suppress("/")
     + _pp.Word(_pp.alphas + _pp.nums + "_-")
     + _pp.Suppress("=")
-    + _pp.Combine(_pp.CharsNotIn("\n") + _pp.LineEnd() + _pp.ZeroOrMore(keyvalspacedline))
+    + _pp.Combine(
+        _pp.CharsNotIn("\n") + _pp.LineEnd() + _pp.ZeroOrMore(keyvalspacedline)
+    )
 )
 
 # Special Case for Numerical Vals:  /bases=12  OR  /bases="12"
@@ -213,14 +227,18 @@ NumFeaturekeyval = _pp.Group(
 
 # Key Only KeyVal: /pseudo
 # post-parse convert it into a pair to resemble the structure of the first three cases i.e. [pseudo, True]
-FlagFeaturekeyval = _pp.Group(_pp.Suppress("/") + _pp.Word(_pp.alphas + _pp.nums + "_-")).setParseAction(
-    lambda s, l_, t: [[t[0][0], True]]
-)
+FlagFeaturekeyval = _pp.Group(
+    _pp.Suppress("/") + _pp.Word(_pp.alphas + _pp.nums + "_-")
+).setParseAction(lambda s, l_, t: [[t[0][0], True]])
 
 Feature = _pp.Group(
-    _pp.Word(_pp.alphas + _pp.nums + "_-").setParseAction(lambda s, l_, t: [["type", t[0]]])
+    _pp.Word(_pp.alphas + _pp.nums + "_-").setParseAction(
+        lambda s, l_, t: [["type", t[0]]]
+    )
     + featLocation.setResultsName("location")
-    + _pp.OneOrMore(NumFeaturekeyval | QuoteFeaturekeyval | NoQuoteFeaturekeyval | FlagFeaturekeyval)
+    + _pp.OneOrMore(
+        NumFeaturekeyval | QuoteFeaturekeyval | NoQuoteFeaturekeyval | FlagFeaturekeyval
+    )
 )
 
 FeaturesEntry = (
@@ -234,7 +252,9 @@ FeaturesEntry = (
 
 # sequence is just a column-spaced big table of dna nucleotides
 # should it recognize full IUPAC alphabet?  NCBI uses n for unknown region
-Sequence = _pp.OneOrMore(_pp.Suppress(_pp.Word(_pp.nums)) + _pp.OneOrMore(_pp.Word("ACGTacgtNn")))
+Sequence = _pp.OneOrMore(
+    _pp.Suppress(_pp.Word(_pp.nums)) + _pp.OneOrMore(_pp.Word("ACGTacgtNn"))
+)
 
 # Group(  ) hides the setResultsName names def'd inside, such that one needs to first access this group and then access the dict of contents inside
 SequenceEntry = _pp.Suppress(_pp.Literal("ORIGIN")) + Sequence.setParseAction(
@@ -352,7 +372,9 @@ def wrapstring(str_, rowstart, rowend, padfirst=True):
         if linenum == 0 and not padfirst:
             wrappedstr += str_[linenum * rowlen : (linenum + 1) * rowlen] + "\n"
         else:
-            wrappedstr += " " * leftpad + str_[linenum * rowlen : (linenum + 1) * rowlen] + "\n"
+            wrappedstr += (
+                " " * leftpad + str_[linenum * rowlen : (linenum + 1) * rowlen] + "\n"
+            )
     #    if str_.startswith("/translation="):
     #        print(str_)
     #        print(wrappedstr)
@@ -480,7 +502,9 @@ def toGB(jseq):
                         fstr += wrapstring("/" + str(k) + "=" + str(feat[k]), 21, 80)
                     # standard: wrap val in quotes
                     else:
-                        fstr += wrapstring("/" + str(k) + "=" + '"' + str(feat[k]) + '"', 21, 80)
+                        fstr += wrapstring(
+                            "/" + str(k) + "=" + '"' + str(feat[k]) + '"', 21, 80
+                        )
             featuresstr += fstr
 
     # the spaced, numbered sequence
@@ -511,11 +535,11 @@ def gbtext_clean(gbtext):
     ... //'''
     >>> from pydna.readers import read
     >>> read(s)  # doctest: +SKIP
-    /home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/site-packages/Bio/GenBank/Scanner.py:1388: BiopythonParserWarning: Malformed LOCUS line found - is this correct?
+    ... /site-packages/Bio/GenBank/Scanner.py:1388: BiopythonParserWarning: Malformed LOCUS line found - is this correct?
     :'LOCUS       New_DNA      3 bp    DNA   CIRCULAR SYN        19-JUN-2013\\n'
       "correct?\\n:%r" % line, BiopythonParserWarning)
     Traceback (most recent call last):
-      File "/home/bjorn/python_packages/pydna/pydna/readers.py", line 48, in read
+      File "... /pydna/readers.py", line 48, in read
         results = results.pop()
     IndexError: pop from empty list
     <BLANKLINE>
@@ -523,7 +547,7 @@ def gbtext_clean(gbtext):
     <BLANKLINE>
     Traceback (most recent call last):
       File "<stdin>", line 1, in <module>
-      File "/home/bjorn/python_packages/pydna/pydna/readers.py", line 50, in read
+      File "... /pydna/readers.py", line 50, in read
         raise ValueError("No sequences found in data:\\n({})".format(data[:79]))
     ValueError: No sequences found in data:
     (LOCUS       New_DNA      3 bp    DNA   CIRCULAR SYN        19-JUN-2013
@@ -570,14 +594,3 @@ def gbtext_clean(gbtext):
     Result = _namedtuple("Result", "gbtext jseq")
     result = Result(_pretty_str(toGB(jseq).strip()), jseq)
     return result
-
-
-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/genbankrecord.py

@@ -11,7 +11,9 @@ import os as _os
 
 
 class GenbankRecord(_Dseqrecord):
-    def __init__(self, record, *args, item="accession", start=None, stop=None, strand=1, **kwargs):
+    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
@@ -64,7 +66,9 @@ class GenbankRecord(_Dseqrecord):
         return obj
 
     @classmethod
-    def from_SeqRecord(cls, record, *args, item="accession", start=None, stop=None, strand=1, **kwargs):
+    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
@@ -95,7 +99,9 @@ class GenbankRecord(_Dseqrecord):
 
     def __repr__(self):
         """returns a short string representation of the object"""
-        return "Gbnk({}{} {})".format({True: "-", False: "o"}[not self.circular], len(self), self._repr)
+        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"""
@@ -121,7 +127,7 @@ class GenbankRecord(_Dseqrecord):
 
         code = (
             "from pydna.genbank import Genbank\n"
-            f"gb = Genbank('{_os.environ['pydna_email']}')\n"
+            f"gb = Genbank('{_os.getenv('pydna_email')}')\n"
             f"seq = gb.nucleotide('{self.item}'"
         )
         if self.start and self.start:
@@ -141,7 +147,7 @@ class GenbankRecord(_Dseqrecord):
 
         code = (
             "from Bio import Entrez, SeqIO\n"
-            f"Entrez.email = '{_os.environ['pydna_email']}'\n"
+            f"Entrez.email = '{_os.getenv('pydna_email')}'\n"
             "handle = Entrez.efetch(db='nuccore',\n"
             f"                       id='{self.item}',\n"
             "                       rettype='gbwithparts',\n"
@@ -160,12 +166,3 @@ class GenbankRecord(_Dseqrecord):
         code += "record = SeqIO.read(handle, 'genbank')"
 
         return _ps(code)
-
-
-if __name__ == "__main__":
-    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/goldengate.py

@@ -27,9 +27,9 @@ 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
+# import logging as _logging
 
-_module_logger = _logging.getLogger("pydna." + __name__)
+# _module_logger = _logging.getLogger("pydna." + __name__)
 
 BsaI, BsmBI, BbsI, FokI
 

pydna/ladders.py

@@ -19,7 +19,10 @@ a gel image. Exampel can be found in scripts/molecular_weight_standards.ods.
 from pydna.fakeseq import FakeSeq as _FakeSeq
 
 
-PennStateLadder = [_FakeSeq(int(n)) for n in (10000, 7750, 5000, 4000, 3000, 2000, 1500, 1000, 750, 500)]
+PennStateLadder = [
+    _FakeSeq(int(n))
+    for n in (10000, 7750, 5000, 4000, 3000, 2000, 1500, 1000, 750, 500)
+]
 
 
 GeneRuler_1kb = [
@@ -131,13 +134,3 @@ FakeGel = [
     ],
     PennStateLadder,
 ]
-
-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

@@ -9,9 +9,10 @@ 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__)
+# import logging as _logging
+
+# _module_logger = _logging.getLogger("pydna." + __name__)
 
 
 def ligate(fragments: list):
@@ -51,18 +52,11 @@ def ligate(fragments: list):
 
     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]
+    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/parsers.py

@@ -7,7 +7,7 @@
 
 """Provides two functions, parse and parse_primers"""
 
-import os as _os
+# import os as _os
 import re as _re
 import io as _io
 import textwrap as _textwrap
@@ -40,7 +40,9 @@ except ImportError:
 
 # gb_fasta_embl_regex = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
 
-gb_fasta_embl_regex = r"(?:^>.+\n^(?:^[^>]+?)(?=\n\n|>|^LOCUS|^ID))|(?:(?:^LOCUS|^ID)(?:(?:.|\n)+?)^//)"
+gb_fasta_embl_regex = (
+    r"(?:^>.+\n^(?:^[^>]+?)(?=\n\n|>|^LOCUS|^ID))|(?:(?:^LOCUS|^ID)(?:(?:.|\n)+?)^//)"
+)
 
 # The gb_fasta_embl_regex is meant to be able to extract sequences from
 # text where sequences are mixed with other contents as well
@@ -95,7 +97,7 @@ def embl_gb_fasta(text):
             except ValueError:
                 handle.seek(0)
                 try:
-                    parsed = _SeqIO.read(handle, "fasta")
+                    parsed = _SeqIO.read(handle, "fasta-blast")
                 except ValueError:
                     handle.close()
                     continue
@@ -206,12 +208,3 @@ def parse(data, ds=True):
 def parse_primers(data):
     """docstring."""
     return [_Primer(x) for x in parse(data, ds=False)]
-
-
-if __name__ == "__main__":
-    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/primer.py

@@ -14,7 +14,9 @@ from pydna.seqrecord import SeqRecord as _SeqRecord
 class Primer(_SeqRecord):
     """Primer and its position on a template, footprint and tail."""
 
-    def __init__(self, record, *args, amplicon=None, position=None, footprint=0, **kwargs):
+    def __init__(
+        self, record, *args, amplicon=None, position=None, footprint=0, **kwargs
+    ):
         if hasattr(record, "features"):  # Seqrecord
             self.__dict__.update(record.__dict__)
             self.__dict__.update(kwargs)
@@ -57,14 +59,3 @@ class Primer(_SeqRecord):
         answer.position = None
         answer._fp = len(self)
         return answer
-
-
-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/readers.py

@@ -54,14 +54,3 @@ def read_primer(data):
     The usage is similar to the :func:`parse_primer` function."""
 
     return _Primer(read(data, ds=False))
-
-
-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/seq.py

@@ -25,9 +25,10 @@ from Bio.Seq import Seq as _Seq
 from pydna._pretty import PrettyTable as _PrettyTable
 
 from typing import List as _List, Optional as _Optional, Tuple as _Tuple
-import logging as _logging
 
-_module_logger = _logging.getLogger("pydna." + __name__)
+# import logging as _logging
+
+# _module_logger = _logging.getLogger("pydna." + __name__)
 
 
 class Seq(_Seq):
@@ -43,7 +44,9 @@ class Seq(_Seq):
         **kwargs,
     ) -> "ProteinSeq":
         """Translate.."""
-        p = super().translate(*args, stop_symbol=stop_symbol, to_stop=to_stop, cds=cds, gap=gap, **kwargs)
+        p = super().translate(
+            *args, stop_symbol=stop_symbol, to_stop=to_stop, cds=cds, gap=gap, **kwargs
+        )
         return ProteinSeq(p._data)
 
     def gc(self) -> float:
@@ -78,10 +81,17 @@ class Seq(_Seq):
 
     def express(self, organism: str = "sce") -> _PrettyTable:
         """docstring."""
-        x = _PrettyTable(["cds", "len", "cai", "gc", "sta", "stp", "n-end"] + _rare_codons[organism] + ["rare"])
+        x = _PrettyTable(
+            ["cds", "len", "cai", "gc", "sta", "stp", "n-end"]
+            + _rare_codons[organism]
+            + ["rare"]
+        )
         val = []
 
-        val.append(f"{self._data.upper().decode('ASCII')[:3]}..." f"{self._data.upper().decode('ASCII')[-3:]}")
+        val.append(
+            f"{self._data.upper().decode('ASCII')[:3]}..."
+            f"{self._data.upper().decode('ASCII')[-3:]}"
+        )
         val.append(len(self) / 3)
         val.append(self.cai(organism))
         val.append(self.gc())
@@ -103,7 +113,9 @@ class Seq(_Seq):
 
     def orfs2(self, minsize: int = 30) -> _List[str]:
         """docstring."""
-        orf = _re.compile(f"ATG(?:...){{{minsize},}}?(?:TAG|TAA|TGA)", flags=_re.IGNORECASE)
+        orf = _re.compile(
+            f"ATG(?:...){{{minsize},}}?(?:TAG|TAA|TGA)", flags=_re.IGNORECASE
+        )
         start = 0
         matches: _List[slice] = []
         s = self._data.decode("ASCII")
@@ -203,7 +215,9 @@ class ProteinSeq(_Seq):
         ----------
         .. [#] http://wiki.christophchamp.com/index.php/SEGUID
         """
-        return _lsseguid(self._data.decode("utf8").upper(), alphabet="{protein-extended}")
+        return _lsseguid(
+            self._data.decode("utf8").upper(), alphabet="{protein-extended}"
+        )
 
     def __getitem__(self, key):
         result = super().__getitem__(key)
@@ -232,14 +246,3 @@ class ProteinSeq(_Seq):
         Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
         """
         return self._pa().instability_index()
-
-
-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/seqrecord.py

@@ -35,10 +35,10 @@ from copy import copy as _copy
 from pydna import _PydnaWarning
 from warnings import warn as _warn
 
-import logging as _logging
+# import logging as _logging
 import datetime
 
-_module_logger = _logging.getLogger("pydna." + __name__)
+# _module_logger = _logging.getLogger("pydna." + __name__)
 
 
 class SeqRecord(_SeqRecord):
@@ -87,7 +87,9 @@ class SeqRecord(_SeqRecord):
             self.seq = _Seq(self.seq)
 
         self.seq._data = b"".join(self.seq._data.split())  # remove whitespaces
-        self.annotations = {_pretty_str(k): _pretty_str(v) for k, v in self.annotations.items()}
+        self.annotations = {
+            _pretty_str(k): _pretty_str(v) for k, v in self.annotations.items()
+        }
 
     @classmethod
     def from_Bio_SeqRecord(clc, sr: _SeqRecord):
@@ -109,7 +111,9 @@ class SeqRecord(_SeqRecord):
         if len(value) > 16:
             shortvalue = value[:16]
             _warn(
-                ("locus property {} truncated" "to 16 chars {}").format(value, shortvalue),
+                ("locus property {} truncated" "to 16 chars {}").format(
+                    value, shortvalue
+                ),
                 _PydnaWarning,
                 stacklevel=2,
             )
@@ -239,7 +243,9 @@ class SeqRecord(_SeqRecord):
             f.qualifiers["ApEinfo_fwdcolor"] = [cols[i % len(cols)]]
             f.qualifiers["ApEinfo_revcolor"] = [cols[::-1][i % len(cols)]]
 
-    def add_feature(self, x=None, y=None, seq=None, type_="misc", strand=1, *args, **kwargs):
+    def add_feature(
+        self, x=None, y=None, seq=None, type_="misc", strand=1, *args, **kwargs
+    ):
         """Add a feature of type misc to the feature list of the sequence.
 
         Parameters
@@ -327,7 +333,9 @@ class SeqRecord(_SeqRecord):
         |   0 | L:ft2         | --> | 2   | 4   |   2 | misc |  no  |
         +-----+---------------+-----+-----+-----+-----+------+------+
         """
-        x = _PrettyTable(["Ft#", "Label or Note", "Dir", "Sta", "End", "Len", "type", "orf?"])
+        x = _PrettyTable(
+            ["Ft#", "Label or Note", "Dir", "Sta", "End", "Len", "type", "orf?"]
+        )
         x.align["Ft#"] = "r"  # Left align
         x.align["Label or Note"] = "l"  # Left align
         x.align["Len"] = "r"
@@ -357,7 +365,8 @@ class SeqRecord(_SeqRecord):
                     len(sf),
                     sf.type,
                     {True: "yes", False: "no"}[
-                        self.extract_feature(i).isorf() or self.extract_feature(i).reverse_complement().isorf()
+                        self.extract_feature(i).isorf()
+                        or self.extract_feature(i).reverse_complement().isorf()
                     ],
                 ]
             )
@@ -480,7 +489,9 @@ class SeqRecord(_SeqRecord):
                 f"Stamp change.\nNew: {chksum}\nOld: {oldstamp[0]}",
                 _PydnaWarning,
             )
-        self.annotations["comment"] = (f"{oldcomment}\n" f"{tool} {chksum} {now()} {comment}").strip()
+        self.annotations["comment"] = (
+            f"{oldcomment}\n" f"{tool} {chksum} {now()} {comment}"
+        ).strip()
         return _pretty_str(chksum)
 
     def lcs(self, other, *args, limit=25, **kwargs):
@@ -729,14 +740,3 @@ class ProteinSeqRecord(SeqRecord):
     def __format__(self, format):
         """docstring."""
         return _pretty_str(_SeqRecord.__format__(self, format))
-
-
-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 | doctest.NORMALIZE_WHITESPACE))
-    _os.environ["pydna_cached_funcs"] = cached

pydna/sequence_picker.py

@@ -7,11 +7,12 @@
 
 from pydna.dseqrecord import Dseqrecord
 import os as _os
-import logging as _logging
+
+# import logging as _logging
 from Bio.Blast import NCBIWWW
 from Bio.Blast import NCBIXML
 
-_module_logger = _logging.getLogger("pydna." + __name__)
+# _module_logger = _logging.getLogger("pydna." + __name__)
 
 
 email = _os.getenv("pydna_email")
@@ -51,13 +52,3 @@ def genbank_accession(s: str) -> Dseqrecord:
         description=(f"{best_alignment.accession} " f"REGION: {start}..{stop}"),
     )
     return result
-
-
-if __name__ == "__main__":
-    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
-    pass

pydna/tm.py

@@ -213,7 +213,9 @@ def dbd_program(amplicon, tm=tm_dbd, ta=ta_dbd):
 
     """
     PfuSso7d_extension_rate = 15  # seconds/kB PCR product
-    extension_time_PfuSso7d = max(10, int(PfuSso7d_extension_rate * len(amplicon) / 1000))  # seconds
+    extension_time_PfuSso7d = max(
+        10, int(PfuSso7d_extension_rate * len(amplicon) / 1000)
+    )  # seconds
 
     # The program returned is eaither a two step or three step progrem
     # This depends on the tm and length of the primers in the
@@ -324,7 +326,10 @@ def tmbresluc(primer: str, *args, primerc=500.0, saltc=50, **kwargs):
         dH += _thermodynamic_data.dHBr[n1 - 97][n2 - 97]
         dS += _thermodynamic_data.dSBr[n1 - 97][n2 - 97]
 
-    tm = (dH / (1.9872 * _math.log(pri / 1600) + dS) + (16.6 * _math.log(saltc)) / _math.log(10)) - 273.15
+    tm = (
+        dH / (1.9872 * _math.log(pri / 1600) + dS)
+        + (16.6 * _math.log(saltc)) / _math.log(10)
+    ) - 273.15
 
     return tm
 
@@ -365,25 +370,18 @@ def tm_neb(primer, conc=0.5, prodcode="q5-0"):
     try:
         res = requests.get(url, params=params, headers=headers)
     except requests.exceptions.ConnectionError as e:
-        raise requests.exceptions.ConnectionError("Could not connect to NEB API.") from e
+        raise requests.exceptions.ConnectionError(
+            "Could not connect to NEB API."
+        ) from e
     if res.status_code != 200:
         if "error" in res.json():
             raise requests.exceptions.HTTPError(res.status_code, res.json()["error"])
         else:
-            raise requests.exceptions.HTTPError(res.status_code, res.text)  # pragma: no cover
+            raise requests.exceptions.HTTPError(
+                res.status_code, res.text
+            )  # pragma: no cover
     r = res.json()
     if r["success"]:
         return r["data"]["tm1"]
     else:
         raise requests.exceptions.HTTPError(r["error"])
-
-
-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