File gel_old.py has 1496 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# doctest: +NORMALIZE_WHITESPACE
# doctest: +SKIP

File dseq.py has 1427 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

File dseqrecord.py has 1063 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

Function run has a Cognitive Complexity of 113 (exceeds 5 allowed). Consider refactoring.

Open

    def run(
        self,
        field=5.0,  # V/cm
        temperature=295.15,  # K
        runtime=None,  # seconds

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File seqrecord.py has 562 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

Function gelplot_imshow has a Cognitive Complexity of 57 (exceeds 5 allowed). Consider refactoring.

Open

def gelplot_imshow(
    distances,
    bandwidths,
    intensities,
    lanes,

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File design.py has 536 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

File _thermodynamic_data.py has 515 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the pydna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included

File gel2.py has 495 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import matplotlib

File utils.py has 463 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

Dseq has 47 functions (exceeds 20 allowed). Consider refactoring.

Open

class Dseq(_Seq):
    """Dseq holds information for a double stranded DNA fragment.

    Dseq also holds information describing the topology of
    the DNA fragment (linear or circular).

Dseqrecord has 47 functions (exceeds 20 allowed). Consider refactoring.

Open

class Dseqrecord(_SeqRecord):
    """Dseqrecord is a double stranded version of the Biopython SeqRecord [#]_ class.
    The Dseqrecord object holds a Dseq object describing the sequence.
    Additionally, Dseqrecord hold meta information about the sequence in the
    from of a list of SeqFeatures, in the same way as the SeqRecord does.

File amplify.py has 427 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

Function __init__ has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(
        self,
        watson,
        crick=None,
        ovhg=None,

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Function run has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.

Open

    def run(
        self,
        till_len=0.75,  # percent of gel_len
        till_time=None,  # hours
        exposure=0.5,  # [0-1]

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SeqRecord has 40 functions (exceeds 20 allowed). Consider refactoring.

Open

class SeqRecord(_SeqRecord):
    """
    A subclass of the Biopython SeqRecord class.

    Has a number of extra methods and uses

Function eq has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.

Open

def eq(*args, **kwargs):
    """Compare two or more DNA sequences for equality.

    Compares two or more DNA sequences for equality i.e. if they
    represent the same double stranded DNA molecule.

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File assembly.py has 380 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/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

Function map_trace_files has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.

Open

    def map_trace_files(self, pth, limit=25):  # TODO allow path-like objects
        import glob

        traces = []
        for name in glob.glob(pth):

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Function assemble_circular has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.

Open

    def assemble_circular(self, length_bound=None):
        cps = {}  # circular assembly
        cpsrc = {}
        cpaths = sorted(_nx.simple_cycles(self.G, length_bound=length_bound), key=len)
        cpaths_sorted = []

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