File genbankfixer.py has 377 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

Function guess_alphabet has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

def guess_alphabet(sequence):
    """
    guess_alphabet(sequence)

    returns an apropriate Biopython alphabet based on the content of the sequence.

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Function embl_gb_fasta has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

def embl_gb_fasta(text, ds, path=None):

    chunks = extract_from_text(text)
    result_list = []

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Function assemble_linear has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

    def assemble_linear(self, start=None, end=None, max_nodes=None):
        G = _nx.MultiDiGraph(self.G)

        G.add_nodes_from(["begin", "begin_rc", "end", "end_rc"], length=0)

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Function ligate has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

def ligate(fragments: list):
    """docstring."""
    G = _nx.DiGraph()
    G.add_nodes_from(["begin", "end"])
    fragments = fragments[:]

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Function primer_design has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

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def primer_design(template, fp=None, rp=None, limit=13, target_tm=55.0, tm_func=_tm_default, **kwargs):
    """This function designs a forward primer and a reverse primer for PCR amplification
    of a given template sequence.

    The template argument is a Dseqrecord object or equivalent containing the template sequence.

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Function run has 89 lines of code (exceeds 25 allowed). Consider refactoring.

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

Function fuse_by_pcr has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

def fuse_by_pcr(fragments, limit=15):
    """docstring."""

    def anneal(x, y, limit=limit):
        """docstring."""

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Function __repr__ has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

    def __repr__(self):
        """Returns a representation of the sequence, truncated if
        longer than 30 bp"""

        if len(self) > Dseq.trunc:

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Function tm_default has 27 arguments (exceeds 4 allowed). Consider refactoring.

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def tm_default(

Function products has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

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    def products(self):
        if self._products:
            return self._products

        self._products = []

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Function gel has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

def gel(samples=None, gel_length=600, margin=50, interpolator=interpolator(mwstd=_mwstd)):
    import numpy as np
    from PIL import Image as Image
    from PIL import ImageDraw as ImageDraw

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Function assembly_fragments has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

def assembly_fragments(f, overlap=35, maxlink=40):
    """This function return a list of :mod:`pydna.amplicon.Amplicon` objects where
    primers have been modified with tails so that the fragments can be fused in
    the order they appear in the list by for example Gibson assembly or homologous
    recombination.

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Function all_simple_paths_edges has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

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def all_simple_paths_edges(G, source, target, cutoff=None, data=False):
    if data == True:
        edge_data = lambda u, v, n, E, I: (u, v, dict([E[n][I[n]]]))
    else:
        edge_data = lambda u, v, n, E, I: (u, v)

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Function run has 22 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(

Function toGB has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

def toGB(jseq):
    "parses json jseq data and prints out ApE compatible genbank"

    # construct the LOCUS header string
    #  LOCUS format:

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Function SmallestRotation has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

def SmallestRotation(s):
    """Find the rotation of s that is smallest in lexicographic order.
    Duval 1983 describes how to modify his algorithm to do so but I think
    it's cleaner and more general to work from the ChenFoxLyndon output."""

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Function all_circular_paths_edges has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

def all_circular_paths_edges(G):
    for path in sorted(_nx.simple_cycles(G), key=len, reverse=True):
        edges = list(zip(path, path[1:] + [path[0]]))
        N = []
        for u, v in edges:

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Function cutsite_is_valid has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def cutsite_is_valid(self, cutsite):
        """Returns False if:
        - Cut positions fall outside the sequence (could be moved to Biopython)
        - Overhang is not double stranded
        - Recognition site is not double stranded or is outside the sequence

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Function add_feature has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    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
        ----------

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