Function diff_plot has a Cognitive Complexity of 19 (exceeds 15 allowed). Consider refactoring.

Open

def diff_plot(
    motifs,
    pwms,
    names,
    freq,

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Avoid deeply nested control flow statements.

Open

                    if abs(matrix[i][n]) * height >= 0.5:
                        plt.text(
                            x,
                            y,
                            nuc,

Avoid deeply nested control flow statements.

Open

                    if len(res):
                        for _, gene_name, _, gene_id, *_ in res:
                            motif_set = True
                            if gene_name is not None:
                                f.write(f"{motif}\t{gene_name}\tOrthologs\tN\n")

Avoid deeply nested control flow statements.

Open

                        if "x" not in line and "n" not in line:
                            line = line.strip().upper()
                            align.append(line)
                            if not pfm:
                                pfm = [[0 for _ in range(4)] for _ in range(len(line))]

Avoid deeply nested control flow statements.

Open

                        with open(score_file) as f:
                            for line in f:
                                l1, l2, m, sd = line.strip().split("\t")[:4]
                                self.scoredist[metric][f"{match}_{combine}"].setdefault(
                                    int(l1), {}

Avoid deeply nested control flow statements.

Open

                        if not pfm:
                            pfm = [[0 for x in range(4)] for x in range(len(match))]
                        for pos in range(len(match)):

Function matrix_ic has a Cognitive Complexity of 18 (exceeds 15 allowed). Consider refactoring.

Open

def matrix_ic(self, ppm1, ppm2, bg=None):
    if bg is None:
        bg = [0.25, 0.25, 0.25, 0.25]

    # xxCATGYT

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Avoid deeply nested control flow statements.

Open

                        if not pfm:
                            pfm = [[0 for x in range(4)] for x in range(len(match))]
                        for pos in range(len(match)):

Avoid deeply nested control flow statements.

Open

                        for pos in range(len(match)):
                            if match[pos] in nucs:
                                pfm[pos][nucs[match[pos]]] += 1
                            else:
                                for i in range(4):

Function _read_motifs_pfm has a Cognitive Complexity of 18 (exceeds 15 allowed). Consider refactoring.

Open

def _read_motifs_pfm(handle):
    p = re.compile(
        r"(\d+(\.\d+)?(e-\d+)?)\s+(\d+(\.\d+)?(e-\d+)?)\s+(\d+(\.\d+)?(e-\d+)?)\s+(\d+(\.\d+)?(e-\d+)?)"  # noqa: E501
    )
    motifs = []

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Avoid deeply nested control flow statements.

Open

                        for pos in range(len(match)):
                            if match[pos] in nucs:
                                pfm[pos][nucs[match[pos]]] += 1
                            else:
                                for i in range(4):

Avoid deeply nested control flow statements.

Open

                    if warn_no_summit:
                        logger.warning(
                            "No summit present in narrowPeak file, "
                            "using the peak center."
                        )

Function _upgrade_config has a Cognitive Complexity of 18 (exceeds 15 allowed). Consider refactoring.

Open

    def _upgrade_config(self, config_fname=None):
        changed = False
        dflt = configparser.ConfigParser()
        dflt.read(self.default_config)

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Avoid deeply nested control flow statements.

Open

                    if len(vals) > 5:
                        strand = vals[5]

Avoid deeply nested control flow statements.

Open

                        if m1 not in scores:
                            scores[m1] = {}
                        scores[m1][m2] = s

Avoid deeply nested control flow statements.

Open

                        if len(row) == 4:
                            row = [float(x) for x in row]
                            pfm.append(row)

Function plot_logo has a Cognitive Complexity of 17 (exceeds 15 allowed). Consider refactoring.

Open

def plot_logo(
    self,
    fname=None,
    kind="information",
    title=True,

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Avoid too many return statements within this function.

Open

                    return self.max_partial(m1.pfm, m2.pfm, metric, combine)

Avoid too many return statements within this function.

Open

                    return self.max_subtotal(m1.pfm, m2.pfm, metric, combine)

Avoid too many return statements within this function.

Open

                return "unknown"