Function compare_motifs has a Cognitive Complexity of 25 (exceeds 15 allowed). Consider refactoring.

Open

    def compare_motifs(
        self, m1, m2, match="total", metric="wic", combine="mean", pval=False
    ):
        """Compare two motifs.

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Function _scan_jobs has a Cognitive Complexity of 25 (exceeds 15 allowed). Consider refactoring.

Open

    def _scan_jobs(self, scan_func, scan_seqs):
        if self.ncpus > 1:
            median_len = np.median([len(x) for x in scan_seqs])
            chunksize = 200000 // int(median_len)  # 1000 seqs for len 200
            # prepare for parallel processing

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Function write_equalsize_bedfile has a Cognitive Complexity of 24 (exceeds 15 allowed). Consider refactoring.

Open

def write_equalsize_bedfile(bedfile, size, outfile):
    """Read input from <bedfile>, set the size of all entries to <size> and
    write the result to <outfile>.
    Input file needs to be in BED or WIG format."""
    if size is None or size <= 0:

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Function cluster_motifs_with_report has a Cognitive Complexity of 24 (exceeds 15 allowed). Consider refactoring.

Open

def cluster_motifs_with_report(infile, outfile, outdir, threshold, title=None):
    # Cluster significant motifs

    if title is None:
        title = infile

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Function determine_file_type has a Cognitive Complexity of 24 (exceeds 15 allowed). Consider refactoring.

Open

def determine_file_type(fname):
    """
    Detect file type.

    The following file types are supported:

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Function format_factors has a Cognitive Complexity of 23 (exceeds 15 allowed). Consider refactoring.

Open

    def format_factors(
        self, max_length=5, html=False, include_indirect=True, extra_str=",(...)"
    ):
        # create a list of factors, in order of de novo > direct/indirect > occurrence
        if hasattr(self, "factor_info"):

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Function parse has a Cognitive Complexity of 23 (exceeds 15 allowed). Consider refactoring.

Open

    def parse(self, fo):
        """
        Convert GADEM output to motifs

        Parameters

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Function select_nonredundant_motifs has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def select_nonredundant_motifs(
    roc_report, pfmfile, fg_table, bg_table, tolerance=0.001
):
    pfmfile = pfmfile_location(pfmfile)
    motifs = read_motifs(pfmfile)

Function parse has a Cognitive Complexity of 22 (exceeds 15 allowed). Consider refactoring.

Open

    def parse(self, fo):
        """
        Convert MDmodule output to motifs

        Parameters

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Function motifs has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def motifs(args):
    """Calculate ROC_AUC and other metrics and optionally plot ROC curve."""
    if args.outdir is None:
        raise ValueError("an output directory is required!")
    if not os.path.exists(args.outdir):

Function match has a Cognitive Complexity of 21 (exceeds 15 allowed). Consider refactoring.

Open

def match(args):
    sample = dict([(m.id, m) for m in read_motifs(args.pfmfile)])
    db = dict([(m.id, m) for m in read_motifs(args.dbpfmfile)])

    mc = MotifComparer()

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Function _initialize_matrices has a Cognitive Complexity of 21 (exceeds 15 allowed). Consider refactoring.

Open

    def _initialize_matrices(self, seqs, k=1, alphabet=None):
        if alphabet is None:
            alphabet = ["A", "C", "G", "T"]

        self.frequencies = {}

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Function cli has a Cognitive Complexity of 21 (exceeds 15 allowed). Consider refactoring.

Open

def cli(sys_args):
    config = MotifConfig()
    params = config.get_default_params()
    default_pfm_file = os.path.join(config.get_motif_dir(), params["motif_db"])
    default_pfm = params["motif_db"]

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Function roc_auc_xlim has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def roc_auc_xlim(x_bla, y_bla, xlim=0.1):
    """
    Computes the ROC Area Under Curve until a certain FPR value.

    Parameters

Function motif2factor_from_orthologs has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def motif2factor_from_orthologs(
    database: str = "gimme.vertebrate.v5.0",
    database_references: List[str] = None,
    extra_orthologs_references: List[str] = None,
    new_reference: List[str] = None,

Function score_matrices has a Cognitive Complexity of 20 (exceeds 15 allowed). Consider refactoring.

Open

    def score_matrices(self, matrix1, matrix2, metric, combine):

        if metric in self.metrics and combine in self.combine:
            s = score(matrix1.tolist(), matrix2.tolist(), metric, combine)

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Function _unknownfactor2symbols has a Cognitive Complexity of 20 (exceeds 15 allowed). Consider refactoring.

Open

def _unknownfactor2symbols(factor, fields):
    """
    Query mygeneinfo for different aliases of our gene
    """

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Function diff has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def diff(args):

    infiles = args.inputfiles.split(",")
    bgfile = args.bgfile
    outfile = args.outputfile

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

Open

    def _circle(
        self,
        subset=None,
        show_text=True,
        color=None,

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

Open

    def __init__(self, fname=None, split_whitespace=False, fdict=None):
        """Instantiate fasta object. Optional Fasta-formatted file as argument"""
        self.ids = []
        self.seqs = []
        p = re.compile(r"[^abcdefghiklmnpqrstuvwyzxABCDEFGHIKLMNPQRSTUVWXYZ]")

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