Avoid too many return statements within this function.

Open

                    return self.pvalue(

Avoid too many return statements within this function.

Open

                    return "unknown"

Avoid too many return statements within this function.

Open

                    return "narrowpeak"

Avoid too many return statements within this function.

Open

                    return self.max_total(

Avoid too many return statements within this function.

Open

    return "unknown"

Avoid too many return statements within this function.

Open

            return 30

Avoid too many return statements within this function.

Open

                    return self.max_subtotal(

Avoid too many return statements within this function.

Open

            return metric(m1, m2)

Avoid too many return statements within this function.

Open

            return 22

Avoid too many return statements within this function.

Open

        return length

Avoid too many return statements within this function.

Open

        return "region"

Avoid too many return statements within this function.

Open

            return "bed"

Avoid too many return statements within this function.

Open

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

Function check_bed_file has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.

Open

def check_bed_file(fname):
    """Check if the inputfile is a valid bed-file"""
    if not os.path.exists(fname):
        logger.error(f"Inputfile {fname} does not exist!")
        sys.exit(1)

• Read up
  Read up

Function pp_predict_motifs has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.

Open

def pp_predict_motifs(
    fastafile,
    outfile,
    analysis="small",
    organism="hg19",

• Read up
  Read up

Function parse_cutoff has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.

Open

def parse_cutoff(motifs, cutoff, default=0.9):
    """Provide either a file with one cutoff per motif or a single cutoff
    returns a hash with motif id as key and cutoff as value
    """
    cutoffs = {}

• Read up
  Read up

Function factor2orthogroups has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.

Open

def factor2orthogroups(factor, references, database, strategy):
    """
    Returns all the orthogroups a factor belongs to. This is NOT a trivial task.

    Some of the factors shouldn't be considered (blacklisted), some have an

• Read up
  Read up

Function pfmfile_location has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.

Open

def pfmfile_location(infile=None):
    """Return the path to the pfmfile"""
    config = MotifConfig()

    if infile is None:

• Read up
  Read up

Function parse has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.

Open

    def parse(self, fname):
        """
        Convert RPMCMC output to motifs

        Parameters

• Read up
  Read up