Showing 82 of 82 total issues
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"