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Avoid deeply nested control flow statements.
Open

                if info_percentage <= min_sequence: # Are all my samples complete? or at least with N percentage of information?
                    print("Sample", os.path.basename(opened_files[i]), "only has", str(round(100.0*info_percentage,2)), "% coverage for", m["ID"])
                    num_samples_low_coverage+=1
                    has_enough_coverage[i] = False
            # Check that this gene has enough information on at least N percent of the samples print it to the filtered output
Severity: Major
Found in codon_from_fasta.py - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

                    for file, m in enumerate(markers):
                    if m["ID"] == current_marker:
                        # eprint("LIB ", opened_files[file], " contains gene ", current_marker)
                        m["seq"] = m["seq"].ljust(longest_seq, "N") # Pad the genes with ? for the lenght of unknowns
                        printed = 0
    Severity: Major
    Found in codon_from_fasta.py - About 45 mins to fix

      Function read_markers has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
      Open

      def read_markers(files, current_marker, markers):
    have_seqs = False
    for counter, file in enumerate(files):
        if (current_marker != markers[counter]["ID"] and current_marker != ""):
            markers[counter]["seq"] = ""
      Severity: Minor
      Found in codon_from_fasta.py - About 45 mins to fix

      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

      Avoid deeply nested control flow statements.
      Open

                      if (m["ID"] != current_marker):
                    num_samples_low_coverage+=1
                    has_enough_coverage[i] = False
                    print("File ", os.path.basename(opened_files[i]), " doesn't contain gene ", current_marker)
                    continue
      Severity: Major
      Found in codon_from_fasta.py - About 45 mins to fix

        Avoid deeply nested control flow statements.
        Open

                        if (len(m["seq"]) > 0):
                    info_percentage = 1.0 - m["seq"].count("N") / float(max_length)
                else:
                    info_percentage = 0.0
                if info_percentage <= min_sequence: # Are all my samples complete? or at least with N percentage of information?
        Severity: Major
        Found in codon_from_fasta.py - About 45 mins to fix
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