csv_string_to_codons_dict() raises ValueError when reading a custom codon table - proposed workaround

[lcareypando]

I've used pandas df.to_csv() to write out a custom codon table
codon_table.csv

reading this table gives an error when reading the last line. adding the length check ( if len(line)>3:) solves this problem.

def csv_string_to_codons_dict(csv_string):
    """Transform a CSV string of a codon table to a dict."""
    result = {}
    for line in csv_string.split("\n")[1:]:
        if len(line)>3: # new check
            aa, codon, freq = line.split(",")
            if aa not in result:
                result[aa] = {}
            result[aa][codon] = float(freq)
    return result

[veghp]

Thank you. The issue seems to arise when the csv is terminated with an empty line, which is common and probably a preferable format as well. I'll address this later this month together with DNA Chisel; the function may be replaced with something from the csv package. But in any case perhaps it's better to remove all trailing newlines from the string.

[lcareypando]

Hi Peter,
Thanks so much for addressing this!
best wishes, and thanks for the great packages.