INNER CODE UNIT · Python

frac_gc

open2c/bioframe · src/bioframe/extras.py:269

def frac_gc(df, fasta_records, mapped_only=True, return_input=True):
    """
    Calculate the fraction of GC basepairs for each interval in a dataframe.

    Parameters
    ----------
    df : pandas.DataFrame
        A sets of genomic intervals stored as a DataFrame.

    fasta_records : OrderedDict
        Dictionary of chromosome names to sequence records.
        Created by: bioframe.load_fasta('/path/to/fasta.fa')

    mapped_only: bool
        if True, ignore 'N' in the fasta_records for calculation.
        if True and there are no mapped base-pairs in an interval, return np.nan.

    return_input: bool

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