flowcraft/templates/process_viral_assembly.py
def _get_gc_content(sequence, length):
        """Get GC content and proportions.

        Parameters
        ----------
        sequence : str
            The complete sequence of the contig.
        length : int
            The length of the sequence contig.

        Returns
        -------
        x : dict
            Dictionary with the at/gc/n counts and proportions

        """

        # Get AT/GC/N counts
        at = sum(map(sequence.count, ["A", "T"]))
        gc = sum(map(sequence.count, ["G", "C"]))
        n = length - (at + gc)

        # Get AT/GC/N proportions
        at_prop = at / length
        gc_prop = gc / length
        n_prop = n / length

        return {"at": at, "gc": gc, "n": n,
                "at_prop": at_prop, "gc_prop": gc_prop, "n_prop": n_prop}
def _get_gc_content(sequence, length):
        """Get GC content and proportions.

        Parameters
        ----------
        sequence : str
            The complete sequence of the contig.
        length : int
            The length of the sequence contig.

        Returns
        -------
        x : dict
            Dictionary with the at/gc/n counts and proportions

        """

        # Get AT/GC/N counts
        at = sum(map(sequence.count, ["A", "T"]))
        gc = sum(map(sequence.count, ["G", "C"]))
        n = length - (at + gc)

        # Get AT/GC/N proportions
        at_prop = at / length
        gc_prop = gc / length
        n_prop = n / length

        return {"at": at, "gc": gc, "n": n,
                "at_prop": at_prop, "gc_prop": gc_prop, "n_prop": n_prop}
Get GC content and proportions.

        Parameters
        ----------
        sequence : str
            The complete sequence of the contig.
        length : int
            The length of the sequence contig.

        Returns
        -------
        x : dict
            Dictionary with the at/gc/n counts and proportions