Source code for bandwagon.ladders

"""Definition of custom ladders for BandWagon."""

from .BandsPattern import Band, BandsPattern

try:
    import pandas

    PANDAS_AVAILABLE = True
except ImportError:
    PANDAS_AVAILABLE = False


def custom_ladder(label, bands_migrations):
    """Generate a BandsPattern object meant to be used as a ladder.

    By default the ladder is dark red on a white background.
    """
    migrations = bands_migrations.values()
    min_migrations = min(migrations)
    ladder_span = max(migrations) - min_migrations
    if min_migrations < 0.1 * ladder_span:
        shift = 0
    else:
        shift = min_migrations - 0.1 * ladder_span
    return BandsPattern(
        [
            Band(size, migration_distance=migration - shift, band_color="#8B0000",)
            for (size, migration) in bands_migrations.items()
        ],
        background_color="#ffffff",
        label=label,
    )


def ladder_from_aati_fa_calibration_table(filepath=None, dataframe=None, label=None):
    """Extract a BandPattern from an AATI Fragment Analyzer calibration file.

    The calibration table is generated after each run from the migration
    times of the ladder and is generally in a file called something like
    ``2016 11 08 16H 57M Size Calibration.csv``.

    This method requires Pandas installed.

    Parameters
    ----------

    filepath
      Path to the calibration file.

    dataframe
      Pandas dataframe obtained by reading the file, can be provided instead of
      ``filepath``.

    label
      Label that will be given to the ladder when plotted.
    """
    if not PANDAS_AVAILABLE:
        raise ImportError("The Pandas library is required for this method.")

    if filepath is not None:
        dataframe = pandas.read_csv(filepath)

    dataframe["migration"] = (
        1.1 * dataframe["Time (sec)"].max() - dataframe["Time (sec)"]
    )

    return custom_ladder(
        label,
        {row["Ladder Size (bp)"]: row["migration"] for i, row in dataframe.iterrows()},
    )


LADDER_100_to_4k = custom_ladder(
    "100-4k",
    {
        100: 205,
        200: 186,
        300: 171,
        400: 158,
        500: 149,
        650: 139,
        850: 128,
        1000: 121,
        1650: 100,
        2000: 90,
        3000: 73,
        4000: 65,
    },
)