Module synbiopython.lab_automation.tools

Miscellaneous useful functions.

In particular, methods for converting to and from plate coordinates.

View Source

"""Miscellaneous useful functions.

In particular, methods for converting to and from plate coordinates.

"""

import numpy as np

from collections import OrderedDict

from fuzzywuzzy import process

import re

def round_at(value, rounding=None):

    """Round value at the nearest rounding"""

    if rounding is None:

        return value

    else:

        return np.round(value / rounding) * rounding

def dicts_to_columns(dicts):

    return {key: [d[key] for d in dicts] for key in dicts[0]}

def replace_nans_in_dict(dictionary, replace_by="null"):

    for key, value in dictionary.items():

        if isinstance(value, dict):

            replace_nans_in_dict(value, replace_by=replace_by)

        elif value is np.nan:

            dictionary[key] = replace_by

def human_seq_size(n):

    "Return the given sequence as a human friendly 35b, 1.4k, 15k, etc."

    if n < 1000:

        return "%db" % n

    elif n < 10000:

        return "%.1fk" % (n / 1000)

    else:

        return "%dk" % np.round(n / 1000)

unit_factors = {

    prefix + unit: factor

    for unit in "glL"

    for prefix, factor in [("", 1), ("m", 1e-3), ("u", 1e-6), ("n", 1e-9)]

}

volume_values_and_units = sorted(

    [(value, unit) for (unit, value) in unit_factors.items() if unit.endswith("L")]

)

def find_best_volume_unit(vols):

    med = np.median(vols)

    for value, unit in volume_values_and_units:

        if (not unit.endswith("g")) and (med <= 999 * value):

            return unit

    return unit

def human_volume(vol, unit="auto"):

    if unit == "auto":

        unit = find_best_volume_unit([vol])

    vol = np.round(vol / unit_factors[unit], 2)

    if int(vol) == vol:

        return "%d %s" % (vol, unit)

    else:

        return "%s %s" % (("%.02f" % vol).rstrip("0"), unit)

Variables

unit_factors

volume_values_and_units

Functions

dicts_to_columns

def dicts_to_columns(
    dicts
)

View Source

def dicts_to_columns(dicts):

    return {key: [d[key] for d in dicts] for key in dicts[0]}

find_best_volume_unit

def find_best_volume_unit(
    vols
)

View Source

def find_best_volume_unit(vols):

    med = np.median(vols)

    for value, unit in volume_values_and_units:

        if (not unit.endswith("g")) and (med <= 999 * value):

            return unit

    return unit

human_seq_size

def human_seq_size(
    n
)

Return the given sequence as a human friendly 35b, 1.4k, 15k, etc.

View Source

def human_seq_size(n):

    "Return the given sequence as a human friendly 35b, 1.4k, 15k, etc."

    if n < 1000:

        return "%db" % n

    elif n < 10000:

        return "%.1fk" % (n / 1000)

    else:

        return "%dk" % np.round(n / 1000)

human_volume

def human_volume(
    vol,
    unit='auto'
)

View Source

def human_volume(vol, unit="auto"):

    if unit == "auto":

        unit = find_best_volume_unit([vol])

    vol = np.round(vol / unit_factors[unit], 2)

    if int(vol) == vol:

        return "%d %s" % (vol, unit)

    else:

        return "%s %s" % (("%.02f" % vol).rstrip("0"), unit)

replace_nans_in_dict

def replace_nans_in_dict(
    dictionary,
    replace_by='null'
)

View Source

def replace_nans_in_dict(dictionary, replace_by="null"):

    for key, value in dictionary.items():

        if isinstance(value, dict):

            replace_nans_in_dict(value, replace_by=replace_by)

        elif value is np.nan:

            dictionary[key] = replace_by

round_at

def round_at(
    value,
    rounding=None
)

Round value at the nearest rounding

View Source

def round_at(value, rounding=None):

    """Round value at the nearest rounding"""

    if rounding is None:

        return value

    else:

        return np.round(value / rounding) * rounding