constants

Constants for electropherogram analysis

Author: Anja Hess

Date: 2023-AUG-06

Attributes

DISTANCE	Minimum required distance of two peaks to be discriminated.
MIN_PEAK_HEIGHT_FACTOR	Factor by which to multiply the maximum peak height to set the minimum peak height to be detected.
MAX_PEAK_WIDTH_FACTOR	Fraction of entire gel length to set the maximum accepted peak width - ONLY FOR THE LADDER, not for sample peaks
PEAK_PROMINENCE	Tuple, minimum peak prominence
INTERPOLATE_FUNCTION	Function to interpolate missing base pair values based on user-annotated values
BACKGROUND_SUBSTRACTION_STATS
HALO_FACTOR
ARTIFICIAL_MAX
ACCEPTED_FORMATS	Possible input formats
LOGFILE_NAME
YCOL	Standardized y axis name
XCOL	Standardized x axis name
YLABEL	Standardized y labe name
XLABEL	Standardized x label name
XLABEL_PRIOR_SIZE	Standardized x label name before interpolation
ALTERNATE_FORMAT	The second format apart from .pdf to save images to
PALETTE	Standardized color palette
LADDER_DICT	Dictionary with standardized peak size options (beta)
NUC_DICT
NUC_DICT_250	Dictionary with standardized peak size options (beta)

Module Contents

constants.DISTANCE = 20

Minimum required distance of two peaks to be discriminated.

constants.MIN_PEAK_HEIGHT_FACTOR = 0.2

Factor by which to multiply the maximum peak height to set the minimum peak height to be detected.

constants.MAX_PEAK_WIDTH_FACTOR = 1

Fraction of entire gel length to set the maximum accepted peak width - ONLY FOR THE LADDER, not for sample peaks

constants.PEAK_PROMINENCE = (0.2, None)

Tuple, minimum peak prominence

constants.INTERPOLATE_FUNCTION = 'linear'

Function to interpolate missing base pair values based on user-annotated values

constants.BACKGROUND_SUBSTRACTION_STATS = 0.1

constants.HALO_FACTOR = 0

constants.ARTIFICIAL_MAX = 100000

constants.ACCEPTED_FORMATS = ['.csv', '.png', '.jpeg', '.jpg']

Possible input formats

constants.LOGFILE_NAME = 'dnavi.log'

constants.YCOL = 'normalized_fluorescent_units'

Standardized y axis name

constants.XCOL = 'bp_pos'

Standardized x axis name

constants.YLABEL = 'Sample Intensity [Normalized FU]'

Standardized y labe name

constants.XLABEL = 'Size [bp]'

Standardized x label name

constants.XLABEL_PRIOR_SIZE = 'Size'

Standardized x label name before interpolation

constants.ALTERNATE_FORMAT = 'svg'

The second format apart from .pdf to save images to

constants.PALETTE = ['cadetblue', '#fbc27b', '#d56763', 'darkgrey', '#a7c6c9', '#2d435b', '#d56763', 'darkred',...

Standardized color palette

constants.LADDER_DICT

Dictionary with standardized peak size options (beta)

constants.NUC_DICT

constants.NUC_DICT_250

Dictionary with standardized peak size options (beta)