bio-aid

Package containing tools for genetic and genomic analysis in python in the Malkova Lab.

Includes a collection of functions from my other repositories for easier development of new projects

Installation

The latest release of the bio-aid package can be installed through pip (https://pypi.org/project/bio-aid/) by using the following command:

pip install --upgrade bio-aid

bio-aid currently consists of a base module and three sub modules: deepSeqInsH, MMBSearchTK, varaintTK.

To easily import and access the functions inside of the bio-aid package, include the following in your python scripts:

import BioAid as ba

Diluter

This simple program calculates volumes for serial dilutions of yeast cultures, that can subsequently be used for colony plating. To access diluter, in python type:

ba.dilute()

and follow instructions on the prompt.

PopDub

Utillity for finding population doublings for the Telomere project.

To get results you will need to adjust initial and final population densities:

• set initial_population to the cell count on the beginning of your experiment used as inoculum.

• set final_population_ml to the /ml cell count at the time you want to measure population doublings.

• set final_culture_volume to the volume of your final culture.

Finally, run the function:

ba.calculatePopulationDoublings(initial_population, final_population_ml, final_culture_volume)

RepeatSearch

This tool allows for search of imperfect repeats (Inverted and Direct) in a DNA sequence. Diagram explaining the parameters can be found in the stand-alone repo here

# Set RepeatSearch parameters

sequence="ACGT"           # This is your nucleotide sequence to be searched for repeats

inverted=True             # Sets search to Inverted (True) vs Direct (False) repeats

min_query_length=5        # Sets min length of a query sequence

max_query_length=30       # Sets max length of a query sequence

min_spacer=0              # Set min distance between query and the repeat

window_size=804           # Sets window size within which the search is confined

imperfect_homology=True   # Set True/False, to search for imperfect/perfect homologies.

min_homology=0.8          # Sets minimum homology treshold (a fraction) when imperfect_homology=True,  

fixed_errors=1            # Sets maximum number of errors (del/sub) when imperfect_homology=True (set to False or to an integer)



# To run the Search execute the following:

results_dictionary = ba.searchSequenceForRepeats(

                         sequence=sequence,

                         min_query_length=min_query_length,

                         max_query_length=max_query_length,

                         min_spacer=min_spacer,

                         window_size=window_size,

                         imperfect_homology=imperfect_homology,

                         min_homology=min_homology,

                         fixed_errors=fixed_errors,

                         inverted=inverted)