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-aidbio-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 baDiluter
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_populationto the cell count on the beginning of your experiment used as inoculum. - set
final_population_mlto the /ml cell count at the time you want to measure population doublings. - set
final_culture_volumeto 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)
