James_Foundry_Tools

biomek

main.py

Top level interface for running backdilutions on Biomek, Equal_OD_dilutions
function takes the output from a plate reader along with a dilution factor,
target OD, target volume & other variables and outputs a csv file
formatted for the biomek's "Transfer from file" step to the "output files"
folder.
Prints a warning in case of a well's OD being too low and drops them from
the experiment  

dilution_calculator.py

Handles calculations related to diluting cultures for main.py

biomek_file_writer.py

general purpose csv writer formatted for the biomek, breaks down transfers
that exceed maximum allowed volume into multiple smaller transfers
automatically, can save to .csv or return csv formatted file to console

flow_cytometry

BD_accuri_parser.py

built off the open source project "FlowIO", reads .fcs files outputted by
the flow cytometer and combines with a strain map to provide easily
graphable and retrievable results
can make multistrain comparing any combination of two measurements, across
an arbitrary number of strains. Can take custom dimensions for side by side
comparison or generate dimensions automatically
Can also retrieve results for a single strain for custom figures.

microtiter

plate_reader_tools.py

contains an array of basic tools used throughout the package including:
	Reading one-shot plate reader outputs
	Reading growth curve data from sunrises 
	Conversion between matrix format and list format
	Conversion between well coordinates (A1-H12) and numbers (1-96)
	Reading strain & treatment maps for other modules

curve_maker.py

Contains higher level tools for analyzing growth curves.
curve_maker accepts a strain map path and a sunrise path and outputs a
long format dataframe with columns as Time, well, name & OD. Ideal for
combining output of multiple experiments into a single dataframe
curve_viewer recieves the output of curve_maker (works better with
raw_time set to False) and produces a line plot using the seaborn.relplot
function. 
	accepts an optional  context variable with “notepad”, “paper”, “talk”,
	and “poster” as options,
	accepts optional: legend_name, and a list of names from the strain map
	to plot
mu_max recieves the output from curve_maker and produces the mu max of each
well, retaining identifier information 
mu_max_plot provides a high level function for plotting mu max results,
designed specifically for multiple strains & treatments with a control
strain