Command line arguments

At any time, you can run SimBLE with the -h or --help flag to see all available arguments (also below):

simble -h

Available arguments:

argument	abbr	default	description
Frequently used
--output	-o	cwd/results	folder for results
--number	-n	1	number of clones to simulate
--processes	-p	1	number of processes (multiprocessing)
--neutral			if provided, runs a neutral simulation
--uniform			if provided, runs a uniform neutral simulation
--migration-rate		0	expected number of cells that leave the germinal center each generation
--samples	-s	[0 200 25]	start, stop, step, to specify sample times for germinal center
Sampling
--other-samples		GC sample times	start, stop, step, to specify "Other" location sample times
--sample-size		50	specify sample size for 'GC' location
--sample-size-other		12	specify sample size for the 'Other' location
Model parameters
--sequence-length		370	length of the sequence to simulate if uniform
--antigen	-a	1000	amount of antigen
--heavy-shm		0.0008908272571108565	expected number of heavy chain mutations each division per site
--light-shm		0.0004923076923076923	expected number of light chain mutations each division per site
--target-mutations-heavy		5	number of amino acid mutations the target heavy chain should have
--target-mutations-light		2	number of amino acid mutations the target light chain should have
--cdr-dist			cdr distribution (constant or exponential)
--cdr-var			cdr variable
--fwr-dist			fwr distribution (constant or exponential)
--fwr-var			fwr variable
--multiplier	-m	2	selection multiplier
Program settings
--quiet	-q		if present, progress bar suppressed
--verbose	-v		if present, verbose information provided
--fasta			if present, also write a fasta file
--config			path to a config file (still in development)
--dev			if present, run in dev mode (not recommended)
--seed			an RNG seed to reproduce specific simulations