Documentation for BFB Simulations
Lena Krockenberger 8/17/22

BFBSimulator Parameters:
usage: BFBSimulator.py num_cycles chr_str start_pos end_pos genome
                       [-h] [-l L] [-ld {expo,simple}] [-df DF] [-dl DL]
                       [-dd {expo,simple}] [-xf XF] [-xl XL]
                       [-xd {expo,simple}] [-o O] [-rev] [-p P] [-b B]
                       [-bl BL]
                      
positional arguments:
  num_cycles		Number of BFB cycles to simulate
  chr_str		Name of the chromosome to simulate BFB on
  start_pos	Start position of the genome section to simulate BFB on (0-indexed, inclusive)
end_pos	End position of the genome section to simulate BFB on (0-indexed, exclusive)
  genome		FASTA file of the genome

optional arguments:
  -h, --help		show this help message and exit
  -l L			Mean length of the BFB segments (default 600000)
  -ld {expo,simple}	Distribution of the BFB segment lengths. "expo"(default): exponential; "simple": all use the same value as the mean length
  -df DF		Probability for each BFB segment to have one deletion (default 0.1)
  -dl DL		Mean deletion length of the BFB segments (default 50000)
  -dd {expo,simple}	Distribution of the BFB segment deletion lengths. "expo"(default): exponential; "simple": all use the same value as the mean deletion length
  -xf XF		Probability for each BFB segment to have one duplication (default 0.1)
  -xl XL		Mean duplication length of the BFB segments (default 10000)
  -xd {expo,simple}	Distribution of the BFB segment duplication lengths. "expo"(default): exponential; "simple": all use the same value as the mean duplication length
  -o O			Prefix of the output files
  -rev	If this option is specified, BFB simulation will append string to the 5' side of the region
-p P	For each segment, the probability that deletion is simulated before duplication (default 0.5)
-b B	Probability that there is a deletion when appending duplicated segment. (default 0.1)
  -bl BL		Length of deletion when appending duplicated segment. (default 50000)

Simple Case - (low segment count, low copy number, no indels, no end deletions):
Ex with ERBB2: 
  num_cycles		5
  chr_str		17
  start_pos	33600000
end_pos	36600000 (add 3,000,000 to start_pos)
  genome		new_hg38.fa (fasta file name)

  -l L			default
  -ld {expo,simple}	default
  -df DF		0 (don’t want deletions)
  -dl DL		0 (don’t want deletions)
  -dd {expo,simple}	simple
  -xf XF		0 (don’t want duplications)
  -xl XL		0 (don’t want duplications)
  -xd {expo,simple}	simple
  -o O			outputs/simple/ERBB2 (can add file paths to output prefixes)
  -rev	defualt
-p P	0 (no deletions)
-b B	0 (no end deletions)
  -bl BL		0 (no end deletions)

Final command:
./BFBSimulator.py 5 17 33600000 36600000 new_hg38.fa -df 0 -dl 0 -dd simple -xf 0 -xl 0 -xd simple -o outputs/simple/ERBB2 -p 0 -b 0 -bl 0

Intermediate Case - (regular segment number and copy number, end deletions, no indels):
Ex with ERBB2:
  num_cycles		10 (larger number of cycles increases copy number)
  chr_str		17
  start_pos	33600000
end_pos	39600000 (add 6,000,000 to start_pos)
  genome		new_hg38.fa (fasta file name)

  -l L			default
  -ld {expo,simple}	default
  -df DF		0 (don’t want deletions)
  -dl DL		0 (don’t want deletions)
  -dd {expo,simple}	simple
  -xf XF		0 (don’t want duplications)
  -xl XL		0 (don’t want duplications)
  -xd {expo,simple}	simple
  -o O			outputs/end_Deletions/ERBB2 (can add file paths to output prefixes)
  -rev	default
-p P	0 (no deletions)
-b B	1 (always simulate end deletion when appending new segment)
  -bl BL		50000

Final Command:
./BFBSimulator.py 10 17 33600000 39600000 new_hg38.fa -df 0 -dl 0 -dd simple -xf 0 -xl 0 -xd simple -o outputs/end_Deletions/ERBB2 -p 0 -b 1 -bl 50000

Complex Case - (regular segment number and copy number, end deletions, indels):
Ex with ERBB2:
  num_cycles		10
  chr_str		17
  start_pos	33600000
end_pos	39600000 (add 6,000,000 to start_pos)
  genome		new_hg38.fa (fasta file name)

  -l L			default
  -ld {expo,simple}	default
  -df DF		default
  -dl DL		default
  -dd {expo,simple}	default
  -xf XF		default
  -xl XL		default
  -xd {expo,simple}	default
  -o O			outputs/complex/ERBB2 (can add file paths to output prefixes)
  -rev	default
-p P	default
-b B	default
  -bl BL		default

Final Command:
./BFBSimulator.py 10 17 33600000 39600000 new_hg38.fa -o outputs/complex/ERBB2 

Script for Running Simulations – simulations.sh
Usage: ./simulations.sh
Parameters: none
When running simulations.sh, 5 different oncogenes are simulated through each of the 3 cases (simple, intermediate, and complex). The 5 genes include: ERBB2, MYC, EGFR, BCL2, and PIK3CA. 
Simple case: 1 simulation per gene with the same parameters for “simple case” detailed above (5 simulations total)
Intermediate case: 3 simulations per gene with the same parameters for “intermediate case” detailed above (15 simulations total)
Complex case: 2 simulations per gene with the same parameters for “complex case” detailed above (10 simulations total)
In total, simulations.sh runs 30 simulations of varying complexity. 
To modify details of the simulations, the script must be edited.