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config.yaml
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descriptions:
general:
input: Folder containing input scHi-C contacts in csv format. If 'None' simulated
scHi-C maps are going to be used.
output: Output folder for storing simulation results
n: Number of scHi-C frames to be generated. Only applicable if input==None.
m: Size of scHi-C frames to be generated (number of beads). Only applicable if
input==None.
n_contacts: Number of contacts to be drawn from each in silico structure. Only
applicable if input==None.
artificial_structure: 'Index of the in silico structure to be generated as simulation
input.
Only applicable if input==None. Available structure indices: TODO'
genome: 'Genome assembly of the input data. Currently supported assemblies: hg19,
hg38, mm10, GRCm39.'
chrom: Chromosome to be modeled. The input files are going to be filtered for
intra-chromosomal contacts within this chromosome.
simulation:
platform: TODO
resolutions: Resolutions to be used for hierarchical modeling. Expected to be
in the form of comma separated integer of float numbers in the units of Mb.
N_steps: TODO
burnin: TODO
MC_step: TODO
sim_step: TODO
forcefield:
ev_formula: 'Type of the Excluded Volume (EV) repulsion. Available types: TODO'
ev_min_dist: Excluded Volume (EV) minimal distance
ev_coef: Excluded Volume (EV) force coefficient
ev_coef_evol: 'Enable or disable the changing EV coefficient value.
If True the coefficient will start as 0 at the beginning of the simulation and
reach ev_coef at the end.
If False the coefficient will have stable value of ev_coef.'
bb_formula: 'Type of the Backbone (BB) potential. Available types: TODO'
bb_opt_dist: Backbone (BB) optimal distance
bb_lin_thresh: 'Backbone (BB) distance after which the potential grows linearly.
Must be strictly greater than bb_opt_dist.
Only applicable if bb_formula is TODO'
bb_coef: Backbone (BB) force coefficient
bb_coef_evol: 'Enable or disable the changing BB coefficient value.
If True the coefficient will start as 0 at the beginning of the simulation and
reach bb_coef at the end.
If False the coefficient will have stable value of bb_coef.'
sc_formula: 'Type of the Single cell contact (SC) potential. Available types:
TODO'
sc_opt_dist: Single cell contact (SC) optimal distance
sc_lin_thresh: 'Single cell contact (SC) distance after which the potential grows
linearly.
Must be strictly greater than sc_opt_dist.
Only applicable if bb_formula is TODO'
sc_coef: Single cell contact (SC) force coefficient
sc_coef_evol: 'Enable or disable the changing SC coefficient value.
If True the coefficient will start as 0 at the beginning of the simulation and
reach sc_coef at the end.
If False the coefficient will have stable value of sc_coef.'
ff_formula: 'Type of the Frame force (FF) potential. Available types: TODO'
ff_opt_dist: Frame force (FF) optimal distance
ff_lin_thresh: 'Frame force (FF) distance after which the potential grows linearly.
Must be strictly greater than ff_opt_dist.
Only applicable if bb_formula is TODO'
ff_coef: Frame force (FF) force coefficient
ff_coef_evol: 'Enable or disable the changing FF coefficient value.
If True the coefficient will start as 0 at the beginning of the simulation and
reach ff_coef at the end.
If False the coefficient will have stable value of ff_coef.'
general:
input: examples/example1_cell_cycle
output: results
n: 10
m: 100
n_contacts: 50
artificial_structure: 1
genome: mm10
chrom: chr1
simulation:
platform: OpenCL
resolutions: 5,2
N_steps: 100
burnin: 5
MC_step: 1
sim_step: 20
forcefield:
ev_formula: harmonic
ev_min_dist: 1.0
ev_coef: 1000.0
ev_coef_evol: false
bb_formula: harmonic
bb_opt_dist: 1.0
bb_lin_thresh: 2.0
bb_coef: 1000.0
bb_coef_evol: false
sc_formula: harmonic
sc_opt_dist: 1.0
sc_lin_thresh: 2.0
sc_coef: 1000.0
sc_coef_evol: false
ff_formula: harmonic
ff_opt_dist: 1.0
ff_lin_thresh: 2.0
ff_coef: 1000.0
ff_coef_evol: false