pastis.config.get_default_options¶

pastis.config.get_default_options()¶

Returns default options

Here are all the options:

output_namestructure.pdb, str

The name of the PDB file to write. The name of the algorithm used will be appended to this filename. The coordinates of each beads will also be outputted in a text file structure.pdb.txt. For example, running the algorithm MDS with an output_name structure.pdb will yield the files MDS.structure.pdb and MDS.structure.pdb.txt

countsdata/counts.npy, str

The numpy ndarray of counts

organism_structurefiles/budding_yeast_structure

The path to the filename containing the organism structure. This file should contain the lengths of the chromosomes of the organism.

resolution10000, integer

Resolution to which perform the optimization.

chromosomes“1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16”, str

coma separated list of chromosomes onto which the optimization should be performed.

binary_mds“MDS_all”

Path to the binary MDS_all

binary_pm“PM_all”

Path to the binary PM_all

alpha-3., float

Coefficient of the power law used in converting interaction counts to wish distances

beta1., float

Scaling factor of the structure.

seed0, integer

Random seed used when generating the starting point in the optimization.