MSA Occupancy Calculation

MSA residue coevolution calculation application.

prody.apps.evol_apps.evol_occupancy.evol_occupancy(msa, **kwargs)[source]

Calculate occupancy of rows and columns in MSA.

Parameters:: msa – MSA file

Calculation Options

Parameters:: occaxis (str) – calculate row or column occupancy or both., one of 'row', 'col', 'both', default is 'row'

Output Options

Parameters:

prefix (str) – output filename prefix, default is msa filename with _occupancy suffix
label (str) – index for column based on msa label
numformat (str) – number output format, default is '%12g'