RNADiscrepancy

A python library for RNA isodiscrepancy and discrepancy

Quick Start

Install from PyPI:

pip install RNADiscrepancy

Basic usage:

import RNADiscrepancy
path_cif = '../../test/2gdi.cif'
to_find = [('B', '4'), ('B', '78'), #a CWW
           ('B', '51'),('B', '69')  #a TWH
          ]
positions = RNADiscrepancy.get_cif_positions(path_cif, to_find,
                                             author_chain=False,
                                             author_position=False)
first_base_pair = (positions['B', '4'], positions['B', '78'])
second_base_pair = (positions['B', '51'], positions['B', '69'])
print(RNADiscrepancy.isodiscrepancy(first_base_pair, second_base_pair))
#15.130358196427407

Modules discrepancy:

import RNADiscrepancy

path_cif = '2gdi.cif'
to_find = [('B', '4'), ('B', '78'), ('B', '5'), #a CWW + neighbor
           ('B', '51'),('B', '69'), ('B', '52')  #a TWH + neighbor
          ]
positions = RNADiscrepancy.get_cif_positions(path_cif, to_find,
                                             author_chain=False,
                                             author_position=False)
first_module = (positions['B', '4'], positions['B', '78'], positions['B', '5'], positions['B', '51'])
second_module = (positions['B', '51'], positions['B', '69'], positions['B', '52'], positions['B', '4'])
print(RNADiscrepancy.discrepancy(first_module, second_module)
#1.7206629733676666

Modules