parser.py

import numpy as py

sequence_bps = input("Enter Sequence bps file: ")
IRE_bps = input("Enter IRE bps file: ")
shift = input("Enter position of IRE: ")

IRE = {(1,34): 0.9963,
       (2, 33): 0.9980,
       (3, 32): 0.9982,
       (4, 31): 0.9869, 
       (6, 28): 0.4434,
       (5, 30): 0.9869,
       (7, 29): 0.5971, 
       (8, 26): 0.4558,
       (9, 28): 0.8125,
       (10, 27): 0.8200,
       (11, 26): 0.8224, 
       (12, 21): 0.5144,
       (13, 20): 0.4505,
       (14, 23): 0.8479, 
       (15, 22): 0.8481, 
       (16, 21): 0.6457,
       (17, 21): 0.0281,
       (18, 25): 0.0031, 
       (19, 26): 0.0042,
       (20, 28): 0.0114, 
       (21, 27): 0.0123,
       (22, 29): 0.0448, 
       (23, 29): 0.0123,
       (24, 33): 0.0021,
       (25, 31): 0.0050,
       (26, 35): 0.0205,
       (27, 34): 0.0219,
       (28, 33): 0.0194 
       }
IRE2 = {(1, 28): 0.565990427,
        (2, 27): 0.834558937,
        (3, 26): 0.852239847,
        (4, 25): 0.845962168,
        (5, 25): 0.522992586,
        (6, 24): 0.791836762,
        (7, 22): 0.067498629,
        (8, 23): 0.984339729,
        (9, 22): 0.992869075,
        (10, 21): 0.996729211,
        (11, 20): 0.996517286,
        (12, 19): 0.993328370,
        (13, 17): 0.036324522,
        (14, 20): 0.005116260,
        (15, 24): 0.004863894,
        (16, 23): 0.004853327,
        }

"""
Function to parse through the IRE bps file to compare with sequence
"""
def IRE_Parse(file):


"""
Function to parse through the sequence bps files and store all of the bps in dictionary
file: Path of the file
"""
def SequenceParse(file):
    array = py.loadtxt(file)
    Sequence_bps = {}
    for index in range(len(array)):
        i = array[index][0]
        j = array[index][1]
        temp = [i,j]
        Sequence_bps[tuple(temp)] = array[index][2]
    return Sequence_bps


"""
Function to check and see the bps of the IRE inserted into the sequence
IRE_bps: IRE stored as a dictionary.
Sequence_bps: Sequence Candidate stored as a dictionary.
Offset: Index of where the IRE was inserted, Int
"""
def BPS_Comp(IRE_bps, Sequence_bps, Offset):
    results = {}
    for sequence in IRE_bps:
       key = (sequence[0] + shift, sequence[1] + shift)
       if key in Sequence_bps:
           results[key] = Sequence_bps[key]
    return results

"""
Function to Write to the file
results_dictionary: Dictionary generated by BPS_Comp
"""
def Write_File(results_dictionary):
    file = open('results.txt', 'w')
    file.write("i j Sqrt(Prob(i,j))" + "\n")
    BPS = results.items()
    for result_bps in BPS:
        file.write(" ".join(map(str, result_bps)) + "\n")
    file.close()
    
Candidate = SequenceParse(sequence_bps)
results = BPS_Comp(IRE2, Candidate, 0)
Write_File(results)