annotate PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 4:908b8ce0326c draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"

import sys
import itertools
import pandas as pd
import random
import os
from itertools import permutations
from random import shuffle
import argparse, sys
import pandas as pd


def MutatedPeptides(input_file, index_list, AA, outputFile):


    index_list = [int(x) for x in index_list.split(',')]
    out_put = []
    AA = AA.split(',')
    l = len(index_list)

    replacements = [x for x in itertools.permutations(AA,l)]


    counter = 0
    to_modify = [x for x in input_file]

    for replacement in replacements:
        for i,index in enumerate(index_list):
            to_modify[index_list[i]-1] = replacement[i]

        counter = counter + 1
        out_put.append("".join(to_modify).upper())

    w = open(outputFile, 'w')

    for i, f in enumerate(out_put):


        w.write(">sequence_"+str(i)+'\n')
        w.write(f+'\n')

def RandomPeptides(AAs, pep_length, out_pep_num, outputFile):


    if int(pep_length) > 20:
        print ("Max peptide lenth 20")
        exit()
    else:
        pass

    if int(out_pep_num) > 10000:
        print ("Max peptide library 10000")
        exit()
    else:
        pass

    out_pep_lib = []
    raw = AAs.split(',')

    for x in range(int(out_pep_num)):
        un_seq = []
        for i in range(int(pep_length)):
            un_seq.append(random.choice(raw))
        out_pep_lib.append("".join(un_seq))


    w = open(outputFile, 'w')


    for i, f in enumerate(out_pep_lib):

        w.write(">sequence_"+str(i)+'\n')
        w.write(f+'\n')

def SlidingWindowPeptide(infile, window_size, frag_size, outputFile):


    if int(window_size) > 10:
        print ("Max window_size 10")
        exit()
    else:
        pass
    if int(frag_size) >  20:
        print ("Max frag size is 20")
        exit()
    else:
        pass


    pep_list = []

    f = open(infile)

    lines = f.readlines()

    flines = []

    for line in lines:
        if '>' in line:
            pass
        else:
            flines.append(line.strip('\n'))
    sequence = "".join(flines)

    for i in range(int(frag_size)):
        if int(frag_size) == len(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]):
            pep_list.append(sequence[i*int(window_size):i*int(window_size)+int(frag_size)])
        else:
            break

    w = open(outputFile, 'w')


    for i, f in enumerate(pep_list):

        w.write(">sequence_"+str(i)+'\n')
        w.write(f+'\n')

if __name__=='__main__':

    parser = argparse.ArgumentParser(description='Deployment tool')
    subparsers = parser.add_subparsers()

    Mp = subparsers.add_parser('MutatedPeptides')
    Mp.add_argument("-s","--sequence")
    Mp.add_argument("-m","--mutation_site_list")
    Mp.add_argument("-a","--AA_list")
    Mp.add_argument("-d", "--outputFile", required=None, default='out.fasta',   help="Path to out file")

    Rp = subparsers.add_parser('RandomPeptides')
    Rp.add_argument("-a","--AA_list")
    Rp.add_argument("-l","--pep_length")
    Rp.add_argument("-o","--out_pep_lenght")
    Rp.add_argument("-d", "--outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'),   help="Path to out file")

    Sp = subparsers.add_parser('SlidingWindowPeptide')
    Sp.add_argument("-i","--InFile")
    Sp.add_argument("-w","--winSize")
    Sp.add_argument("-s","--FragSize")
    Sp.add_argument("-d", "--outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'),   help="Path to out file")

    args = parser.parse_args()

    if sys.argv[1] == 'MutatedPeptides':
        MutatedPeptides(args.sequence, args.mutation_site_list, args.AA_list, args.outputFile)

    elif sys.argv[1] == 'RandomPeptides':
        RandomPeptides(args.AA_list, args.pep_length, args.out_pep_lenght, args.outputFile)

    elif sys.argv[1] == 'SlidingWindowPeptide':
        SlidingWindowPeptide(args.InFile, args.winSize, args.FragSize, args.outputFile)

    else:
        print("Incorrect option provided: %s" % (sys.argv[1]))