Mercurial > repos > jay > pdaug_sequence_based_peptide_generation
view PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 2:cda6264267f7 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 8b18552f6d2b2261efebe1075ff4c18a295b94dd"
author | jay |
---|---|
date | Tue, 29 Dec 2020 19:00:54 +0000 |
parents | 93f7668caa55 |
children | 4a58c72769df |
line wrap: on
line source
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("In Correct Option:")