Mercurial > repos > jay > pdaug_word_vector_descriptor
view PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 7:9749ee65cf47 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
---|---|
date | Sun, 09 Jan 2022 04:53:41 +0000 |
parents | 8de738fa6552 |
children |
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("Incorrect option provided: %s" % (sys.argv[1]))