Mercurial > repos > jay > pdaug_peptide_core_functions
view PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 6:6822d43a5f84 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:17:01 +0000 |
parents | 48eedcb9bfa7 |
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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]))