Mercurial > repos > jay > pdaug_peptide_ngrams
annotate PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 0:7557b48b2872 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author  jay 

date  Wed, 28 Oct 2020 02:10:12 +0000 
parents  
children  d7e684975db3 
rev  line source 

0
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 import sys 
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2 import itertools 
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3 import pandas as pd 
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4 import random 
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5 import os 
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6 from itertools import permutations 
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7 from random import shuffle 
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8 import argparse, sys 
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9 import pandas as pd 
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10 
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11 
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12 def MutatedPeptides(input_file, index_list, AA, outputFile): 
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13 
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14 
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15 index_list = [int(x) for x in index_list.split(',')] 
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16 out_put = [] 
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17 AA = AA.split(',') 
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18 l = len(index_list) 
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19 
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20 replacements = [x for x in itertools.permutations(AA,l)] 
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21 
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22 
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23 counter = 0 
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24 to_modify = [x for x in input_file] 
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25 
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26 for replacement in replacements: 
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27 for i,index in enumerate(index_list): 
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28 to_modify[index_list[i]1] = replacement[i] 
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29 
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30 counter = counter + 1 
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31 out_put.append("".join(to_modify).upper()) 
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32 
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33 w = open(outputFile, 'w') 
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34 
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35 for i, f in enumerate(out_put): 
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36 
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37 
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38 w.write(">sequence_"+str(i)+'\n') 
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39 w.write(f+'\n') 
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40 
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41 def RandomPeptides(AAs, pep_length, out_pep_num, outputFile): 
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42 
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43 
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44 if int(pep_length) > 20: 
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45 print ("Max peptide lenth 20") 
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46 exit() 
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47 else: 
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48 pass 
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49 
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50 if int(out_pep_num) > 10000: 
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51 print ("Max peptide library 10000") 
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52 exit() 
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53 else: 
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54 pass 
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55 
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56 out_pep_lib = [] 
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57 raw = AAs.split(',') 
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58 
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59 for x in range(int(out_pep_num)): 
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60 un_seq = [] 
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61 for i in range(int(pep_length)): 
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62 un_seq.append(random.choice(raw)) 
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63 out_pep_lib.append("".join(un_seq)) 
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64 
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65 
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66 w = open(outputFile, 'w') 
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67 
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68 
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69 for i, f in enumerate(out_pep_lib): 
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70 
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71 w.write(">sequence_"+str(i)+'\n') 
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72 w.write(f+'\n') 
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73 
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74 def SlidingWindowPeptide(infile, window_size, frag_size, outputFile): 
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75 
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76 
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77 if int(window_size) > 10: 
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78 print ("Max window_size 10") 
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79 exit() 
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80 else: 
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81 pass 
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82 if int(frag_size) > 20: 
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83 print ("Max frag size is 20") 
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84 exit() 
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85 else: 
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86 pass 
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87 
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88 
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89 pep_list = [] 
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90 
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91 f = open(infile) 
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92 
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93 lines = f.readlines() 
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94 
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95 flines = [] 
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96 
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97 for line in lines: 
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98 if '>' in line: 
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99 pass 
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100 else: 
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101 flines.append(line.strip('\n')) 
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102 sequence = "".join(flines) 
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103 
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104 for i in range(int(frag_size)): 
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105 if int(frag_size) == len(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]): 
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106 pep_list.append(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]) 
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107 else: 
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108 break 
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109 
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110 w = open(outputFile, 'w') 
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111 
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112 
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113 for i, f in enumerate(pep_list): 
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114 
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115 w.write(">sequence_"+str(i)+'\n') 
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116 w.write(f+'\n') 
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117 
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118 if __name__=='__main__': 
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119 
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120 parser = argparse.ArgumentParser(description='Deployment tool') 
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121 subparsers = parser.add_subparsers() 
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122 
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123 Mp = subparsers.add_parser('MutatedPeptides') 
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124 Mp.add_argument("s","sequence") 
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125 Mp.add_argument("m","mutation_site_list") 
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126 Mp.add_argument("a","AA_list") 
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127 Mp.add_argument("d", "outputFile", required=None, default='out.fasta', help="Path to out file") 
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128 
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129 Rp = subparsers.add_parser('RandomPeptides') 
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130 Rp.add_argument("a","AA_list") 
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131 Rp.add_argument("l","pep_length") 
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132 Rp.add_argument("o","out_pep_lenght") 
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133 Rp.add_argument("d", "outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'), help="Path to out file") 
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134 
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135 Sp = subparsers.add_parser('SlidingWindowPeptide') 
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136 Sp.add_argument("i","InFile") 
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137 Sp.add_argument("w","winSize") 
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138 Sp.add_argument("s","FragSize") 
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139 Sp.add_argument("d", "outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'), help="Path to out file") 
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140 
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141 args = parser.parse_args() 
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142 
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143 if sys.argv[1] == 'MutatedPeptides': 
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144 MutatedPeptides(args.sequence, args.mutation_site_list, args.AA_list, args.outputFile) 
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145 
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146 elif sys.argv[1] == 'RandomPeptides': 
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147 RandomPeptides(args.AA_list, args.pep_length, args.out_pep_lenght, args.outputFile) 
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148 
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149 elif sys.argv[1] == 'SlidingWindowPeptide': 
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150 SlidingWindowPeptide(args.InFile, args.winSize, args.FragSize, args.outputFile) 
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151 
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152 else: 
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153 print("In Correct Option:") 
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154 