Mercurial > repos > jay > pdaug_peptide_sequence_analysis

annotate PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 0:e59674e3a391 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
author jay
date Fri, 20 Nov 2020 19:47:44 +0000
parents
children d11a54691a2f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
parents:
diff changeset
1 import sys
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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2 import itertools
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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diff changeset
3 import pandas as pd
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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4 import random
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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diff changeset
5 import os
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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6 from itertools import permutations
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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7 from random import shuffle
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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8 import argparse, sys
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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9 import pandas as pd
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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12 def MutatedPeptides(input_file, index_list, AA, outputFile):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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15 index_list = [int(x) for x in index_list.split(',')]
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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16 out_put = []
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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17 AA = AA.split(',')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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18 l = len(index_list)
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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20 replacements = [x for x in itertools.permutations(AA,l)]
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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23 counter = 0
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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24 to_modify = [x for x in input_file]
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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26 for replacement in replacements:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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diff changeset
27 for i,index in enumerate(index_list):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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28 to_modify[index_list[i]-1] = replacement[i]
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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30 counter = counter + 1
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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31 out_put.append("".join(to_modify).upper())
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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33 w = open(outputFile, 'w')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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35 for i, f in enumerate(out_put):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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37
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38 w.write(">sequence_"+str(i)+'\n')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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39 w.write(f+'\n')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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41 def RandomPeptides(AAs, pep_length, out_pep_num, outputFile):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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42
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43
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44 if int(pep_length) > 20:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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45 print ("Max peptide lenth 20")
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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46 exit()
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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47 else:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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48 pass
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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50 if int(out_pep_num) > 10000:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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51 print ("Max peptide library 10000")
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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52 exit()
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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53 else:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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54 pass
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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55
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56 out_pep_lib = []
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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57 raw = AAs.split(',')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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59 for x in range(int(out_pep_num)):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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60 un_seq = []
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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61 for i in range(int(pep_length)):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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62 un_seq.append(random.choice(raw))
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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63 out_pep_lib.append("".join(un_seq))
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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64
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66 w = open(outputFile, 'w')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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67
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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')
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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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):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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75
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76
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77 if int(window_size) > 10:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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78 print ("Max window_size 10")
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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79 exit()
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80 else:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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81 pass
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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82 if int(frag_size) > 20:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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83 print ("Max frag size is 20")
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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84 exit()
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85 else:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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86 pass
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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87
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88
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89 pep_list = []
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91 f = open(infile)
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93 lines = f.readlines()
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95 flines = []
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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96
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97 for line in lines:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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98 if '>' in line:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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99 pass
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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100 else:
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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101 flines.append(line.strip('\n'))
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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102 sequence = "".join(flines)
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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103
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104 for i in range(int(frag_size)):
e59674e3a391 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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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