Mercurial > repos > jay > pdaug_sequence_similarity_network
annotate PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py @ 5:9012052b1dad draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:00:07 +0000 |
parents | e650de82bcc7 |
children | 1fafae68b9bb |
rev | line source |
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e650de82bcc7
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 from modlamp.core import BaseSequence |
e650de82bcc7
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2 import pandas as pd |
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3 import os, sys |
e650de82bcc7
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4 import argparse |
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5 |
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6 |
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7 parser = argparse.ArgumentParser(description='Deployment tool') |
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8 subparsers = parser.add_subparsers() |
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9 |
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10 mutateAA = subparsers.add_parser('mutateAA') |
e650de82bcc7
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11 mutateAA.add_argument("-I","--InFile", required=True, default=None, help="Input fasta sequence") |
e650de82bcc7
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12 mutateAA.add_argument("-N","--nr", required=True, default=None, help="Number of mutations to perform per sequence") |
e650de82bcc7
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13 mutateAA.add_argument("-P","--Prob", required=True, default=None, help="Probability of mutating a sequence") |
e650de82bcc7
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14 mutateAA.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Mutated output fasta") |
e650de82bcc7
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15 |
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16 filterduplicates = subparsers.add_parser('filterduplicates') |
e650de82bcc7
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17 filterduplicates.add_argument("-I","--InFile", required=True, default=None, help="Input file") |
e650de82bcc7
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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18 filterduplicates.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") |
e650de82bcc7
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19 |
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20 |
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21 keepnaturalaa = subparsers.add_parser('keepnaturalaa') |
e650de82bcc7
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22 keepnaturalaa.add_argument("-I","--InFile", required=True, default=None, help="Inputt file") |
e650de82bcc7
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23 keepnaturalaa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") |
e650de82bcc7
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24 |
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25 |
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26 filteraa = subparsers.add_parser('filteraa') |
e650de82bcc7
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27 filteraa.add_argument("-I","--InFile", required=True, default=None, help="Input file") |
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28 filteraa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") |
e650de82bcc7
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29 filteraa.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide") |
e650de82bcc7
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30 |
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31 args = parser.parse_args() |
e650de82bcc7
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32 |
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33 if sys.argv[1] == 'mutateAA': |
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34 |
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35 Pep = [] |
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36 Index = [] |
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37 |
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38 f = open(args.InFile) |
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39 lines = f.readlines() |
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40 |
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41 for line in lines: |
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42 if '>' in line: |
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43 line = line.strip('\n') |
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44 line = line.strip('\r') |
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45 Index.append(line) |
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46 else: |
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47 line = line.strip('\n') |
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48 line = line.strip('\r') |
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49 Pep.append(line) |
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50 |
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51 b = BaseSequence(len(Pep)) |
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52 b.sequences = Pep |
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53 b.mutate_AA(int(args.nr), float(args.Prob)) |
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54 OutPep = b.sequences |
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55 |
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56 OutFasta = open(args.FastOut, 'w') |
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57 |
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58 for i,O in enumerate(OutPep): |
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59 |
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60 OutFasta.write(Index[i]+'\n') |
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61 OutFasta.write(O+'\n') |
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62 |
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63 |
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64 elif sys.argv[1] == 'filterduplicates': |
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65 |
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66 Pep = [] |
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67 Index = [] |
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68 |
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69 f = open(args.InFile) |
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70 lines = f.readlines() |
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71 |
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72 for line in lines: |
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73 if '>' in line: |
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74 line = line.strip('\n') |
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75 line = line.strip('\r') |
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76 Index.append(line) |
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77 else: |
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78 line = line.strip('\n') |
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79 line = line.strip('\r') |
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80 Pep.append(line) |
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81 |
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82 b = BaseSequence(len(Pep)) |
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83 |
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84 b.sequences = Pep |
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85 |
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86 b.filter_duplicates() |
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87 |
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88 OutPep = b.sequences |
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89 |
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90 OutFasta = open(args.FastOut, 'w') |
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91 |
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92 for i,O in enumerate(OutPep): |
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93 |
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94 OutFasta.write(Index[i]+'\n') |
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95 OutFasta.write(O+'\n') |
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96 |
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97 |
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98 elif sys.argv[1] == 'keepnaturalaa': |
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99 |
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100 Pep = [] |
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101 Index = [] |
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102 |
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103 f = open(args.InFile) |
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104 lines = f.readlines() |
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105 |
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106 for line in lines: |
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107 if '>' in line: |
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108 line = line.strip('\n') |
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109 line = line.strip('\r') |
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110 Index.append(line) |
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111 else: |
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112 line = line.strip('\n') |
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113 line = line.strip('\r') |
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114 Pep.append(line) |
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115 |
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116 b = BaseSequence(len(Pep)) |
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117 b.sequences = Pep |
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118 b.keep_natural_aa() |
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119 |
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120 OutFasta = open(args.FastOut, 'w') |
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121 |
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122 OutPep = b.sequences |
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123 |
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124 for i,O in enumerate(OutPep): |
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125 |
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126 OutFasta.write(Index[i]+'\n') |
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127 OutFasta.write(O+'\n') |
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128 |
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129 |
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130 elif sys.argv[1] == 'filteraa': |
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131 |
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132 Pep = [] |
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133 Index = [] |
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134 |
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135 f = open(args.InFile) |
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136 lines = f.readlines() |
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137 |
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138 for line in lines: |
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139 if '>' in line: |
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140 line = line.strip('\n') |
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141 line = line.strip('\r') |
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142 Index.append(line) |
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143 else: |
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144 line = line.strip('\n') |
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145 line = line.strip('\r') |
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146 Pep.append(line) |
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147 |
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148 |
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149 b = BaseSequence(len(Pep)) |
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150 b.sequences = Pep |
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151 |
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152 FilterAA = args.FilterAA.split(',') |
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153 |
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154 b.filter_aa(FilterAA) |
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155 |
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156 OutPep = b.sequences |
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157 |
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158 OutFasta = open(args.FastOut, 'w') |
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159 |
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160 for i,O in enumerate(OutPep): |
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161 |
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162 OutFasta.write(Index[i]+'\n') |
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163 OutFasta.write(O+'\n') |
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164 |
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165 |
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166 |
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167 |
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168 |