Mercurial > repos > jay > pdaug_peptide_core_descriptors

annotate PDAUG_AA_Property_Based_Peptide_Descriptor/PDAUG_AA_Property_Based_Peptide_Descriptor.py @ 0:0fc091fb7e8f draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:12:57 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 from modlamp.descriptors import *
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2 import pandas as pd
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3 import os
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7 def PepFasta(InFile):
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8 file = open(InFile)
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9 lines = file.readlines()
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11 Index = []
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12 Peptides = []
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14 for line in lines:
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15 if '>' in line:
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16 Index.append(line.strip('\n'))
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17 else:
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18 Peptides.append(line.strip('\n'))
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20 return Peptides, Index
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23 def AutoCorrCal(InFile, window, ScaleName, OutFile):
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25 list_pep_name,_ = PepFasta(InFile)
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27 AMP = PeptideDescriptor(list_pep_name, ScaleName)
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28 AMP.calculate_autocorr(int(window))
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29 df = AMP.descriptor
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31 columns = ["CroAut_"+str(i) for i in range(len(df[0]))]
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32 df = pd.DataFrame(df, columns=columns)
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33 df.to_csv(OutFile, index=False,sep='\t')
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35 def CrossCorrCal(InFile, window, ScaleName, OutFile):
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37 list_pep_name,_ = PepFasta(InFile)
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39 AMP = PeptideDescriptor(list_pep_name, ScaleName)
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40 AMP.calculate_crosscorr(int(window))
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41 df = AMP.descriptor
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43 columns = ["CroCor_"+str(i) for i in range(len(df[0]))]
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44 df = pd.DataFrame(df, columns=columns)
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45 df.to_csv(OutFile, index=False,sep='\t')
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47 def CalculateMovementCal(InFile, window, angle, modality, ScaleName, OutFile):
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50 list_pep_name,_ = PepFasta(InFile)
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52 AMP = PeptideDescriptor(list_pep_name, ScaleName)
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53 AMP.calculate_moment(int(window), int(angle), modality)
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54 df = AMP.descriptor
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56 df = pd.DataFrame(df, columns=['Movement'])
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57 df.to_csv(OutFile, index=False,sep='\t')
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59 def CalculateGlobalCal(InFile, WindowSize, modality, ScaleName, OutFile):
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61 list_pep_name,_ = PepFasta(InFile)
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62
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63 AMP = PeptideDescriptor(list_pep_name, ScaleName)
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64 AMP.calculate_global(int(WindowSize), modality)
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65 df = AMP.descriptor
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67 df = pd.DataFrame(df, columns=['Global'])
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68 df.to_csv(OutFile, index=False, sep='\t')
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70 def CalculateProfileCal(InFile, prof_type, WindowSize, ScaleName, OutFile):
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72 list_pep_name,_ = PepFasta(InFile)
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74 AMP = PeptideDescriptor(list_pep_name, ScaleName)
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75 AMP.calculate_profile(prof_type, int(WindowSize))
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76 df = AMP.descriptor
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78 df = pd.DataFrame(df, columns=['hyPhoPro','hyPhoMov'])
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79 df.to_csv(OutFile, index=False, sep='\t')
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81 def CalculateArcCal(InFile, modality, OutFile):
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83 list_pep_name,_ = PepFasta(InFile)
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84
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85 AMP = PeptideDescriptor(list_pep_name, scalename="peparc")
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86 AMP.calculate_arc(modality)
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87 df = AMP.descriptor
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88
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89 columns = ["Arc_"+str(i) for i in range(len(df[0]))]
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90 df = pd.DataFrame(df, columns=columns)
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91 df.to_csv(OutFile, index=False, sep='\t')
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93 if __name__=="__main__":
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95 import argparse
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97 parser = argparse.ArgumentParser(description='Deployment tool')
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98 subparsers = parser.add_subparsers()
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99
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100 Aut = subparsers.add_parser('AutoCorrCal')
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101 Aut.add_argument("-i","--InFile", required=True, default=None, help="")
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102 Aut.add_argument("-w","--WindowSize", required=False, default=7, help="")
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103 Aut.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="")
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104 Aut.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="")
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105
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106 Cro = subparsers.add_parser('CrossCorrCal')
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107 Cro.add_argument("-i","--InFile", required=True, default=None, help="")
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108 Cro.add_argument("-w","--WindowSize", required=False, default=7, help="")
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109 Cro.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="")
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110 Cro.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="")
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111
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112 Mov = subparsers.add_parser('CalculateMovement')
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113 Mov.add_argument("-i","--InFile", required=True, default=None, help="")
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114 Mov.add_argument("-w","--WindowSize", required=False, default=1000, help="")
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115 Mov.add_argument("-a","--Angle", required=False, default=100, help="")
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116 Mov.add_argument("-m","--Modality", required=False, default="max", help="")
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117 Mov.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="")
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118 Mov.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="")
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119
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120 Glo = subparsers.add_parser('GlobalCal')
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121 Glo.add_argument("-i","--InFile", required="", default="", help="")
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122 Glo.add_argument("-w","--WindowSize", required=False, default=1000, help="")
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123 Glo.add_argument("-m","--Modality", required=False, default="max", help="")
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124 Glo.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="")
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125 Glo.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="")
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126
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127 Pro = subparsers.add_parser('ProfileCal')
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128 Pro.add_argument("-i","--InFile", required=True, default=None, help="")
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129 Pro.add_argument("-p","--ProfType", required=False, default="text", help="")
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130 Pro.add_argument("-w","--WindowSize", required=False, default=7, help="")
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131 Pro.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="")
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132 Pro.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="")
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133
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134 Arc = subparsers.add_parser('ArcCal')
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135 Arc.add_argument("-i","--InFile", required=True, default=None, help="")
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136 Arc.add_argument("-m","--Modality", required=False, default="max", help="")
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137 Arc.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="")
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138
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139 args = parser.parse_args()
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140
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141 if sys.argv[1] == 'AutoCorrCal':
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142 AutoCorrCal(args.InFile, args.WindowSize, args.ScaleName, args.OutFile)
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143 elif sys.argv[1] == 'CrossCorrCal':
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144 CrossCorrCal(args.InFile, args.WindowSize, args.ScaleName, args.OutFile)
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145 elif sys.argv[1] == 'CalculateMovement':
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146 CalculateMovementCal(args.InFile, args.WindowSize, args.Angle, args.Modality, args.ScaleName, args.OutFile)
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147 elif sys.argv[1] == 'GlobalCal':
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148 CalculateGlobalCal(args.InFile, args.WindowSize, args.Modality, args.ScaleName, args.OutFile)
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149 elif sys.argv[1] == 'ProfileCal':
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150 CalculateProfileCal(args.InFile, args.ProfType, args.WindowSize, args.ScaleName, args.OutFile)
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151 elif sys.argv[1] == 'ArcCal':
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152 CalculateArcCal(args.InFile, args.Modality, args.OutFile)
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153 else:
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154 print ("You entered Wrong Values: ")