Mercurial > repos > jay > pdaug_sequence_similarity_network

annotate PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py @ 0:e650de82bcc7 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 a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:50:00 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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diff changeset
1 from modlamp.descriptors import *
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import os
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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3 import pandas as pd
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 def Descriptor_calcultor(DesType, inputfile, ph, amide,OutFile ):
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6
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7 list_pep_name = []
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8 f = open(inputfile)
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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9 lines = f.readlines()
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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11 for line in lines:
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12 if ">" in line:
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13 pass
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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14 else:
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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15 list_pep_name.append(line.strip('\n'))
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16
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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17 desc = GlobalDescriptor(list_pep_name)
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18
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19 if DesType == "Length":
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20 desc.length()
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21 df = desc.descriptor
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22 dfN = desc.featurenames
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23
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24 elif DesType == "Weight":
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25
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26 desc.calculate_MW()
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27 df = desc.descriptor
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 dfN = desc.featurenames
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29
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30 elif DesType == "Charge":
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31 desc.calculate_charge(ph=int(ph), amide=amide)
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32 df = desc.descriptor
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33 dfN = desc.featurenames
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34
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35 elif DesType == "ChargeDensity":
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36 desc.charge_density(ph=int(ph), amide=amide)
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37 df = desc.descriptor
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 dfN = desc.featurenames
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39
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40 elif DesType == "IsoelectricPoint":
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41 desc.isoelectric_point(amide=amide)
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42 df = desc.descriptor
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 dfN = desc.featurenames
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44
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45 elif DesType == "InstabilityIndex":
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46 desc.instability_index()
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 df = desc.descriptor
e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 dfN = desc.featurenames
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49
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50 elif DesType == "Aromaticity":
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51 desc.aromaticity()
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52 df = desc.descriptor
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53 dfN = desc.featurenames
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54
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55 elif DesType == "AliphaticIndex":
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56 desc.aliphatic_index()
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57 df = desc.descriptor
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58 dfN = desc.featurenames
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59
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60 elif DesType == "BomanIndex":
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61 desc.boman_index()
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62 df = desc.descriptor
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63 dfN = desc.featurenames
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64
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65 elif DesType == "HydrophobicRatio":
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66 desc.hydrophobic_ratio()
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67 df = desc.descriptor
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68 dfN = desc.featurenames
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69
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70 elif DesType == "All":
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71 desc.calculate_all(ph=int(ph), amide=amide)
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72 df = desc.descriptor
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73 dfN = desc.featurenames
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74 else:
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75 pass
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76
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77 df = desc.descriptor
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78 dfN = desc.featurenames
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79 dfOut = pd.DataFrame(df,columns=dfN)
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80
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81 dfOut.to_csv(OutFile, index=False, sep='\t')
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82
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83 if __name__=="__main__":
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84
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85 import argparse
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86
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87 parser = argparse.ArgumentParser()
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88
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89 parser.add_argument("-t", "--DesType",
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90 required=True,
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91 default=None,
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92 help="Descriptors Type")
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93
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94 parser.add_argument("-i", "--InFile",
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95 required=True,
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96 default=None,
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97 help="Peptide File")
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98
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99 parser.add_argument("-p", "--Ph",
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100 required=False,
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101 default=7.0,
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102 help="Ph 0-14")
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103
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104 parser.add_argument("-a", "--Amide",
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105 required=False,
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106 default="True",
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107 help="True or False")
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108
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109 parser.add_argument("-O", "--OutFile",
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110 required=False,
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111 default="out.tsv",
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112 help="True or False")
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113
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114
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115 args = parser.parse_args()
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116
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117 Descriptor_calcultor(args.DesType, args.InFile, args.Ph, args.Amide, args.OutFile)