Mercurial > repos > jay > pdaug_peptide_sequence_analysis
annotate PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py @ 9:90e3b1968ae6 draft default tip
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 19:36:54 +0000 |
parents | e59674e3a391 |
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rev | line source |
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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parents:
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1 from modlamp.descriptors import * |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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2 import os |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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3 import pandas as pd |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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4 |
e59674e3a391
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5 def Descriptor_calcultor(DesType, inputfile, ph, amide,OutFile ): |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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6 |
e59674e3a391
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7 list_pep_name = [] |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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8 f = open(inputfile) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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9 lines = f.readlines() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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10 |
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11 for line in lines: |
e59674e3a391
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12 if ">" in line: |
e59674e3a391
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13 pass |
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14 else: |
e59674e3a391
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15 list_pep_name.append(line.strip('\n')) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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16 |
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17 desc = GlobalDescriptor(list_pep_name) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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18 |
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19 if DesType == "Length": |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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20 desc.length() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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21 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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22 dfN = desc.featurenames |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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23 |
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24 elif DesType == "Weight": |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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25 |
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26 desc.calculate_MW() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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27 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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28 dfN = desc.featurenames |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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29 |
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30 elif DesType == "Charge": |
e59674e3a391
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31 desc.calculate_charge(ph=int(ph), amide=amide) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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32 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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33 dfN = desc.featurenames |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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34 |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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35 elif DesType == "ChargeDensity": |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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36 desc.charge_density(ph=int(ph), amide=amide) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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37 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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38 dfN = desc.featurenames |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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39 |
e59674e3a391
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40 elif DesType == "IsoelectricPoint": |
e59674e3a391
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41 desc.isoelectric_point(amide=amide) |
e59674e3a391
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42 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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43 dfN = desc.featurenames |
e59674e3a391
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44 |
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45 elif DesType == "InstabilityIndex": |
e59674e3a391
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46 desc.instability_index() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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47 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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48 dfN = desc.featurenames |
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49 |
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50 elif DesType == "Aromaticity": |
e59674e3a391
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51 desc.aromaticity() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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52 df = desc.descriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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53 dfN = desc.featurenames |
e59674e3a391
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54 |
e59674e3a391
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55 elif DesType == "AliphaticIndex": |
e59674e3a391
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56 desc.aliphatic_index() |
e59674e3a391
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57 df = desc.descriptor |
e59674e3a391
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58 dfN = desc.featurenames |
e59674e3a391
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59 |
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60 elif DesType == "BomanIndex": |
e59674e3a391
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61 desc.boman_index() |
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62 df = desc.descriptor |
e59674e3a391
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63 dfN = desc.featurenames |
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64 |
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65 elif DesType == "HydrophobicRatio": |
e59674e3a391
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66 desc.hydrophobic_ratio() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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67 df = desc.descriptor |
e59674e3a391
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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) |
e59674e3a391
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72 df = desc.descriptor |
e59674e3a391
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73 dfN = desc.featurenames |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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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 |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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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') |
e59674e3a391
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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() |
e59674e3a391
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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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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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91 default=None, |
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92 help="Descriptors Type") |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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93 |
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94 parser.add_argument("-i", "--InFile", |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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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) |