Mercurial > repos > jay > pdaug_peptide_ngrams
annotate PDAUG_AA_Property_Based_Peptide_Descriptor/PDAUG_AA_Property_Based_Peptide_Descriptor.py @ 9:755dd6018caa 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 20:06:27 +0000 |
parents | 7557b48b2872 |
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7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 from modlamp.descriptors import * |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import pandas as pd |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import os |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 |
7557b48b2872
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5 |
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6 |
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7 def PepFasta(InFile): |
7557b48b2872
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8 file = open(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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9 lines = file.readlines() |
7557b48b2872
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10 |
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11 Index = [] |
7557b48b2872
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12 Peptides = [] |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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13 |
7557b48b2872
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14 for line in lines: |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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15 if '>' in line: |
7557b48b2872
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16 Index.append(line.strip('\n')) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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17 else: |
7557b48b2872
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18 Peptides.append(line.strip('\n')) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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19 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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20 return Peptides, Index |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 |
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22 |
7557b48b2872
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23 def AutoCorrCal(InFile, window, ScaleName, OutFile): |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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24 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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25 list_pep_name,_ = PepFasta(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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26 |
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27 AMP = PeptideDescriptor(list_pep_name, ScaleName) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 AMP.calculate_autocorr(int(window)) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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29 df = AMP.descriptor |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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31 columns = ["CroAut_"+str(i) for i in range(len(df[0]))] |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 df = pd.DataFrame(df, columns=columns) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 df.to_csv(OutFile, index=False,sep='\t') |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 def CrossCorrCal(InFile, window, ScaleName, OutFile): |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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37 list_pep_name,_ = PepFasta(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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39 AMP = PeptideDescriptor(list_pep_name, ScaleName) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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40 AMP.calculate_crosscorr(int(window)) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 df = AMP.descriptor |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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42 |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 columns = ["CroCor_"+str(i) for i in range(len(df[0]))] |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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44 df = pd.DataFrame(df, columns=columns) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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45 df.to_csv(OutFile, index=False,sep='\t') |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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46 |
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47 def CalculateMovementCal(InFile, window, angle, modality, ScaleName, OutFile): |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 |
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49 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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50 list_pep_name,_ = PepFasta(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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51 |
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52 AMP = PeptideDescriptor(list_pep_name, ScaleName) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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53 AMP.calculate_moment(int(window), int(angle), modality) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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54 df = AMP.descriptor |
7557b48b2872
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55 |
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56 df = pd.DataFrame(df, columns=['Movement']) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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57 df.to_csv(OutFile, index=False,sep='\t') |
7557b48b2872
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58 |
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59 def CalculateGlobalCal(InFile, WindowSize, modality, ScaleName, OutFile): |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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60 |
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61 list_pep_name,_ = PepFasta(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 |
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63 AMP = PeptideDescriptor(list_pep_name, ScaleName) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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64 AMP.calculate_global(int(WindowSize), modality) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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65 df = AMP.descriptor |
7557b48b2872
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66 |
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67 df = pd.DataFrame(df, columns=['Global']) |
7557b48b2872
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68 df.to_csv(OutFile, index=False, sep='\t') |
7557b48b2872
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69 |
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70 def CalculateProfileCal(InFile, prof_type, WindowSize, ScaleName, OutFile): |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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71 |
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72 list_pep_name,_ = PepFasta(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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73 |
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74 AMP = PeptideDescriptor(list_pep_name, ScaleName) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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75 AMP.calculate_profile(prof_type, int(WindowSize)) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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76 df = AMP.descriptor |
7557b48b2872
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77 |
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78 df = pd.DataFrame(df, columns=['hyPhoPro','hyPhoMov']) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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79 df.to_csv(OutFile, index=False, sep='\t') |
7557b48b2872
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80 |
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81 def CalculateArcCal(InFile, modality, OutFile): |
7557b48b2872
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82 |
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83 list_pep_name,_ = PepFasta(InFile) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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84 |
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85 AMP = PeptideDescriptor(list_pep_name, scalename="peparc") |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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86 AMP.calculate_arc(modality) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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87 df = AMP.descriptor |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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88 |
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89 columns = ["Arc_"+str(i) for i in range(len(df[0]))] |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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90 df = pd.DataFrame(df, columns=columns) |
7557b48b2872
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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91 df.to_csv(OutFile, index=False, sep='\t') |
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92 |
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93 if __name__=="__main__": |
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94 |
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95 import argparse |
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96 |
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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: ") |