Mercurial > repos > jay > pdaug_basic_plots
annotate PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py @ 0:7d247e27ff11 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:52:18 +0000 |
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children | 58a5249e47cb |
rev | line source |
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7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 import modlamp |
7d247e27ff11
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2 from modlamp.datasets import load_AMPvsTM |
7d247e27ff11
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3 from modlamp.datasets import load_AMPvsUniProt |
7d247e27ff11
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4 from modlamp.datasets import load_ACPvsTM |
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5 from modlamp.datasets import load_ACPvsRandom |
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6 from modlamp.database import query_apd |
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7 from modlamp.database import query_camp |
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8 import os |
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9 import pandas as pd |
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10 |
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11 def DataGen(DataBaseType, OutFile, IDs): |
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12 |
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13 if DataBaseType == 'AMPvsTM': |
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14 data = load_AMPvsTM() |
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15 |
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16 elif DataBaseType == 'AMPvsUniProt': |
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17 data = load_AMPvsUniProt() |
7d247e27ff11
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18 |
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19 elif DataBaseType == 'ACPvsTM': |
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20 data = load_ACPvsTM() |
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21 |
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22 elif DataBaseType == 'ACPvsRandom': |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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23 data = load_ACPvsRandom() |
7d247e27ff11
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24 |
7d247e27ff11
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25 elif DataBaseType == 'query_apd': |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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26 |
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27 data = query_apd([int(i) for i in IDs.split(',')]) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 df = pd.DataFrame(data, columns=['Peptides']) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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29 df.to_csv(OutFile, index=False, sep='\t') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 exit() |
7d247e27ff11
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31 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 elif DataBaseType == 'query_camp': |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 data = query_camp([int(i) for i in IDs.split(',')]) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 df = pd.DataFrame(data, columns=['Peptides']) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 df.to_csv(OutFile, index=False, sep='\t') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 exit() |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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37 |
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38 else: |
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39 print ("Enter Correct Values") |
7d247e27ff11
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40 exit() |
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41 |
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42 Target = data.target.tolist() |
7d247e27ff11
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43 Target_list = set(Target) |
7d247e27ff11
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44 df = data.sequences |
7d247e27ff11
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45 |
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46 |
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47 Target = pd.DataFrame(Target, columns=['Target']) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 df = pd.DataFrame(df, columns=['Peptide']) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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49 |
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50 df = pd.DataFrame(df) |
7d247e27ff11
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51 df = pd.concat([df, Target], axis=1) |
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52 |
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53 df.to_csv(OutFile, index=False, sep='\t') |
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54 |
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55 |
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56 if __name__=="__main__": |
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57 |
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58 import argparse |
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59 parser = argparse.ArgumentParser() |
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60 |
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61 parser.add_argument("-d", "--DataBaseType", |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 required=True, |
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63 default=None, |
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64 help="Name of the dataset ") |
7d247e27ff11
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65 |
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66 parser.add_argument("-o", "--OutFile", |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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67 required=False, |
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68 default='Out.tsv', |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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69 help="Out put file name for str descriptors") |
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70 |
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71 parser.add_argument("-L", "--List", |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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72 required=False, |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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73 default=None, |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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74 help="List of integer as ID") |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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75 |
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76 args = parser.parse_args() |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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77 DataGen(args.DataBaseType, args.OutFile, args.List) |