Mercurial > repos > jay > pdaug_addclasslabel
annotate PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py @ 8:b9659a0a327d draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Mon, 10 Jan 2022 05:04:27 +0000 |
parents | 8c2ee62ce9d8 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 import modlamp |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 from modlamp.datasets import load_AMPvsTM |
2df11ea23f10
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3 from modlamp.datasets import load_AMPvsUniProt |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 from modlamp.datasets import load_ACPvsTM |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 from modlamp.datasets import load_ACPvsRandom |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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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 == 'AMPvsTMP': |
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14 data = load_AMPvsTM() |
2df11ea23f10
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15 |
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16 elif DataBaseType == 'AMPvsUniProt': |
2df11ea23f10
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17 data = load_AMPvsUniProt() |
2df11ea23f10
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18 |
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19 elif DataBaseType == 'ACPvsTMP': |
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20 data = load_ACPvsTM() |
2df11ea23f10
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21 |
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22 elif DataBaseType == 'ACPvsRandom': |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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23 data = load_ACPvsRandom() |
2df11ea23f10
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24 |
2df11ea23f10
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25 elif DataBaseType == 'query_apd': |
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26 |
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27 data = query_apd([int(i) for i in IDs.split(',')]) |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 df = pd.DataFrame(data, columns=['Peptides']) |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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29 df.to_csv(OutFile, index=False, sep='\t') |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 exit() |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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31 |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 elif DataBaseType == 'query_camp': |
2df11ea23f10
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33 data = query_camp([int(i) for i in IDs.split(',')]) |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 df = pd.DataFrame(data, columns=['Peptides']) |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 df.to_csv(OutFile, index=False, sep='\t') |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 exit() |
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37 |
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38 else: |
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39 print ("Enter Correct Values") |
2df11ea23f10
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40 exit() |
2df11ea23f10
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41 |
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42 peptide_data = data.sequences |
8c2ee62ce9d8
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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43 class_label = int(len(peptide_data)/2)*[data.target_names[0]]+int(len(peptide_data)/2)*[data.target_names[1]] |
8c2ee62ce9d8
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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44 peptide_data = pd.DataFrame(peptide_data, columns=['name']) |
8c2ee62ce9d8
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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45 class_label = pd.DataFrame(class_label, columns=['class_label']) |
8c2ee62ce9d8
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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46 df = pd.concat([peptide_data,class_label], axis=1) |
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47 |
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48 df.to_csv(OutFile, index=False, sep='\t') |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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49 |
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50 |
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51 if __name__=="__main__": |
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52 |
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53 import argparse |
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54 parser = argparse.ArgumentParser() |
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55 |
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56 parser.add_argument("-d", "--DataBaseType", |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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57 required=True, |
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58 default=None, |
2df11ea23f10
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59 help="Name of the dataset ") |
2df11ea23f10
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60 |
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61 parser.add_argument("-o", "--OutFile", |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 required=False, |
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63 default='Out.tsv', |
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64 help="Out put file name for str descriptors") |
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65 |
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66 parser.add_argument("-L", "--List", |
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67 required=False, |
8c2ee62ce9d8
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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68 default=None, |
8c2ee62ce9d8
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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69 help="List of integer as ID") |
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70 |
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71 args = parser.parse_args() |
2df11ea23f10
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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72 DataGen(args.DataBaseType, args.OutFile, args.List) |