Mercurial > repos > jay > pdaug_tsvtofasta
annotate PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py @ 2:728e1fb64e91 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 398e58899356c3f437267285021f15dfd168f249"
author | jay |
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date | Fri, 27 Nov 2020 22:37:57 +0000 |
parents | c3f0b3a6339e |
children | 95c09c06f655 |
rev | line source |
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0
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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1 import pandas as pd |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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2 from pydpi.pypro import PyPro |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import os |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 def BinaryDescriptor(seq): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 BinaryCode = { |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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9 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 'A':"1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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11 'C':"0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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12 'D':"0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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13 'E':"0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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14 'F':"0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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15 'G':"0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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16 'H':"0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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17 'I':"0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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18 'K':"0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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19 'L':"0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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20 'M':"0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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21 'N':"0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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22 'P':"0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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23 'Q':"0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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24 'R':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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25 'S':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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26 'T':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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27 'V':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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28 'W':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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29 'Y':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1", |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 } |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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31 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 lines = [] |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 Df = [] |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 for s in seq: |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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37 des = [] |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 for n in s: |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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39 des.append(BinaryCode[n.upper()]) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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40 lines.append(','.join(des).split(',')) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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42 df = pd.DataFrame(lines) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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44 return df |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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45 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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46 def Decriptor_generator(InFile, Lamda, Weight, DesType, Out_file): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 list_pep_name = [] |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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49 f = open(InFile) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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50 lines = f.readlines() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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51 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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52 for line in lines: |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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53 if ">" in line: |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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54 pass |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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55 else: |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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56 list_pep_name.append(line.strip('\n')) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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57 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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58 out_df = pd.DataFrame() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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59 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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60 for seq in list_pep_name: |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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61 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 protein = PyPro() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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63 protein.ReadProteinSequence(seq) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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64 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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65 if DesType == 'PAAC': |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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66 DS = protein.GetPAAC(lamda=int(Lamda), weight=float(Weight)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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67 df = pd.DataFrame(DS, index=[0]) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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68 elif DesType == 'APAAC': |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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69 DS = protein.GetAPAAC(lamda=int(Lamda), weight=float(Weight)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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70 df = pd.DataFrame(DS, index=[0]) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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71 elif DesType == 'CTD': |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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72 DS = protein.GetCTD() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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73 df = pd.DataFrame(DS, index=[0]) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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74 elif DesType == 'DPComp': |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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75 DS = protein.GetDPComp() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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76 df = pd.DataFrame(DS, index=[0]) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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77 elif DesType == 'GearyAuto': |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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78 DS = protein.GetGearyAuto() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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79 df = pd.DataFrame(DS, index=[0]) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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80 elif DesType == 'MoranAuto': |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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81 DS = protein.GetMoranAuto() |
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82 df = pd.DataFrame(DS, index=[0]) |
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83 elif DesType == 'MoreauBrotoAuto': |
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84 DS = protein.GetMoreauBrotoAuto() |
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85 df = pd.DataFrame(DS, index=[0]) |
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86 elif DesType == 'QSO': |
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87 DS = protein.GetQSO() |
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88 df = pd.DataFrame(DS, index=[0]) |
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89 elif DesType == 'SOCN': |
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90 DS = protein.GetSOCN() |
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91 df = pd.DataFrame(DS, index=[0]) |
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92 elif DesType == 'TPComp': |
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93 DS = protein.GetTPComp() |
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94 df = pd.DataFrame(DS, index=[0]) |
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95 elif DesType == 'All': |
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96 DS_1 = protein.GetPAAC(lamda=int(Lamda), weight=float(Weight)) |
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97 DS_2 = protein.GetAPAAC(lamda=int(Lamda), weight=float(Weight)) |
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98 DS_3 = protein.GetCTD() |
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99 DS_4 = protein.GetDPComp() |
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100 DS_5 = protein.GetGearyAuto() |
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101 DS_6 = protein.GetMoranAuto() |
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102 DS_7 = protein.GetMoreauBrotoAuto() |
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103 DS_8 = protein.GetQSO() |
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104 DS_9 = protein.GetSOCN() |
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105 DS_10 = protein.GetTPComp() |
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106 |
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107 DS = {} |
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108 |
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109 for D in (DS_1, DS_2, DS_3, DS_4, DS_5, DS_6, DS_7, DS_8, DS_9, DS_10): |
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110 DS.update(D) |
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111 |
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112 df = pd.DataFrame(DS, index=[0]) |
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113 |
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114 if DesType == 'BinaryDescriptor': |
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115 out_df = BinaryDescriptor(list_pep_name) |
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116 else: |
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117 out_df = pd.concat([out_df, df], axis=0) |
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118 |
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119 |
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120 out_df.to_csv(Out_file, index=False, sep='\t') |
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121 |
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122 |
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123 if __name__=="__main__": |
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124 |
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125 |
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126 import argparse |
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127 |
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128 parser = argparse.ArgumentParser() |
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129 |
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130 parser.add_argument("-I", "--InFile", |
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131 required=True, |
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132 default=None, |
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133 help="pep file") |
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134 |
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135 parser.add_argument("-l", "--Lamda", |
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136 required=False, |
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137 default=50, |
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138 help="pep file") |
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139 |
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140 parser.add_argument("-w", "--Weight", |
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141 required=False, |
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142 default=0.5, |
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143 help="pep file") |
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144 |
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145 parser.add_argument("-t", "--DesType", |
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146 required=True, |
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147 default=None, |
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148 help="out put file name for str Descriptors") |
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149 |
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150 parser.add_argument("-O", "--Out_file", |
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151 required=False, |
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152 default="Out.tsv", |
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153 help="Path to target tsv file") |
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154 |
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155 args = parser.parse_args() |
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156 Decriptor_generator(args.InFile, args.Lamda, args.Weight, args.DesType, args.Out_file) |
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157 |
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158 |