Mercurial > repos > jay > pdaug_tsvtofasta
annotate PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py @ 0:c3f0b3a6339e draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:47:48 +0000 |
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children | fc5508bfa640 |
rev | line source |
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c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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1 from modlamp.sequences import * |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import argparse, sys |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import pandas as pd |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 import os |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 def Random_seq(seq_num, lenmin_s, lenmax_s, S_proba, OutFasta): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 b = Random(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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9 b.generate_sequences(proba=float(S_proba)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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11 OutPep = b.sequences |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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12 OutFasta = open(OutFasta, 'w') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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13 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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14 for i,O in enumerate(OutPep): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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15 OutFasta.write(">sequence_"+str(i)+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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16 OutFasta.write(O+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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17 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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18 def Helices_seq(seq_num, lenmin_s, lenmax_s, OutFasta): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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19 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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20 h = Helices(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 h.generate_sequences() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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22 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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23 OutPep = h.sequences |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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24 OutFasta = open(OutFasta, 'w') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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25 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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26 for i,O in enumerate(OutPep): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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27 OutFasta.write(">sequence_"+str(i)+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 OutFasta.write(O+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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29 |
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30 |
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31 def Kinked_seq(seq_num, lenmin_s, lenmax_s, OutFasta): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 |
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33 k = Kinked(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 k.generate_sequences() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 OutPep = k.sequences |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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37 OutFasta = open(OutFasta, 'w') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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39 for i,O in enumerate(OutPep): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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40 OutFasta.write(">sequence_"+str(i)+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 OutFasta.write(O+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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42 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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44 def Oblique_seq(seq_num, lenmin_s, lenmax_s, OutFasta): |
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 o = Oblique(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 o.generate_sequences() |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 o.sequences |
c3f0b3a6339e
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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 OutPep = o.sequences |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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51 OutFasta = open(OutFasta, 'w') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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52 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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53 for i,O in enumerate(OutPep): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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54 OutFasta.write(">sequence_"+str(i)+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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55 OutFasta.write(O+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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56 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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58 def Centrosymmetric_seq(seq_num, lenmin_s, lenmax_s, symmetry_s, OutFasta): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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59 |
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60 s = Centrosymmetric(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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61 s.generate_sequences(symmetry=symmetry_s) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 |
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63 OutPep = s.sequences |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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64 OutFasta = open(OutFasta, 'w') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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65 |
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66 for i,O in enumerate(OutPep): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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67 OutFasta.write(">sequence_"+str(i)+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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68 OutFasta.write(O+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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69 |
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71 def HelicesACP_seq(seq_num, lenmin_s, lenmax_s, OutFasta): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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73 helACP = HelicesACP(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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74 helACP.generate_sequences() |
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75 |
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76 OutPep = helACP.sequences |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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77 OutFasta = open(OutFasta, 'w') |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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78 |
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79 for i,O in enumerate(OutPep): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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80 OutFasta.write(">sequence_"+str(i)+'\n') |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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81 OutFasta.write(O+'\n') |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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82 |
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84 def Hepahelices_seq(seq_num, lenmin_s, lenmax_s, OutFasta): |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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85 |
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86 h = Hepahelices(int(seq_num), int(lenmin_s),int(lenmax_s)) |
c3f0b3a6339e
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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87 h.generate_sequences() |
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88 |
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89 OutPep = h.sequences |
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90 OutFasta = open(OutFasta, 'w') |
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91 |
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92 for i,O in enumerate(OutPep): |
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93 OutFasta.write(">sequence_"+str(i)+'\n') |
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94 OutFasta.write(O+'\n') |
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95 |
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96 |
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97 def AMPngrams_seq(seq_num, lenmin_s, lenmax_s, OutFasta): |
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98 |
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99 s = AMPngrams(int(seq_num), int(lenmin_s),int(lenmax_s)) |
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100 s.generate_sequences() |
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101 |
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102 OutPep = s.sequences |
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103 OutFasta = open(OutFasta, 'w') |
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104 |
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105 for i,O in enumerate(OutPep): |
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106 OutFasta.write(">sequence_"+str(i)+'\n') |
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107 OutFasta.write(O+'\n') |
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108 |
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109 def AmphipathicArc_seq(seq_num, lenmin_s, lenmax_s, gen_seq, hyd_gra, OutFasta): |
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110 |
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111 amphi_hel = AmphipathicArc(int(seq_num), int(lenmin_s),int(lenmax_s)) |
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112 amphi_hel.generate_sequences(int(gen_seq)) |
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113 OutFasta = open(OutFasta, 'w') |
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114 |
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115 if hyd_gra == 'true': |
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116 |
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117 amphi_hel.make_H_gradient() |
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118 OutPep = amphi_hel.sequences |
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119 |
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120 for i,O in enumerate(OutPep): |
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121 OutFasta.write(">sequence_"+str(i)+'\n') |
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122 OutFasta.write(O+'\n') |
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123 |
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124 elif hyd_gra == 'false': |
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125 |
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126 OutPep = amphi_hel.sequences |
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127 |
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128 for i,O in enumerate(OutPep): |
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129 OutFasta.write(">sequence_"+str(i)+'\n') |
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130 OutFasta.write(O+'\n') |
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131 |
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132 if __name__=='__main__': |
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133 |
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134 parser = argparse.ArgumentParser(description='Deployment tool') |
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135 subparsers = parser.add_subparsers() |
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136 |
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137 Ran = subparsers.add_parser('Random') |
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138 Ran.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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139 Ran.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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140 Ran.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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141 Ran.add_argument("-p","--S_proba", required=False, default='AMP', help="AA probability to be used to generate sequences,'rand', 'AMP', 'AMPnoCM', 'randnoCM', 'ACP'") |
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142 Ran.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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143 |
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144 Hal = subparsers.add_parser('Helices') |
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145 Hal.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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146 Hal.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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147 Hal.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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148 Hal.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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149 |
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150 Kin = subparsers.add_parser('Kinked') |
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151 Kin.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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152 Kin.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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153 Kin.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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154 Kin.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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155 |
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156 Obl = subparsers.add_parser('Oblique') |
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157 Obl.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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158 Obl.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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159 Obl.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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160 Obl.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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161 |
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162 Cen = subparsers.add_parser('Centrosymmetric') |
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163 Cen.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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164 Cen.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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165 Cen.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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166 Cen.add_argument("-S","--symmetry_s", required=False, default="asymmetric", help="symmetric,asymmetric") |
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167 Cen.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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168 |
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169 Hel = subparsers.add_parser('HelicesACP') |
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170 Hel.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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171 Hel.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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172 Hel.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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173 Hel.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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174 |
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175 Hep = subparsers.add_parser('Hepahelices') |
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176 Hep.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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177 Hep.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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178 Hep.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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179 Hep.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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180 |
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181 AMP = subparsers.add_parser('AMPngrams') |
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182 AMP.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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183 AMP.add_argument("-m","--n_min", required=False, default=3, help="minimum number of ngrams to take for sequence assembly") |
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184 AMP.add_argument("-M","--n_max", required=False, default=1, help="maximum number of ngrams to take for sequence assembly") |
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185 AMP.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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186 |
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187 Arc = subparsers.add_parser('AmphipathicArc') |
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188 Arc.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") |
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189 Arc.add_argument("-m","--lenmin_s", required=False, default=7, help="") |
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190 Arc.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") |
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191 Arc.add_argument("-a","--arcsize", help="Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture") |
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192 Arc.add_argument("-y","--hyd_gra", default='False', help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic.") |
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193 Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") |
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194 |
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195 args = parser.parse_args() |
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196 |
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197 if sys.argv[1] == 'Random': |
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198 Random_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.S_proba, args.OutFasta) |
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199 elif sys.argv[1] == 'Helices': |
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200 Helices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) |
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201 elif sys.argv[1] == 'Kinked': |
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202 Kinked_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) |
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203 elif sys.argv[1] == 'Oblique': |
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204 Oblique_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) |
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205 elif sys.argv[1] == 'Centrosymmetric': |
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206 Centrosymmetric_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.symmetry_s, args.OutFasta) |
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207 elif sys.argv[1] == 'HelicesACP': |
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208 HelicesACP_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) |
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209 elif sys.argv[1] == 'Hepahelices': |
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210 Hepahelices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) |
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211 elif sys.argv[1] == 'AMPngrams': |
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212 AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta) |
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213 elif sys.argv[1] == 'AmphipathicArc': |
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214 AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta) |
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215 else: |
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216 print("You entered Wrong Values: ") |