Mercurial > repos > jay > pdaug_basic_plots
annotate PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py @ 5:4c3242563796 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author | jay |
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date | Thu, 28 Jan 2021 03:46:16 +0000 |
parents | 7d247e27ff11 |
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rev | line source |
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0
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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1 import sys |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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2 import itertools |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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3 import pandas as pd |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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4 import random |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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5 import os |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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6 from itertools import permutations |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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7 from random import shuffle |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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8 import argparse, sys |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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9 import pandas as pd |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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11 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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12 def MutatedPeptides(input_file, index_list, AA, outputFile): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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13 |
7d247e27ff11
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14 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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15 index_list = [int(x) for x in index_list.split(',')] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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16 out_put = [] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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17 AA = AA.split(',') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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18 l = len(index_list) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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19 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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20 replacements = [x for x in itertools.permutations(AA,l)] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 |
7d247e27ff11
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22 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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23 counter = 0 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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24 to_modify = [x for x in input_file] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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25 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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26 for replacement in replacements: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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27 for i,index in enumerate(index_list): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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28 to_modify[index_list[i]-1] = replacement[i] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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29 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 counter = counter + 1 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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31 out_put.append("".join(to_modify).upper()) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 w = open(outputFile, 'w') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 for i, f in enumerate(out_put): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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37 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 w.write(">sequence_"+str(i)+'\n') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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39 w.write(f+'\n') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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40 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 def RandomPeptides(AAs, pep_length, out_pep_num, outputFile): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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42 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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44 if int(pep_length) > 20: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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45 print ("Max peptide lenth 20") |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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46 exit() |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 else: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 pass |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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49 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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50 if int(out_pep_num) > 10000: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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51 print ("Max peptide library 10000") |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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52 exit() |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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53 else: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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54 pass |
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55 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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56 out_pep_lib = [] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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57 raw = AAs.split(',') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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58 |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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59 for x in range(int(out_pep_num)): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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60 un_seq = [] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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61 for i in range(int(pep_length)): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 un_seq.append(random.choice(raw)) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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63 out_pep_lib.append("".join(un_seq)) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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64 |
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65 |
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66 w = open(outputFile, 'w') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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67 |
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68 |
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69 for i, f in enumerate(out_pep_lib): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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70 |
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71 w.write(">sequence_"+str(i)+'\n') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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72 w.write(f+'\n') |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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73 |
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74 def SlidingWindowPeptide(infile, window_size, frag_size, outputFile): |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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75 |
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76 |
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77 if int(window_size) > 10: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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78 print ("Max window_size 10") |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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79 exit() |
7d247e27ff11
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80 else: |
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81 pass |
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82 if int(frag_size) > 20: |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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83 print ("Max frag size is 20") |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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84 exit() |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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85 else: |
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86 pass |
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87 |
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88 |
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89 pep_list = [] |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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90 |
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91 f = open(infile) |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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92 |
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93 lines = f.readlines() |
7d247e27ff11
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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94 |
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95 flines = [] |
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96 |
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97 for line in lines: |
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98 if '>' in line: |
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99 pass |
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100 else: |
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101 flines.append(line.strip('\n')) |
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102 sequence = "".join(flines) |
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103 |
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104 for i in range(int(frag_size)): |
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105 if int(frag_size) == len(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]): |
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106 pep_list.append(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]) |
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107 else: |
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108 break |
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109 |
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110 w = open(outputFile, 'w') |
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111 |
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112 |
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113 for i, f in enumerate(pep_list): |
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114 |
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115 w.write(">sequence_"+str(i)+'\n') |
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116 w.write(f+'\n') |
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117 |
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118 if __name__=='__main__': |
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119 |
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120 parser = argparse.ArgumentParser(description='Deployment tool') |
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121 subparsers = parser.add_subparsers() |
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122 |
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123 Mp = subparsers.add_parser('MutatedPeptides') |
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124 Mp.add_argument("-s","--sequence") |
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125 Mp.add_argument("-m","--mutation_site_list") |
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126 Mp.add_argument("-a","--AA_list") |
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127 Mp.add_argument("-d", "--outputFile", required=None, default='out.fasta', help="Path to out file") |
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128 |
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129 Rp = subparsers.add_parser('RandomPeptides') |
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130 Rp.add_argument("-a","--AA_list") |
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131 Rp.add_argument("-l","--pep_length") |
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132 Rp.add_argument("-o","--out_pep_lenght") |
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133 Rp.add_argument("-d", "--outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'), help="Path to out file") |
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134 |
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135 Sp = subparsers.add_parser('SlidingWindowPeptide') |
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136 Sp.add_argument("-i","--InFile") |
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137 Sp.add_argument("-w","--winSize") |
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138 Sp.add_argument("-s","--FragSize") |
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139 Sp.add_argument("-d", "--outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'), help="Path to out file") |
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140 |
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141 args = parser.parse_args() |
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142 |
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143 if sys.argv[1] == 'MutatedPeptides': |
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144 MutatedPeptides(args.sequence, args.mutation_site_list, args.AA_list, args.outputFile) |
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145 |
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146 elif sys.argv[1] == 'RandomPeptides': |
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147 RandomPeptides(args.AA_list, args.pep_length, args.out_pep_lenght, args.outputFile) |
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148 |
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149 elif sys.argv[1] == 'SlidingWindowPeptide': |
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150 SlidingWindowPeptide(args.InFile, args.winSize, args.FragSize, args.outputFile) |
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151 |
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152 else: |
5
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153 print("Incorrect option provided: %s" % (sys.argv[1])) |
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154 |