Mercurial > repos > jay > pdaug_sequence_similarity_network

annotate PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py @ 8:c4bd95cae91f draft default tip

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author jay
date Wed, 12 Jan 2022 19:45:18 +0000
parents e650de82bcc7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import tempfile
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2 import pandas as pd
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3 import shutil
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4 import sys
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5 import glob
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6 import fragbuilder
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7 import openbabel
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8 from fragbuilder import peptide
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10 import os
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13 def read_pep_file(pep_infile):
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15 file = open(pep_infile)
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16 lines = file.readlines()
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18 Index = []
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19 list_pep_name = []
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21 for line in lines:
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22 if '>' in line:
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23 Index.append(line.strip('\n'))
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24 else:
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25 line = line.strip('\n')
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26 line = line.strip('\r')
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27 list_pep_name.append(line.strip('\n'))
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29 return list_pep_name
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31 def structure_gen(pep_seq, out_dir):
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33 if not os.path.exists(os.path.join(out_dir, 'DataFile')):
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34 os.makedirs(os.path.join(out_dir, 'DataFile'))
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36 b = len(pep_seq)
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38 for seq in pep_seq:
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40 pep = peptide.Peptide(seq, nterm = "charged", cterm = "neutral")
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41 pep.regularize()
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42 pep.write_pdb(os.path.join(out_dir, 'DataFile', seq+".pdb"))
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44 obConversion = openbabel.OBConversion()
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45 obConversion.SetInAndOutFormats("pdb", "sdf")
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46 mol = openbabel.OBMol()
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47 obConversion.ReadFile(mol, os.path.join(out_dir, 'DataFile', seq+".pdb"))
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49 mol.AddHydrogens()
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52 def main_process(str_pep_file, out_dir):
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54 my_pep = read_pep_file(str_pep_file)
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55 structure_gen(my_pep, out_dir)
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58 if __name__=="__main__":
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61 import argparse
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62 parser = argparse.ArgumentParser()
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64 parser.add_argument("-p", "--pep", required=True, default=None, help="pep file")
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65 parser.add_argument("-o", "--OutDir", required=None, default=os.getcwd(), help="Path to out file")
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67 args = parser.parse_args()
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68 main_process(args.pep, args.OutDir)
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