pdaug_tsvtofasta: PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

comparison

equal deleted inserted replaced

--1:000000000000
+:c3f0b3a6339e
+import tempfile
+import pandas as pd
+import shutil
+import sys
+import glob
+import fragbuilder
+import openbabel
+from fragbuilder import peptide
+import os
+def read_pep_file(pep_infile):
+file = open(pep_infile)
+lines = file.readlines()
+Index = []
+list_pep_name = []
+for line in lines:
+if '>' in line:
+Index.append(line.strip('\n'))
+else:
+line = line.strip('\n')
+line = line.strip('\r')
+list_pep_name.append(line.strip('\n'))
+return list_pep_name
+def structure_gen(pep_seq, out_dir):
+if not os.path.exists(os.path.join(out_dir, 'DataFile')):
+os.makedirs(os.path.join(out_dir, 'DataFile'))
+b = len(pep_seq)
+for seq in pep_seq:
+pep = peptide.Peptide(seq, nterm = "charged", cterm = "neutral")
+pep.regularize()
+pep.write_pdb(os.path.join(out_dir, 'DataFile', seq+".pdb"))
+obConversion = openbabel.OBConversion()
+obConversion.SetInAndOutFormats("pdb", "sdf")
+mol = openbabel.OBMol()
+obConversion.ReadFile(mol,  os.path.join(out_dir, 'DataFile', seq+".pdb"))
+mol.AddHydrogens()
+def main_process(str_pep_file, out_dir):
+my_pep = read_pep_file(str_pep_file)
+structure_gen(my_pep, out_dir)
+if __name__=="__main__":
+import argparse
+parser = argparse.ArgumentParser()
+parser.add_argument("-p", "--pep", required=True, default=None, help="pep file")
+parser.add_argument("-o", "--OutDir", required=None, default=os.getcwd(), help="Path to out file")
+args = parser.parse_args()
+main_process(args.pep, args.OutDir)

Mercurial > repos > jay > pdaug_tsvtofasta