Mercurial > repos > guerler > springsuite

comparison spring_map.py @ 38:80a4b98121b6 draft

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"planemo upload commit 22cd6b0fa88ce0ddc4052beab306f5ba10754f12"
author guerler
date Wed, 25 Nov 2020 17:38:24 +0000
parents 0be0af9e695d
children 172398348efd
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37:0be0af9e695d 38:80a4b98121b6
6 from spring_package.Molecule import Molecule 6 from spring_package.Molecule import Molecule
7 7
8 8
9 def getId(line): 9 def getId(line):
10 line = line.strip() 10 line = line.strip()
11 if len(line) != 6 or line[4:5] != "_":
12 raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % line)
11 return line[:4].upper() + line[4:6] 13 return line[:4].upper() + line[4:6]
12 14
13 15
14 def getPDB(line, args): 16 def getPDB(line, args):
15 pdb = line[:4].lower() 17 pdb = line[:4].lower()
129 output_file.write("%s\n" % entry) 131 output_file.write("%s\n" % entry)
130 132
131 133
132 if __name__ == "__main__": 134 if __name__ == "__main__":
133 parser = argparse.ArgumentParser(description='Maps binding partners to template library') 135 parser = argparse.ArgumentParser(description='Maps binding partners to template library')
134 parser.add_argument('-l', '--list', help='List of template entries [PDB_CHAIN]', required=True) 136 parser.add_argument('-l', '--list', help='List of template entries `PDB_CHAIN`', required=True)
135 parser.add_argument('-i', '--index', help='PDB Database Index file (dbkit_index)', required=True) 137 parser.add_argument('-i', '--index', help='PDB Database Index file (dbkit_index)', required=True)
136 parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', required=True) 138 parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', required=True)
137 parser.add_argument('-c', '--cross', help='Cross reference (unmapped)', required=True) 139 parser.add_argument('-c', '--cross', help='Cross reference (unmapped)', required=True)
138 parser.add_argument('-o', '--output', help='Cross reference', required=True) 140 parser.add_argument('-o', '--output', help='Cross reference', required=True)
139 parser.add_argument('-g', '--log', help='Log File', required=True) 141 parser.add_argument('-g', '--log', help='Log File', required=True)