UnboundLocal Error onfile

Question

I've got a problem with this file. When I launch it I get an error on line 24.

UnboundLocal Error : local variable 'file_out' referenced before assignment.

Any suggestion on how to correct it will be greatly appreciated. I have to say that I'm a complete noob on python and didn't write this by myself.

#!/usr/local/python

import sys, getopt
import os

usage="python correct_mol2.py -i 2qab_ligand.mol2 -o 2qab_ligand_new.mol2\n"

def main(argv):

    try:
        opts,args = getopt.getopt(sys.argv[1:],'hi:o:')
    except getopt.GetoptError:
        sys.exit(2)

    for opt, arg in opts:
        if opt == '-h':
            print usage
            sys.exit()
        elif opt == '-i':
                file_in = arg
        elif opt == '-o':
            file_out = arg
    x=0
    fout=file("%s"%file_out,"w")
    for line in file(file_in):
#       print line
        if line.find("@<TRIPOS>BOND") >= 0:
            x=0
        if x==0:
            fout.write(line)
        if x==1:
            if line[47:49] == '35' :
                fout.write(line[:47]+"Br"+line[49:])
                continue
            if line[47:49] == '17' :
                fout.write(line[:47]+"Cl"+line[49:])
                continue
            if line[47:48] == '9' :
                fout.write(line[:47]+"F"+line[48:])
                continue
            if (line[47] == 'H' and line[48] ==' ') or line[47] == 'F' or line[47:49] == 'Br' or line[47:49] == 'Cl' :
                fout.write(line)
                continue
            else:
                fout.write(line[:48]+"."+line[48:54]+line[55:])
        if line.find("@<TRIPOS>ATOM") >= 0:
            x=1
    fout.close()

main(sys.argv)

Answer 1

The file_out argument is only set if the -o argument is set.

You need to perhaps set a default before the for opt, arg in opts: loop:

file_out = 'default_filename'

If -o is meant to be a mandatory option, you'll need to explicitly test for the option being absent.

Other comments on your code:

• Use argparse instead; optparse has been deprecated, it's successor is far more flexible and versatile.

• file_out is, when set, already a string. No need to use string formatting on it; you can pass it straight to open() (rather than file(), also deprecated). If you use the file object as a context manager then it'll be closed for you automatically:

  with open(file_out, "w") as fout, open(file_in) as fin:
      for line in fin:
  

• You can use the file object as an iterator, meaning you can advance the file object and get more lines in the for loop as your parsing state changes. Use this to detect Tripos MOL2 records.

  Tripos MOL2 data records use tabs or spaces to separate the lines; split your line into columns, then pick out the specific column to map replacement values for. That's a lot less fragile than slicing the lines to specific columns:

  map = {'35': 'Br', '17': 'Cl', '9': 'F'}
  # when we encounter a mapped value, make it easier on ourselves
  # and map those back to themselves
  map.update((v: v) for v in map.values())
  
  section = None
  for line in fin:
      if line[0] == '@':
          # new section
          section = line.strip().rpartition('>')[-1]
          fout.write(line)
          continue
  
      if section != 'ATOM':
          fout.write(line)
          continue
  
      # parse the ATOM section
      for line in fin:
          if line[0] == '@':  # section end, we are done
              section = line.strip().rpartition('>')[-1]
              fout.write(line)
              break
  
          # atom data lines are whitespace separated
          row = line.split()
  
          # I'm assuming column 7 is the value you are replacing; adjust as required
          row[7] = map.get(row[7], '.')
  
          # re-join line with tabs, write out
          fout.write('\t'.join(row) + '\n')