Question

Hey I am a newbie at python and I need some help. I’ve written down the following code:

 try:
  it = iter(cmLines)
  line=it.next()
  while (line):
    if ("INFERNAL1/a" in line) or ("HMMER3/f" in line) :
      title = line
      line = it.next()
      if word2(line) in namesList: //if second word in line is in list
        output.write(title)
        output.write(line)
        line = it.next()
        while ("//" not in line):
          output.write(line)
          line = it.next()
        output.write(line)
    line = it.next()
except Exception as e:
  print "Loop exited becuase:"
  print type(e)
  print "at " + line
finally:
  output.close()

1. When the loop ends it always throws an Exception that notifies that the loop stopped. Even though it didn’t terminate prematurely. How do I stop that?

2. Is there a better way to write my code? Something more stylish. I have a big file that has lots of information and I am trying to catch only the information I need. Every slice of information is of the format:

   Infernal1/a ...
   Name someSpecificName
   ...
   ...
   ...
   ...
   // 
   

Thank you

Answer 1

RocketDonkey’s answer is spot-on. Because of the complexity of the way you’re iterating, there is no simple way to do this with a for loop, so you’re going to need to explicitly handle StopIteration.

However, if you rethink the problem a bit, there are other ways around this. For example, a trivial state machine:

try:
    state = 0
    for line in cmLines:
        if state == 0:
            if "INFERNAL1/a" in line or "HMMER3/f" in line:
                title = line
                state = 1
        elif state == 1:
            if word2(line) in NamesList:
                output.write(title)
                output.write(line)
                state = 2
            else:
                state = 0
        elif state == 2:
            output.write(line)
            if '//' in line:
                state = 0
except Exception as e:
    print "Loop exited becuase:"
    print type(e)
    print "at " + line
finally:
    output.close()

Alternatively, you can write a generator function that delegates to sub-generators (via yield from foo() if you’re in 3.3, via for x in foo(): yield x if not), or various other possibilities, especially if you rethink your problem at a higher level.

That may not be what you want to do here, but it’s usually worth at least thinking about “Can I turn this while loop and two explicit next calls into a for loop?”, even if the answer turns out to be “No, not without making things less readable.”

As a side note, you can probably simplify things by replacing the try/finally with a with statement. Instead of this:

output = open('foo', 'w')
try:
    blah blah
finally:
    output.close()

You can just do this:

with open('foo', 'w') as output:
    blah blah

Or, if output isn’t a normal file, you can still replace the last four lines with:

with contextlib.closing(output):
    blah blah