remove items from list in python

You can also use a list comprehension:

>>> n = ['UUU', 'F', 'CUU', 'L', 'AUU', 'I', 'GUU', 'V', 'UUC', 'F', 'CUC', 'L', 'AUC', 'I', 'GUC', 'V', 'UUA', 'L', 'CUA', 'L', 'AUA', 'I', 'GUA', 'V', 'UUG', 'L', 'CUG', 'L', 'AUG', 'M', 'GUG', 'V', 'UCU', 'S', 'CCU', 'P', 'ACU', 'T', 'GCU', 'A', 'UCC', 'S', 'CCC', 'P', 'ACC', 'T', 'GCC', 'A', 'UCA', 'S', 'CCA', 'P', 'ACA', 'T', 'GCA', 'A', 'UCG', 'S', 'CCG', 'P', 'ACG', 'T', 'GCG', 'A', 'UAU', 'Y', 'CAU', 'H', 'AAU', 'N', 'GAU', 'D', 'UAC', 'Y', 'CAC', 'H', 'AAC', 'N', 'GAC', 'D', 'UAA', 'Stop', 'CAA', 'Q', 'AAA', 'K', 'GAA', 'E', 'UAG', 'Stop', 'CAG', 'Q', 'AAG', 'K', 'GAG', 'E', 'UGU', 'C', 'CGU', 'R', 'AGU', 'S', 'GGU', 'G', 'UGC', 'C', 'CGC', 'R', '', '', '', '', '', 'AGC', 'S', '', '', '', '', '', 'GGC', 'G', 'UGA', 'Stop', '', '', 'CGA', 'R', '', '', '', '', '', 'AGA', 'R', '', '', '', '', '', 'GGA', 'G', 'UGG', 'W', '', '', '', '', '', 'CGG', 'R', '', '', '', '', '', 'AGG', 'R', '', '', '', '', '', 'GGG', 'G', '']    

>>> n = [x for x in n if x != '']   # or more simply [x for x in n if x]
>>> print n

['UUU', 'F', 'CUU', 'L', 'AUU', 'I', 'GUU', 'V', 'UUC', 'F', 'CUC', 'L', 'AUC', 'I', 'GUC', 'V', 'UUA', 'L', 'CUA', 'L', 'AUA', 'I', 'GUA', 'V', 'UUG', 'L', 'CUG', 'L', 'AUG', 'M', 'GUG', 'V', 'UCU', 'S', 'CCU', 'P', 'ACU', 'T', 'GCU', 'A', 'UCC', 'S', 'CCC', 'P', 'ACC', 'T', 'GCC', 'A', 'UCA', 'S', 'CCA', 'P', 'ACA', 'T', 'GCA', 'A', 'UCG', 'S', 'CCG', 'P', 'ACG', 'T', 'GCG', 'A', 'UAU', 'Y', 'CAU', 'H', 'AAU', 'N', 'GAU', 'D', 'UAC', 'Y', 'CAC', 'H', 'AAC', 'N', 'GAC', 'D', 'UAA', 'Stop', 'CAA', 'Q', 'AAA', 'K', 'GAA', 'E', 'UAG', 'Stop', 'CAG', 'Q', 'AAG', 'K', 'GAG', 'E', 'UGU', 'C', 'CGU', 'R', 'AGU', 'S', 'GGU', 'G', 'UGC', 'C', 'CGC', 'R', 'AGC', 'S', 'GGC', 'G', 'UGA', 'Stop', 'CGA', 'R', 'AGA', 'R', 'GGA', 'G', 'UGG', 'W', 'CGG', 'R', 'AGG', 'R', 'GGG', 'G']

To expand a bit on why you shouldn't change a list this way as you're iterating over it, consider the following simplification of what you're doing:

>>> a = range(10)
>>> a
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
>>> for item in a:
...     print item
...     a.remove(item)
... 
0
2
4
6
8
>>> a
[1, 3, 5, 7, 9]

As this illustrates, by changing the list, you're also changing which elements you act on in successive iterations. That's almost never a good idea and appears not to be what you're trying to accomplish.

Instead, how about a list comprehension:

[item for item in mylist if item != '']

Instead of trying to remove the blanks, try instead to make a new array which contains only the non-blank items

a = ['UUU', 'F', 'CUU', 'L', 'AUU', 'I', 'GUU', 'V', 'UUC', 'F', 'CUC', 'L', 'AUC', 'I', 'GUC', 'V', 'UUA', 'L', 'CUA', 'L', 'AUA', 'I', 'GUA', 'V', 'UUG', 'L', 'CUG', 'L', 'AUG', 'M', 'GUG', 'V', 'UCU', 'S', 'CCU', 'P', 'ACU', 'T', 'GCU', 'A', 'UCC', 'S', 'CCC', 'P', 'ACC', 'T', 'GCC', 'A', 'UCA', 'S', 'CCA', 'P', 'ACA', 'T', 'GCA', 'A', 'UCG', 'S', 'CCG', 'P', 'ACG', 'T', 'GCG', 'A', 'UAU', 'Y', 'CAU', 'H', 'AAU', 'N', 'GAU', 'D', 'UAC', 'Y', 'CAC', 'H', 'AAC', 'N', 'GAC', 'D', 'UAA', 'Stop', 'CAA', 'Q', 'AAA', 'K', 'GAA', 'E', 'UAG', 'Stop', 'CAG', 'Q', 'AAG', 'K', 'GAG', 'E', 'UGU', 'C', 'CGU', 'R', 'AGU', 'S', 'GGU', 'G', 'UGC', 'C', 'CGC', 'R', '', '', '', '', '', 'AGC', 'S', '', '', '', '', '', 'GGC', 'G', 'UGA', 'Stop', '', '', 'CGA', 'R', '', '', '', '', '', 'AGA', 'R', '', '', '', '', '', 'GGA', 'G', 'UGG', 'W', '', '', '', '', '', 'CGG', 'R', '', '', '', '', '', 'AGG', 'R', '', '', '', '', '', 'GGG', 'G', '']

b = []
for x in a:
    if len(x)>0:
        b.append(x)

As dylrei mentioned, list comprehension is a pythonic solution, but is has a drawback with (very) huge list since it copies the list. If you have a huge list and the item you want to remove is only a few times in the list, then I suggest the following (less pythonic) solution:

>>> l=[1,2,3,4,5,6,1,2,3,1,2,1,1]
>>> while True:
...     try:
...         l.remove(1)
...     except ValueError:
...         break
... 
>>> l
[2, 3, 4, 5, 6, 2, 3, 2]