Python TypeError: list indices must be integers, not str

Question

I have a list of names:

geneNameList = ['psaA', 'psbF', 'rpl36', 'rpoC1', 'psbK', 'atpB']

and a list of positions:

positionList = ['_1stpos', '_2ndpos', '_3rdpos']

I am trying to add the strings in my position list to each of the names in my list of names so I would end up with a partitionList:

partitionList = ['psaA_1stpos', 'psaA_2ndpos', 'psaA_3rdpos', psbF_1stpos', 'psbF_2ndpos'... 'atpB_3rdpos']

I have this code:

partitionList = []
for i in geneNameList:
    for k in positionList:
        partition = geneNameList[i] + positionList[k] + ' = '
        partitionList.append(partition)

But I keep getting this error:

    partition = geneNameList[i] + positionList[k] + ' = '
TypeError: list indices must be integers, not str

Answer 1

• Change geneNameList[i] + positionList[k] + ' = ' to i + k to add the values of each list.
  • geneNameList[i] implies you're trying to get a value based upon it's index in the list.
  • You are already iterating over the values, so you don't need to index the list.
  • Specifically, the TypeError is caused because you're indexing the list by a value instead of an integer. (eg geneNameList['psaA'] instead of geneNameList[0] )
• This just resolves the issue with your code without changing your way of writing it.

positionList = ['_1stpos', '_2ndpos', '_3rdpos']
geneNameList = ['psaA', 'psbF', 'rpl36', 'rpoC1', 'psbK', 'atpB']

partitionList = []
for i in geneNameList:
    for k in positionList:
        partition = i + k
        partitionList.append(partition)

print(partitionList)

['psaA_1stpos',
 'psaA_2ndpos',
 'psaA_3rdpos',
 'psbF_1stpos',
 'psbF_2ndpos',
 'psbF_3rdpos',
 'rpl36_1stpos',
 'rpl36_2ndpos',
 'rpl36_3rdpos',
 'rpoC1_1stpos',
 'rpoC1_2ndpos',
 'rpoC1_3rdpos',
 'psbK_1stpos',
 'psbK_2ndpos',
 'psbK_3rdpos',
 'atpB_1stpos',
 'atpB_2ndpos',
 'atpB_3rdpos']

Answer 2

You can use itertools.product to create a cross product of each of the gene names and positions and then join them together in a list comprehension to produce your partitionList :

import itertools

geneNameList = ['psaA', 'psbF', 'rpl36', 'rpoC1', 'psbK', 'atpB']

positionList = ['_1stpos', '_2ndpos', '_3rdpos']

partitionList = [''.join(gp) for gp in itertools.product(geneNameList, positionList)]

print(partitionList)

Output:

[
 'psaA_1stpos', 'psaA_2ndpos', 'psaA_3rdpos',
 'psbF_1stpos', 'psbF_2ndpos', 'psbF_3rdpos',
 'rpl36_1stpos', 'rpl36_2ndpos', 'rpl36_3rdpos',
 'rpoC1_1stpos', 'rpoC1_2ndpos', 'rpoC1_3rdpos',
 'psbK_1stpos', 'psbK_2ndpos', 'psbK_3rdpos',
 'atpB_1stpos', 'atpB_2ndpos', 'atpB_3rdpos'
]

If you want the = on the end of each string, just change ''.join(gp) to ''.join(gp) + ' = ' in the comprehension.

Answer 3

You are iterating over objects, not over integers.

Python works something like this:

Imagine that you have a list

[cat (an object with it properties), dog, human]

if you make:

for i in list: 

you will be iterating over cat, dog, and human, but not over the index of the list.

You have to do this:

for i in range(0, len(list)): 

So, now you are iterating over integers (list index) and not objects.