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TypeError: 'str' object is not callable

Im getting an error wile using a condition on a column two of a csv file. The error says:

TypeError                                 Traceback (most recent call last)
<ipython-input-108-e0c74da932d1> in <module>()
      6     gene = columns[2]
      7     length = columns[3]
----> 8     gen_seq_length = len(seq)
      9     gen_seq_length = int(gen_seq_length)
     10     if gen_seq_length >= 90 and gen_seq_length <= 110:

TypeError: 'str' object is not callable

My file contains 4 coulmns: Specie_Name Sequence Gene_name Gene_count

My code is:

data = open ("data.csv")
for column in data:
    columns = column.split(",")
    names = columns[0]
    seq = columns[1]
    gene = columns[2]
    length = columns[3]
    gen_seq_length = len(seq)

    if gen_seq_length >= 90 and gen_seq_length <= 110:
        print (gene)

And i want to Print out the gene names for all genes between 90 and 110 bases long.

Can anyone help?

python
• 15,178 views • link
updated by warrenfelsh • warrenfelsh • written by S AR S AR

I'd recommend avoiding keywords as variable names. For example, your code has length = columns[3], which might override any function that's also called length(). Maybe use xyz_length =

• 1 views • link
written by Ram Ram

I did change this variable earlier it was pos but i was getting same error

• 1 views • link
written by S AR S AR

Hello angelshiza ,

the code you are showing cannot be the (complete) one, where the error message is shown. In the message this line is shown: gen_seq_length = int(gen_seq_length) which is missing in the code.

Could you please provide a full code example and input file with which one can reproduce the problem?

Thanks,

fin swimmer

• 1 views • link
written by finswimmer finswimmer

The error was i assigned variable name with len and length which are already pre-built functions due to which i was getting an error. But now my problem is solve after changing variable names.

Secondly, gen_seq_length = int(gen_seq_length) this line was in my code i commented it .

• 1 views • link
written by S AR S AR

2 answers

The error and its location indicates that len is a string rather than a function. Perhaps len was redefined? Something like len='abc'. As a side note, notice that \r\n will be included in the last field. Consider column.strip().split(',').

• 1 views • link
updated by Ram Ram • written by jomo018 jomo018

\r\n will be included

Could be just \n too, depending on the OS. You're right, the lines need to be strip-ped

• 1 views • link
written by Ram Ram

I did use strip and rstrip but same error was there

• 1 views • link
written by S AR S AR

Did you check if you'd used len as a variable anywhere?

• 1 views • link
written by Ram Ram

Thanks. I wrote the code in new window with change name of variables it worked. My mistake was i used len and length as my variable which that disable the function of len when i called it to get the length of my column. Thank you

• 1 views • link
written by S AR S AR

I've moved the relevant comment to an answer. Please accept it to give the thread closure.

Upvote|Bookmark|Accept

• 1 views • link
written by Ram Ram

TypeError: 'str' object is not callable usually means you are using your () notation on a string, and Python tries to use that str object as a function. e.g. "hello world"(), or "hello"("world"). Or, if you have variable str and trying to call str() function. Finally: Do not declare python variable name same with python built-in function name, keyword etc.

• 0 views • link
updated by Joe Joe • written by warrenfelsh • warrenfelsh

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