python and user defined functions

Question

I was learning python coding and was using a function for calculating the gc percentage in a DNA sequence with undefined character N or n (NAAATTTGGGCCCN) and this created the following problem. is there a way to overcome this ?

def gc(sequence) :
    "This function computes the GC percentage of a dna sequence"
    nbases=sequence.count('n')+sequence.count('N')
    gc_count=sequence.count('c')+sequence.count('C')+sequence.count('g')+sequence.count('G')      #total gc count
    gc_percent=float(gc_count)/(len(sequence-nbases))     # TOTAL GC COUNT DIVIDED BY TOTAL LEN OF THE sequence-TOTAL NO. OF N
    return 100 * gc_percent

What is the following problem? Be more clear with your problem statement — taha, Jun 16 '20 at 18:16
What problem, exactly? If you received an error message, we need to see the full traceback. If you received an unexpected result, we need to see that result, and what you expected. — jasonharper, Jun 16 '20 at 18:16
Oh, I see it now - `len(sequence-nbases)` is trying to subtract a number from a string, you want `len(sequence) - nbases` instead. — jasonharper, Jun 16 '20 at 18:23

score 1 · Answer 1 · edited Jun 17 '20 at 00:45

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As @jasonharper said in the comments, you need to close the len() function. So change len(sequence-nbases) to len(sequence)-nbases.

len(sequence)-nbases

edited Jun 17 '20 at 00:45

Axe319

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answered Jun 16 '20 at 18:41

E. Goldsmi

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it worked. learning to program is a little bit complicated :) THANK YOU – bellet binu Jun 17 '20 at 16:36

score 0 · Accepted Answer · answered Jun 19 '20 at 00:02

def GC_content(dnaseq):
    percent = round(((dnaseq.count("C") + dnaseq.count("G")) / len(dnaseq)) * 100, 3)
    print(f'GC content: {percent} %')

Here is a code I had laying around for the same thing. But I had mine round to 3 decimal places just for consistency in my program. And I would just put something like sequence.upper() so you avoid having to hard code lower and upper-case letters.

python and user defined functions

2 Answers2