Key error in dna complement

Question

import string
import os,sys

file=open("C:\Python27\\New Text Document.txt",'r')\
seq =file.readlines() basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}

def translate(seq):
    aaseq = []
    for str in seq:
       aaseq.append(basecomplement[str])
    return aaseq

for frame in range(1):
    rseqn= (''.join(item.split('|')[0] for item in translate(seq[frame:])))

rseqn = rseqn[::-1]    
print(rseqn)
print(seq)

ERROR HERE IS File

"C:\Users\ram\Desktop\pythonhw\dnacomp.py", line 13, in <module>
rseqn= (''.join(item.split('|')[0] for item in
translate(seq[frame:])))   File

"C:\Users\ram\Desktop\pythonhw\dnacomp.py", line 10, in translate
aaseq.append(basecomplement[str]) KeyError:
'AGTCTGGCATACCAGTACAGACTATCA'

if i use simple string i am also getting sequence but i tried to read the file as input it shows the following error

please clean the code !!! – Hasan Ramezani Oct 03 '14 at 22:20 — Hasan Ramezani, Oct 03 '14 at 22:20

Cory Kramer · Accepted Answer · 2014-10-03T22:58:22.893

2

If I understand what you are trying to get at

def translate(seq):
    basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
    return ''.join(basecomplement[letter] for letter in seq)

Testing

s = 'ATCGGCATAATAC'
>>> translate(s)
'TAGCCGTATTATG'

For translating a file, you would do something like

with open('file.txt', 'r') as f:
    for line in f:
        print(translate(line))

edited Oct 03 '14 at 22:58

answered Oct 03 '14 at 22:21

Cory Kramer

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i understand can i use this function for file as input Cyber – chakri 123 Oct 03 '14 at 22:55
Can you show an example of what your file looks like? – Cory Kramer Oct 03 '14 at 22:56
dna file FASTA formate – chakri 123 Oct 03 '14 at 23:02
if you want me to paste data here i can do it also – chakri 123 Oct 03 '14 at 23:02
i have to use this code in shell or in program – chakri 123 Oct 03 '14 at 23:12

Key error in dna complement

1 Answers1