Python script error

Question

[Abdul Rafay Khan]

> File "dna2prot2-working-test-Copy.py", line 29, in <module> print
> (entry.seq).translate()#This will translate nucleotide sequence to
> amino acid sequence AttributeError: 'NoneType' object has no attribute
> 'translate'

Code:

import sys 
from Bio import SeqIO
from Bio.SeqIO.FastaIO import *
def fasta_reader(filename):   with open(filename) as handle:
    for record in FastaIterator(handle):
        yield record           

for entry in fasta_reader("test.txt"):
    print entry.id) #This is header of fasta entry
    print
    print (entry.seq) #This is sequence of specific fasta entry
    print
    dna=str (entry.seq)
    print ( entry.id)
from Bio.Tools import Translate  

    print (entry.seq).translate()#This will translate nucleotide sequence to amino acid sequence

[WouterDeCoster]

I did my best to properly format the code...

[WouterDeCoster]

And does entry.seq look as expected?

Answer 1

[Selenocysteine]

I think that the issue is that you are trying to translate outside from the for loop, and also that you are trying to translate the output of print instead of the seq item.

Try this:

import sys 
from Bio import SeqIO
from Bio.Tools import Translate  
from Bio.SeqIO.FastaIO import *

def fasta_reader(filename):   

    with open(filename) as handle:
         for record in FastaIterator(handle):
            yield record           

for entry in fasta_reader("test.txt"):
    print  entry.id) #This is header of fasta entry
    print  (entry.seq) #This is sequence of specific fasta entry
    dna = str  (entry.seq)
    print  entry.id)
    print   (entry.seq.translate())

Answer 2

[Thibault D.]

Hi,

The python error is clear: the syntax is not correct. Let's see your line. You have a lonely parenthesis on your print. Try this:

print str( entry.id )

Instead of:

print strentry.id)

This is a syntax error.

[WouterDeCoster]

OPs code was actually correct (I mean, no lonely parenthesis), but not rendered correctly by the biostars code engine. I have adapted the post to fix it.