Biopython Translate function

[dmb107]

Hi all!

I'm having problems using Biopython to translate sequences into all 3 forward reading frames.

I wrote this script (and it works):

######################
#!/bin/python

#translate dna to protein

from Bio import SeqIO
input = open("input.fasta", "rU")

for record in SeqIO.parse(input, "fasta") :
protein_id = record.id
print(">" + protein_id)
print(record.seq.translate(to_stop=True))

input.close()
#########################

But this only gives me the default reading frame. After extensive searching, I still can't find how I edit the script so I can translate the +2 and +3 frames also.

Any help? Thanks!

[maubp]

I thought this was covered in the Biopython Tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html or the docstrings (API documentation), but can't find a specific example.

The basic idea is cut off the first base, or first two bases to get the next frames, e.g.

print("In frame")
print(record.seq.translate(to_stop=True))
print("Offset by one")
print(record.seq[1:].translate(to_stop=True))
print("Offset by two")
print(record.seq[2:].translate(to_stop=True))

[dmb107]

Thank you so much! I was about to rip my hair out! I really appreciate it!

[maubp]

Thank you for asking - this is useful feedback to improve the Biopython documentation:

https://github.com/biopython/biopython/issues/460

[Dean29]

This is very udeful! I like this info!