How to write all the possible translation into a new fasta file?

Question

[macadamopetrus]

Dear all, This is my first time working with Biopython. I tried to translate unambigous rna sequences from a multi-fasta format file (containing 5 different random sequences) with 3 frame shifts (= meaning getting all possible translation of the RNA sequence). I got this part with the help of Biopython Tutorial and Cook book pdf . “onlinehttp://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc35”
Then I tried to write all the possible translation into a new file. And here I am, stuck. What I already tried: 1) Using Bio.SeqRecord I get only 5 translations of the 5 different RNA sequences. So I don’t get the other 2 frame shifted translation sequences under the original one.

2) And I even tried it with records but then I get 3 sequences only translated. But these are from the last sequence (= means 5th sequence from fasta file) of the random RNA with all 3 possible translation of RNA.

I did not find any other method that could write my translated sequences into a new fasta file. Please help I have tried everything. That means that I have even tried to write all the sequences with hand (see site: writing sequence files) even this attempt was not successful because every translated frame was written in one single line. So I got 5 lines, with 1 line containing all possible translations. What I am trying to achieve is to put all the translated sequences into a fasta file. This means there should be in total 15 sequences.

[Eric Lim]

It'd be helpful to post some code snippets to illustrate what you'd tried. Without checking into biopython's ability to translate 3 frames directly from the interface, one approach can be rec.seq.translate(), rec.seq[1:].translate(), and rec.seq[2:].translate().

[macadamopetrus]

I already tried that but then also I would only get 5 translated sequences that are in the frame. The other 2 translations are not there.

[macadamopetrus]

from Bio.SeqRecord import SeqRecord
def make_protein_record(nuc_record):
    """Returns a new SeqRecord with the translated sequence (default table)."""
    return SeqRecord(seq = nuc_record.seq.translate(cds=False), \
                     id = "trans_" + nuc_record.id, \
                     description = "translation of proteins, unambiguous RNA seq")

# so the function return "SeqRecord(seq = nuc_record.seq.translate(cds=False),\" giives in new fasta file 
#only the first 5 translated proteins. 
#But when I add a new code like this :r
        return SeqRecord(seq = seq_record.seq.translate(), \
                      seq1 = seq_record.seq[1:].translate(), \
                       seq2 = seq_record.seq[2:].translate(), \
                       id = "rc_" + record.id, \
                       description = "translation of protein, unambiguous RNA seq")

This code will give: TypeError: __init__() got an unexpected keyword argument 'seq1'

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[macadamopetrus]

Sorry, Thanks :)

Answer 1

[Eric Lim]

Assuming

[/scratch/tmp/biostars/biopython_translate_allframes]$ cat test.fa 
>a
agctagctagc
>b
gctagctgctag
>c
gatcgatcgatcga
>d
gctgctagctagct
>e
gctagctagctag

Something along this should work fine.

with open('test.translated.fa', 'w') as fout:
  for rec in SeqIO.parse('test.fa', 'fasta'):
    for frame in range(0,3):
      SeqIO.write(SeqRecord(seq=rec[frame:].seq.translate(), id=rec.id, description=str(frame)), fout, 'fasta')

[macadamopetrus]

from Bio import SeqIO
for record in SeqIO.parse("rna_1.fasta", "fasta"):
    printrecord.id)
    print(record.seq.translate())
    print(record.seq[1:].translate())
    print(record.seq[2:].translate())

Answer 2

[Joe]

BioPython’s SeqUtils offers a six_frame_translations method, I’d advise using this. Eric’s solution, while neat, probably isn’t really the ‘pythonic’ way - you’d be getting your hands unnecessarily dirty ;)

http://biopython.org/DIST/docs/api/Bio.SeqUtils-module.html

[Eric Lim]

Nice! I knew there must be a way to translate 6-way within the module.