How To Change The Alphabet Of Seqrecords In A Fasta File With Biopython?

Question

[Laura]

Hi, I am new to python. I am trying to translate some dna sequences (from a multifasta file) with the biopython .translate() method. However, it seems that by default the alphabet of the fasta sequences is set to SingleLetterAlphabet, and this is a problem to do the translation. Is there a way to change the Alphabet feature of my fasta sequences to "unambiguous_dna" or similar? Thanks for any help!

[Brad Chapman]

Can you show us the code you have so far? If you're using SeqIO to read in the file, then you want SeqIO.parse("file.fa", "fasta", alphabet=IUPAC.unambiguous_dna)

[Laura]

Thanks for your reply, Brad. When I try it I get the following error:

for seq in SeqIO.parse('orfs.fasta', 'fasta', alphabet=IUPAC.unambiguous_dna): ... seq.translate() ... Traceback (most recent call last): File "<stdin>", line 2, in <module> AttributeError: 'SeqRecord' object has no attribute 'translate'

[Brad Chapman]

The SeqIO parser gives you back SeqRecords (sequences plus name and annotations). translate is a method on Seq objects, so you want to do: 'for rec in SeqIO.parse' and then 'rec.seq.translate()'.

[Laura]

That worked, thank you!!

Answer 1

[Peter]

See the example(s) on translating FASTA files in the Biopython Tutorial, e.g. "Translating a FASTA file of CDS entries".

http://biopython.org/DIST/docs/tutorial/Tutorial.html

http://biopython.org/DIST/docs/tutorial/Tutorial.pdf