Question: Which Alphabet Type Should I Use With Fasta Files In Biopython?
0
gravatar for sameer
7.9 years ago by
sameer10
sameer10 wrote:

If I'm using the FASTA files from the link below, what Alphabet type should I use in Biopython? Would it be IUPAC.unambiguous_dna?

link to FASTA files: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/?C=S;O=A

fasta biopython • 1.8k views
ADD COMMENTlink modified 6.4 years ago by Biostar ♦♦ 20 • written 7.9 years ago by sameer10
1
gravatar for Peter
7.9 years ago by
Peter5.9k
Scotland, UK
Peter5.9k wrote:

This is a duplicate of your question to the Biopython mailing list: http://lists.open-bio.org/pipermail/biopython/2013-March/008415.html

My answer is here: http://lists.open-bio.org/pipermail/biopython/2013-March/008416.html

Essentially I would use genericdna rather than unambiguousdna for now. The IUPAC alphabet object has a white list of expected letters, but current versions of Biopython do not enforce this in the sequence objects. That may change.

from Bio.Alphabet import generic_dna
from Bio.Alphabet.IUPAC import unambiguous_dna

You don't actually need to specify an alphabet at all, but telling Biopython the sequence is DNA will prevent some user errors.

ADD COMMENTlink written 7.9 years ago by Peter5.9k

And as of Biopython 1.78, you can't specify the alphabet - Bio.Alphabet was removed.

ADD REPLYlink written 8 weeks ago by Peter5.9k
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