[BioPython] SeqRecord to Genbank: use SeqIO?
Cedar McKay
cmckay at u.washington.edu
Fri Aug 1 01:45:15 UTC 2008
Hello, I have SeqRecord objects that I'd like to convert to a string
that is in Genbank format. That way I can do whatever with it,
including write it to a file. The only way I can see to do anything
similar is using SeqIO and doing something like:
SeqIO.write(my_records, out_file_handle, "genbank")
which I found here:
http://biopython.org/DIST/docs/tutorial/Tutorial.html#chapter:Bio.SeqIO
The problem is, it doesn't support something like:
SeqIO.write(seq_record, out_file_handle, "genbank")
Because it requires an iterable object I guess? And it has to write to
a file handle for some reason, and won't just give me the string to do
whatever I want with.
I've done a lot of searching and mailing lists, and googling, and
surely I must be missing something? What is the simplest way to get a
string representing a genbank file, starting with a SeqRecord?
I'm sort of shocked that there isn't some sort of
SeqRecord.to_genbank() method.
Hope someone can point me in the right direction!
best,
Cedar
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