[BioPython] Trying to transcribe RNA = error?

[Peter]

On Tue, Jul 15, 2008 at 11:53 PM, Martin MOKREJŠ
<mmokrejs at ribosome.natur.cuni.cz> wrote:
> I agree but it should require whether a plus or minus strand will be
> transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
> somewhat artificial function.

By convention a DNA sequence is taken as the coding strand, so a
simple U to T is enough to transcibe to RNA.  This is somewhat
artificial (and doesn't really capture double strandedness), but does
seem to be a widley used convention.

You could do my_seq.reverse_complement().transcribe() if you did want
the other strand transcribed.

> What would be really meaningful if the object would be a genbank record
> with introns and transcribe() would rip out all the introns or even
> better allow me to choose which-ones to splice-out. Like to retain
> exons 1, 5, 7.

I was thinking it would be nice to take a SeqRecord with SeqFeatures
(i.e. a parsed GenBank file) and ask Biopython to give you the
nucleotide sequence for the feature.  In the case of intron/exons
these are held using the subfeatures, so it would make sense to obey
those.  I see this as a variation on splicing/subsetting (in python
speak) a sequence.

Maybe something like my_record[my_feature] or
my_record.extract_feature(my_feature)
Or my_record.extract_feature(i) which would refer to my_record.features[i]

Peter