[Biopython-dev] [Biopython] Using SeqLocation to extract subsequence

[Kyle Ellrott]

I've posted a branch on my git (
http://github.com/kellrott/biopython/tree/FeatureExtract ).  The
Name/Description guess functions need to be finalized.  I wrote a unit test
that extracts CDS feature dna, and then runs translate on the dna and
compares it to the translation stored in the feature.  It passes all the
genbank files in the Test directory except for the ones that have 'N' in the
DNA sequence (that causes a translation exception) and one_of.gb (it refers
to sequence outside of the file).
More test ideas would be appreciated.

Kyle


There could be a problem if the SeqFeature qualifiers wasn't a
> list, for example a string like ""NC_123456" instead of say
> ["NC_123456"], but the assumption is safe with anything
> from the GenBank or EMBL parsers.
>
> Peter
>