Getting a feature within genbank object

[NRW]

Hi again,
I am trying to get a feature from a genbank record (bacterial genome) to obtain the locus coordinates.  Ideally, I would like to do something like "gb.nucleotide("NC_000913.3", locus_tag="b0003").  When using gb.nucleotide("NC_000913.3"), the Dseqrecord contains the whole genome sequence, but does not contain the sub features (the CDS's, etc).  When getting the gene of interest  using "gb.nucleotide("NP_414544.1")", the coordinates given are relative to the gene (1..933), not the actual coordinates in the genbank record.  Is there any workaround?
Thanks again!

[Björn Johansson]

Hi,

You probably need to download the whole genome  (NC_000913.3) in order to have access to the features. The NC_000913.3 is a protein, and it does not seem to contain the coordinates of NC_000913.3.

I found a bug in pydna that is now fixed that prevented download of the entire record.

see this notebook, especially in the end:

https://gist.github.com/BjornFJohansson/61c5a394b77a2cee136d

I will have a new pydna bugfix version up later today.

You can also change the pydna code in "download.py" line 216

rettype   = "gb" 

into

rettype = "gbwithparts"

/bjorn

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Björn Johansson
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