New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.

Already on GitHub? Sign in to your account

Get a sequence from a Genbank ID #3

audy opened this Issue Jul 17, 2014 · 4 comments


3 participants

audy commented Jul 17, 2014

Is it possible to get a single sequence given a Genbank ID?

I tried:

bionode-ncbi search Genbank AF068820.2

Which returns nothing.

If not, this would be useful 馃樃


This comment has been minimized.

alanrice commented Jul 18, 2014

It isn't possible yet. "assembly" and "SRA" are the only supported NCBI sections at the moment.

Following "assembly" and "SRA" I imagine the syntax to get a sequence would be like

bionode-ncbi download nucleotide AF068820.2

and'nucleotide', 'AF068820.2')


Search and download in this case would be somewhat redundant given a unique Genbank ID, search would return with just one result.


This comment has been minimized.


bmpvieira commented Jul 18, 2014

We can add this using efetch ( could give the same result as efetch and would return the metadata.


This comment has been minimized.

audy commented Jul 18, 2014

Right there would only be download.

Also, pagination. I know the NCBI API has support for this.'nucleotide', ['AF068820.2', ...])

This comment has been minimized.


bmpvieira commented Apr 4, 2015

Moving discussion to #10

@bmpvieira bmpvieira closed this Apr 4, 2015

@bmpvieira bmpvieira self-assigned this Apr 5, 2017

@bmpvieira bmpvieira removed the enhancement label Apr 7, 2017

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment