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Get a sequence from a Genbank ID #3

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audy opened this issue Jul 17, 2014 · 4 comments
Closed

Get a sequence from a Genbank ID #3

audy opened this issue Jul 17, 2014 · 4 comments
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@audy
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@audy 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

@alanrice
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@alanrice 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

ncbi.download('nucleotide', 'AF068820.2')

perhaps?

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

@bmpvieira
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@bmpvieira bmpvieira commented Jul 18, 2014

We can add this using efetch (http://www.ncbi.nlm.nih.gov/books/NBK25499/).
ncbi.download could give the same result as efetch and ncbi.search would return the metadata.

@audy
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@audy audy commented Jul 18, 2014

Right there would only be download.

Also, pagination. I know the NCBI API has support for this.

ncbi.download('nucleotide', ['AF068820.2', ...])
@bmpvieira
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@bmpvieira 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
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