Comments (4)
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.
from bionode-ncbi.
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.
from bionode-ncbi.
Right there would only be download.
Also, pagination. I know the NCBI API has support for this.
ncbi.download('nucleotide', ['AF068820.2', ...])
from bionode-ncbi.
Moving discussion to #10
from bionode-ncbi.
Related Issues (20)
- Implement efetch API
- Download the GFF file of the Cycas taitungensis mitochondrion HOT 9
- Uncaught, unspecified "error" event HOT 1
- How to look up metadata for an SRR file HOT 1
- Tests are broken because of NCBI side metadata changes (again) HOT 2
- rna_from_genomic instead of genomic.fna
- geo is not searchable HOT 5
- download in the examples printing too much info HOT 3
- We need a smaller assembly from NCBI for testing HOT 3
- Git rid of git-lfs
- Error handling when NCBI connection is lost HOT 4
- User-friendly CLI
- Modularize lib structure.
- Output some warning to terminal when there is no output
- Add Blast API HOT 2
- Use progress bar on download HOT 5
- Downloading one run download the whole Bioproject
- TypeError: Cannot create property 'Run' on string ' ' HOT 1
- Dependencies error: Prototype Pollution (lodash dependencies)
- Unexpected error when running 'bionode' HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bionode-ncbi.