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datasnakes / OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
https://orthoevolution.readthedocs.io/en/master/
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Hot Fix: Added function to download .gbff databases #103

Closed sdhutchins closed 6 years ago

sdhutchins commented 6 years ago

Features Added:

from Datasnakes.Tools.ftp import NcbiFTPClient
ncbiftp = NcbiFTPClient(email='xyz@gmail.com')
ncbiftp.getrefseqrelease(database_name='vertebrate_mammalian', seqtype='rna', filetype='gbff', download_path='',  extract=True)
sdhutchins commented 6 years ago

I'll make this a positive PR later tonight. @grabear

sdhutchins commented 6 years ago

@datasnakes/snakes I went ahead and closed it out so I could keep working on this branch.

FYI: You should now be able to download all of the .gbff files and create a command that uses the NcbiFTPClient to do within your genbank class. There's also an update feature in the NcbiFTPClient class. Worth noting that NCBI only updates the refseqrelease file every odd month so every 60ish days.

I'll be sure to include that in the documentation which needs significantly more detail.

Also, this now should give the opportunity for me to tackle the gilists function. I'll do that tonight most likely.

grabear commented 6 years ago

@sdhutchins This is excellent! been waiting to drop this in!