CODEWITHSUNDEEP
biopython
Mehsah Yhook
Mehsah Yhook

Reputation: 93

connecting to Ensembl via biopython

I have just join to the python and biopython work and like to connect Ensebml and fetch some sequences and other data like TSS, list of some genes and etc. But my problem is that I cannot seem to find any method or module in biopython to do so. I know this is a very routin thing in perl using Ensembl API. I really appreciate if some tell me or point me to a document to see how these things are being done in biopython. thanks

Upvotes: 4

Views: 2934

Answers (2)

Lydia
Lydia

Reputation: 33

You need to use and install the pyCogent module. Then the specific bit to do with Ensembl is here: http://pycogent.org/examples/query_ensembl.html

Depending on what you want to do you may prefer to use the REST API from Ensembl which is here: http://beta.rest.ensembl.org

Upvotes: 2

sefakilic
sefakilic

Reputation: 1230

There is a similar question and a few answers in BioStar.

Upvotes: 2

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