Getting data from NCBI using Python

Question

[Quân]

Hi everyone,

It might sound a bit dumpy since I am pretty new with Python.

I have a list of 150 genes from an RNAseq data and I want to extract some information related to each gene from NCBI, including gene coordinates and reference sequence. I was trying some relevant packages (e.g., pyEnsembl) here but none of them seems working.

If any one has encountered a similar problem, could you kindly give some advice on how to extract gene information from NCBI? The idea is I want to write a script so for a larger list of genes in the future, I will not need to do it manually.

Thanks and have all a good day.

Answer 1

[GenoMax]

Take a look at NCBI Datasets package (there is a web option as well as a command line tool) or NCBI Entrezdirect package.

In title you are asking about getting from Ensembl but then referring to NCBI in body of post.