Question: Map rs to gene symbol in python script
gravatar for leireahedo02
8 months ago by
leireahedo020 wrote:

I have snp ids (rs18008665, rs3212227...) Now, I want to map these snp ids to gene symbols using Python script. I have found similar post, but as I have recently started to learn programing and with no bioinformatics knowledge, I´m unable to create the python script which works. Any script example to use?

snp script python gene • 408 views
ADD COMMENTlink modified 8 months ago by Pierre Lindenbaum104k • written 8 months ago by leireahedo020

look at this post: Get gene names from rs SNP ids

ADD REPLYlink written 8 months ago by cpad01124.1k
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum104k wrote:

using bash

$ wget  -O  - ""  |\
xmllint --format --xpath  '//*[name(.)="FxnSet"]/@symbol' - |\
tr " " "\n" | sort | uniq | cut -d '"' -f 2
ADD COMMENTlink written 8 months ago by Pierre Lindenbaum104k

Thank you Pierre. Easy to understand and concise solution, great help

ADD REPLYlink written 7 months ago by leireahedo020
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 778 users visited in the last hour