Question: Map rs to gene symbol in python script
0
gravatar for leireahedo02
4 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 • 276 views
ADD COMMENTlink modified 4 months ago by Pierre Lindenbaum99k • written 4 months ago by leireahedo020

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

ADD REPLYlink written 4 months ago by cpad01122.3k
1
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum99k wrote:

using bash

$ wget  -O  - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=rs18008665&retmode=xml"  |\
xmllint --format --xpath  '//*[name(.)="FxnSet"]/@symbol' - |\
tr " " "\n" | sort | uniq | cut -d '"' -f 2
ADD COMMENTlink written 4 months ago by Pierre Lindenbaum99k

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

ADD REPLYlink written 3 months ago by leireahedo020
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