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Question: Remove/Identify deprecated IDs from a list of Entrez IDs programatically
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gravatar for salamandra
4.0 years ago by
salamandra • 230
salamandra • 230 wrote:

If I have a list of Entrez IDs, how do I identify programatically those that are deprecated in order to remove them from the list?

 
entrez deprecated remove • 1.6k views
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modified 4.0 years ago by Pierre Lindenbaum ♦ 121k • written 4.0 years ago by salamandra • 230

and example of deprecated ID please ?

ADD REPLY • link written 4.0 years ago by Pierre Lindenbaum ♦ 121k

638800 is an example: http://www.ncbi.nlm.nih.gov/gene/?term=638800.

Another example is this: 639384 http://www.ncbi.nlm.nih.gov/gene/?term=639384

ADD REPLY • link written 4.0 years ago by salamandra • 230

so it's a GENE /entrez id

ADD REPLY • link written 4.0 years ago by Pierre Lindenbaum ♦ 121k
1
gravatar for Pierre Lindenbaum
4.0 years ago by
Pierre Lindenbaum ♦ 121k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 121k wrote:

ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz  "comprehensive information about GeneIDs that are no longer current"

extract and sort this list of ID 

curl "ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz" | gunzip -c | tail -n+1 | cut -f 3 | LC_ALL=C sort

sort your list on the ID colum

and use linux join to remove those IDs from your list. http://linux.die.net/man/1/join
ADD COMMENT • link written 4.0 years ago by Pierre Lindenbaum ♦ 121k
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