Remove/Identify deprecated IDs from a list of Entrez IDs programatically

Question

[salamandra]

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?

[Pierre Lindenbaum]

and example of deprecated ID please ?

[salamandra]

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

[Pierre Lindenbaum]

so it's a GENE /entrez id

Answer 1

[Pierre Lindenbaum]

ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz "comprehensive information about GeneIDs that are no longer current"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

and use linux join to remove those IDs from your list. http://linux.die.net/man/1/join