Remove/Identify deprecated IDs from a list of Entrez IDs programatically
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?
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Ram
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salamandra
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salamandra
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ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz "comprehensive information about GeneIDs that are no longer current"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
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Ram
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Pierre Lindenbaum
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Pierre Lindenbaum
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and example of deprecated ID please ?
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
so it's a GENE /entrez id