Efficient means of mass converting Affy SNP IDs to dbSNP rs ids
I am trying to convert a map file for some SNP data I want to use from Affy ids to dbSNP rs ids (ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/, specifically ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/all_snp.map.gz).
I am trying to find an effective way to this. I have the annotation file for the Axiom Human Origins array from which the data comes from, so I know the proper ids.
I was wondering if anyone could suggest a good bash/Python/Perl based method to this. The idea I had in mind was the
sed -i 's/*Affy#*/*rs#*/g' *filename*
method, but I figure this would not be the most efficient as it would be >600,000 replacements. Any suggestions? Thanks!
if you can use a command line tool it will likely be the more efficient
than relying on perl.
I'd suggest you pipe your output instead of doing an inline replace just to
ensure you have an un-tainted file to come back to in the event of a
-- Dylan B. Storey
Post Doctoral Researcher
University of California, Davis
1089 Veterinary Medicine Drive
Davis Ca 95616
"There is a single light of science, and to brighten it anywhere is to
brighten it everywhere."- Isaac Asimov
Posting if anyone might have similar problem.
This is easily done with plink update
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