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!