User:Lindenb/Notebook/UMR915/20100903

Download NCBI C toolbox
was ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/NCBI_C_Toolkit/ncbi_c--Jun_15_2010.tar.gz then tar xvf

mv ncbi_c--Jun_15_2010.tar.gz ncbi ncbi/make/makedis.csh (...) ********************************************************* *The new binaries are located in ./ncbi/build/ directory* *********************************************************

transform NCBI gene to XML
wget ftp://ftp.ncbi.nih.gov/gene/DATA/ASN_BINARY/Mammalia/Homo_sapiens.ags.gz gunzip Homo_sapiens.ags.gz  ncbi/build/gene2xml -b -i Homo_sapiens.ags.ags  <!DOCTYPE Entrezgene-Set PUBLIC "-//NCBI//NCBI Entrezgene/EN" "NCBI_Entrezgene.dtd">     1 0  

gene2xml -b -i ~/tmp/jeter.ags | wc 208,633,889 236,404,514 9,169,335,251