User:Lindenb/Notebook/UMR915/20100903

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Gene2XML NCBI

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
 <?xml version="1.0"?>
 <!DOCTYPE Entrezgene-Set PUBLIC "-//NCBI//NCBI Entrezgene/EN" "NCBI_Entrezgene.dtd">
 <Entrezgene-Set>
  <Entrezgene>
   <Entrezgene_track-info>
     <Gene-track>
       <Gene-track_geneid>1</Gene-track_geneid>
       <Gene-track_status value="live">0</Gene-track_status>
       <Gene-track_create-date>
         <Date>

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