ó gbc@sLdZddlmZddlmZddlZdefd„ƒYZdS(s, Created on 24 sept. 2010 @author: coissac iÿÿÿÿ(t TaxonomyDump(tTaxonomyNt EcoTaxonomyDBcBs5eZd„Zd„Zd„Zd„Zd„ZRS(cCs-||_tjdIJ|jƒtjdIJtjdIJg|_xg|jƒD]Y\}}}|jj|||j|fƒ|dkrP|j|j|j|ƒqPqPWtjdIJx.|j ƒD] \}}|j||j|;ssSorting taxons...sIndexing taxonomy...isIndexing parent and rank...ii(RtcursortexecuteRRtlisttsettsorttdicttmapRtxrangetlenRt _taxonCmpR t _bsearchTaxont_ranksR tclose(RRtnttaxonomytrankstrankidxtindextt((s;lib/python2.7/site-packages/obitools/ecobarcode/taxonomy.pyR.s.   $      ccsR|jjƒ}|jdƒx%|D]\}}}|||fVq#W|jƒdS(Nsˆ select taxid,name,nameclass from ncbitaxonomy.names (RRRR$(RRRRt nameclass((s;lib/python2.7/site-packages/obitools/ecobarcode/taxonomy.pyRSs ccsL|jjƒ}|jdƒx|D]\}}||fVq#W|jƒdS(Ns† select oldtaxid,newtaxid from ncbitaxonomy.merged (RRRR$(RRtoldtaxidtnewtaxid((s;lib/python2.7/site-packages/obitools/ecobarcode/taxonomy.pyR `s ccsD|jjƒ}|jdƒx|D]}|dVq#W|jƒdS(Nsy select taxid from ncbitaxonomy.delnodes i(RRRR$(RRR((s;lib/python2.7/site-packages/obitools/ecobarcode/taxonomy.pyR ms   (t__name__t __module__RRRR R (((s;lib/python2.7/site-packages/obitools/ecobarcode/taxonomy.pyR s  ! % (t__doc__tobitools.ecopcr.taxonomyRRRR(((s;lib/python2.7/site-packages/obitools/ecobarcode/taxonomy.pyts