"""Count taxonomic groups represented in SeqDbFasta object.
Produces an SQLite DB file containing a table with a "Linnean"
(in a broad sense) lineage for each SeqDb record, as well as
the aggregate count tables for each taxonomic level."""
refDataDir = "../../atovtchi/shannon_viral_IO_paper/shannon_viral_paper_2011.v.1"
workDir = refDataDir
#dbPath = pjoin(workDir,"refseq-taxa")
dbPath = "seq-db.mic"
#taxonomyDir = pjoin(workDir,"taxonomy")
topTaxids = micTaxids
dbSeq = SeqDbFasta(path=dbPath)
taxids = dbSeq.getTaxaList()
#taxaTree = loadTaxaTree(ncbiDumpFile=pjoin(taxonomyDir,"nodes.dmp"),
# ncbiNamesDumpFile=pjoin(taxonomyDir,"names.dmp"))
taxaTree = loadTaxaTree()
topNodes = [ taxaTree.getNode(topTaxid) for topTaxid in topTaxids ]
linwr = LinnWriter(taxaTree=taxaTree)
wr = linwr.newWriter()
for taxid in taxids:
node = taxaTree.getNode(taxid)
if sum(( node.isUnder(topNode) for topNode in topNodes )):
wr.send(dict(taxid=taxid,weight=dbSeq.seqLengths(taxid)["len"].sum()))
#wr.send(dict(taxid=taxid))
