def getLineageInfo(blastHits, db=None):
"""
For each taxID present in blastHits, walk through the taxonomic tree,
starting from that taxID, and for each node, store the information
about the node (rank, taxID, parent_taxID, scientificName).
@param blastHits: A L{dark.blast.BlastHits} instance.
@param db: A database connection, with C{cursor} and C{close} methods.
@return: A C{dict} where each key is a taxID and the value is the
taxonomic information
"""
if db is None:
openedDb = True
db = mysql.getDatabaseConnection()
else:
openedDb = False
cursor = db.cursor()
taxIDLookUpDict = {}
for title in blastHits.titles:
taxID = blastHits.titles[title]['taxID']
if taxID not in taxIDLookUpDict:
taxIDLookUpDict[taxID] = _getLineageInfoPerTaxID(taxID, cursor)
cursor.close()
if openedDb:
db.close()
return taxIDLookUpDict
def __init__(self):
self._db = mysql.getDatabaseConnection()
self._cursor = self._db.cursor()
self._cache = {}
