def __generateServices(self, numServices, serviceParameters):
generator = self.__parameterGenerator()
services = []
taxonomy = Taxonomy('Root')
for i in xrange(numServices):
service = []
for i in xrange(serviceParameters):
p = generator.next()
service.append(p)
taxonomy.addChild('Root', p)
services.append(service)
return services, taxonomy
if child.name == lTaxonomy[iTaxLevel]:
node = child
break
## remove nodes with one child
for node in tree.traverse():
if len(node.get_children()) == 1:
if len(node.get_ancestors()) > 0:
ancestor = node.get_ancestors()[0]
ancestor.add_child(node.get_children()[0])
ancestor.remove_child(node)
else:
tree = node.get_children()[0]
return tree
taxonomy = Taxonomy(sTaxdumpDir=sTaxdumpDir)
lTaxonomies = []
for sLine in open(sInFile):
sTaxId = sLine.strip()
lTaxonomy = taxonomy.getTaxonomyByTaxId(sTaxId)
lTaxonomy = list(
map(lambda x: '{} {}'.format(re.sub('^ a-zA-Z0-9_', '', x[1]), x[0]),
lTaxonomy))[::-1]
lTaxonomies.append(lTaxonomy)
## for testing
"""
lTaxonomies = [['cellular organisms', 'eukaryota', 'opisthokonta', 'metazoa', 'eumetazoa', 'bilateria', 'deuterostomia', 'chordata', 'craniata', 'vertebrata', 'h**o sapiens'],\
['cellular organisms', 'eukaryota', 'opisthokonta', 'metazoa', 'eumetazoa', 'bilateria', 'deuterostomia', 'chordata', 'tunicata', 'ascidiacea', 'phlebobranchia', 'cionidae', 'ciona', 'ciona intestinalis'],\
['cellular organisms', 'bacteria', 'terrabacteria group', 'tenericutes', 'mollicutes', 'mycoplasmatales', 'mycoplasmataceae', 'mycoplasma', 'mycoplasma pneumoniae'],\
['cellular organisms', 'archaea', 'euryarchaeota', 'methanomada group', 'methanococci', 'methanococcales', 'methanococcaceae', 'methanococcus', 'methanococcus maripaludis']]
def __createDistributionTaxonomy(self):
taxonomy = Taxonomy('Root')
taxonomy.addChild('Root', 'A')
taxonomy.addChild('Root', 'B')
taxonomy.addChild('A', 'C')
taxonomy.addChild('A', 'D')
taxonomy.addChild('B', 'E')
taxonomy.addChild('B', 'F')
taxonomy.addChild('C', 'G')
taxonomy.addChild('C', 'H')
taxonomy.addChild('D', 'I')
taxonomy.addChild('D', 'J')
taxonomy.addChild('E', 'K')
taxonomy.addChild('E', 'L')
taxonomy.addChild('F', 'M')
taxonomy.addChild('F', 'N')
return taxonomy
