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']]
