def ali_in_tree(self,aliname = 'group2.stk',
rank = 'genus',
**kwargs):
all_seqs = ali.get_seqs(aliname)
alinodes = ali.get_taxnodes(aliname)
aliranks = [t.rank if t else None for t in alinodes]
all_leaves = self.t.get_terminals()
leafnodes = self.leafNodes(reset = mod(reset, 2))
leafranks =[n.rank if n else None for n in leafnodes]
ali_families = ali.get_taxon_forall(rank = rank,aliname = aliname,
**mem.sr(kwargs))
leaf_families= self.getTaxon(rank = rank, **mem.sr(kwargs))
aset = set(ali_families)
lset = set(leaf_families)
a_domains =[(node, ncbi.get_taxon(node,'superkingdom')) for node in aset]
l_domains =[(node, ncbi.get_taxon(node,'superkingdom')) for node in lset]
bac_domain = [x[1] for x in l_domains if ncbi.sciname(x[1])== 'Bacteria'][0]
l_bacs = set((l[0] for l in l_domains if l[1] == bac_domain))
a_bacs = set((a[0] for a in a_domains if a[1] == bac_domain))
leaf_bacteria = [leaf if leaf in l_bacs else None for leaf in leaf_families]
ali_bacteria = [a if a in a_bacs else None for a in ali_families]
return leaf_bacteria, ali_bacteria, leafnodes, alinodes
def setTaxon(aliname = None, rank = None,**kwargs):
assert aliname != None and rank != None
nodes = get_taxnodes(aliname,**mem.sr(kwargs))
taxon = [ncbi.get_taxon(node, rank=rank)
if node else None for node in nodes]
return taxon
def setTaxon(BTInstance = None, rank = None, **kwargs):
assert rank; assert BTInstance
leafnodes = BTInstance.leafNodes(**mem.sr(kwargs))
leaf_families = [ncbi.get_taxon(node, rank=rank)
if node else None for node in leafnodes]
return leaf_families
def set_taxon_forsome(nodes = None, rank = None,**kwargs):
assert nodes != None and rank != None
taxon = [ncbi.get_taxon(node, rank = rank)
if node else None for node in nodes]
return taxon
