def reroot_tree(tstr):
"""Input: a tree path to a Newick tree. Output: a re-rooted version of the tree, based on the outgroup defined in configuration.py"""
t = Tree()
t.read_from_string(tstr.__str__(), "newick")
og = ap.params["outgroup"]
og = re.sub("\[", "", og)
og = re.sub("\]", "", og)
og = re.sub("\"", "", og)
ogs = og.split(",")
mrca = t.mrca(taxon_labels=ogs)
t.reroot_at_edge(mrca.edge, update_splits=False)
ret = t.as_string("newick")
ret = re.sub("\[\&\R\] ", "", ret)
ret = ret.strip()
return ret
def reroot_newick(con, newick):
"""Provide a newick string, this method will re-root the tree
based on the 'outgroup' setting."""
cur = con.cursor()
dendrotree = Tree()
dendrotree.read_from_string(newick, "newick")
sql = "select shortname from Taxa where id in (select taxonid from GroupsTaxa where groupid in (select id from TaxaGroups where name='outgroup'))"
cur.execute(sql)
rrr = cur.fetchall()
outgroup_labels = []
for iii in rrr:
label = re.sub("_", " ", iii[0])
outgroup_labels.append( label.__str__() )
mrca = dendrotree.mrca(taxon_labels=outgroup_labels)
if mrca.edge.tail_node != None and mrca.edge.head_node != None:
dendrotree.reroot_at_edge(mrca.edge, update_splits=True)
newick = dendrotree.as_string("newick")
return newick
