def get_sum_of_branches(treepath):
fin = open(treepath, "r")
newick = fin.readline().strip()
t = Tree()
t.read_from_string(newick.__str__(), "newick")
fin.close()
return t.length()
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 index_mutations(con):
"""Builds an index of all mutations"""
cur = con.cursor()
for msaid in get_alignment_method_ids(con):
for modelid in get_phylo_modelids(con):
newick = get_anc_cladogram(con, msaid, modelid)
t = Tree()
t.read_from_string(newick, "newick")
for edge in t.preorder_edge_iter():
if edge.head_node == None or edge.tail_node == None:
continue
if edge.head_node.label == None or edge.tail_node.label == None:
continue
print msaid, modelid, edge.head_node.label, edge.tail_node.label
anc1name = "Node" + edge.head_node.label.__str__()
anc2name = "Node" + edge.tail_node.label.__str__()
index_mutations_helper(con, msaid, modelid, anc1name, anc2name)
def return_trees_from_trace(path):
print "Parsing trace:", path
trees = []
lnls = []
fin = open(path, "r")
last_tree = None
last_lnl = 0.0
count_unique_trees = 0
for line in fin.xreadlines():
treestring = ""
lnlstring = ""
found_tree = False
for c in line:
if found_tree == False and c != "]" and c != "[" and c != "(":
lnlstring += c
if c == "(":
found_tree = True
if found_tree == True:
treestring += c
lnl = float(lnlstring)
t = Tree()
t.read_from_string(line, "newick")
if last_tree != None: #2nd->nth trees in the list
#sd = last_tree.symmetric_difference(t)
#sd = t.symmetric_difference(last_tree)
if last_lnl < lnl:
trees.append(t)
lnls.append("%.2f"%lnl)
count_unique_trees += 1
else:
trees[trees.__len__()-1] = t
lnls[lnls.__len__()-1] = "%.2f"%lnl
else: #first tree in the list
trees.append(t)
lnls.append("%.2f"%lnl)
count_unique_trees += 1
last_tree = t
last_lnl = lnl
print count_unique_trees, lnl
trees.append(last_tree)
lnls.append("%.2f"%lnl)
fin.close()
return [trees, lnls]
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
def compute_tree_distances(con):
cur = con.cursor()
cur.execute("insert or replace into TreeDistanceMetrics(metricid, name) values(1, 'symmetric')")
cur.execute("insert or replace into TreeDistanceMetrics(metricid, name) values(2, 'euclidean')")
con.commit()
treeid_dendropytree = {}
sql = "select id, almethod, phylomodelid, newick from UnsupportedMlPhylogenies"
con.execute(sql)
x = cur.fetchall()
for ii in x:
treeid = ii[0]
t = Tree()
t.read_from_string(newick, "newick")
treeid_dendropytree[treeid] = t
for ii in treeid_dendropytree:
treeii = treeid_dendropytree[ii]
this_row = []
for jj in treeid_dendropytree:
treejj = treeid_dendropytree[jj]
"""Symmetric Distance"""
distance = treeii.symmetric_difference(treejj)
"""Store the computed distance in the database."""
sql = "insert into TreeDistances(metricid, treeida, treeidb, distance) values("
sql += "1," + ii.__str__() + "," + jj.__str__() + "," + distance.__str__() + ")"
cur.execute(sql)
"""Euclidean Distance"""
distance = treeii.euclidean_distance(treejj)
"""Store the computed distance in the database."""
sql = "insert into TreeDistances(metricid, treeida, treeidb, distance) values("
sql += "2," + ii.__str__() + "," + jj.__str__() + "," + distance.__str__() + ")"
cur.execute(sql)
con.commit()
def match_ancestors_across_models(con):
"""This method fills data in the table AncestorsAcrossModels"""
cur = con.cursor()
modelids = get_phylo_modelids(con)
msaids = get_alignment_method_ids(con)
ancid_childrenids = {} # key = Ancestor ID, value = list of Taxa IDs
"""Pull the map of taxon names to IDs from the database.
We'll access this information a lot, so let's save it in a separate hashtable
rather than repeatedly querying the databse."""
taxonname_id = {}
sql = "select id, shortname from Taxa"
cur.execute(sql)
for ii in cur.fetchall():
id = ii[0]
name = ii[1]
taxonname_id[name] = id
for modelid in modelids:
for msaid in msaids:
sql = "select newick from AncestralCladogram where unsupportedmltreeid in (select id from UnsupportedMlPhylogenies where almethod=" + msaid.__str__(
) + " and phylomodelid=" + modelid.__str__() + ")"
cur.execute(sql)
xx = cur.fetchone()
if xx is None:
write_error(con, "I cannot find the ancestral Newick cladogram for almethod=" +
msaid.__str__() + " and phylomodelid=" + modelid.__str__())
cladonewick = xx[0].__str__()
t = Tree()
t.read_from_string(cladonewick, "newick")
for node in t.nodes():
if node.is_leaf() == False and node.level() > 0:
sql = "select id from Ancestors where name='Node" + node.label + \
"' and almethod=" + msaid.__str__() + " and phylomodel=" + modelid.__str__()
cur.execute(sql)
ancid = cur.fetchone()[0]
ancid_childrenids[ancid] = []
for l in node.leaf_iter():
# print "978:", l
taxonname = l.as_newick_string()
# print "980:", taxonname
taxonname = re.sub("'", "", taxonname)
ancid_childrenids[ancid].append(
taxonname_id[taxonname])
# key = Ancestor ID, value = list of other ancestor IDs with the same
# children.
ancid_matches = {}
for anc1 in ancid_childrenids:
ancid_matches[anc1] = []
mychildren = ancid_childrenids[anc1]
mychildren.sort()
for anc2 in ancid_childrenids:
if anc1 == anc2:
"""Skip the self comparison."""
continue
theirchildren = ancid_childrenids[anc2]
theirchildren.sort()
if mychildren == theirchildren:
ancid_matches[anc1].append(anc2)
sql = "delete from AncestorsAcrossModels"
cur.execute(sql)
con.commit()
for anc1 in ancid_matches:
for anc2 in ancid_matches[anc1]:
sql = "insert into AncestorsAcrossModels (ancid, same_ancid) values(" + anc1.__str__(
) + "," + anc2.__str__() + ")"
cur.execute(sql)
con.commit()