def convert_terminal_node_names(tree_newick_name,
dictionnary,
tree_format='phyloxml',
write_corresp_table=True):
#from Bio import Phylo
from ete3 import Tree
if write_corresp_table:
f = open('corresp_table.tab', 'w')
print('format', tree_format)
print('tree', tree_newick_name)
try:
tree = Tree(tree_newick_name, tree_format)
leaf_names = {}
for leaf in tree:
#n+=1
#print species.name
#print dictionnary[str(species.name)]
#accession = manipulate_biosqldb.taxon_id2accessions(server, str(species.name), "saureus_01_15")[0]
try:
print("%s --> %s" % (leaf.name, dictionnary[str(leaf.name)]))
if write_corresp_table:
f.write("%s\t%s\n" %
(leaf.name, dictionnary[str(leaf.name)]))
if dictionnary[str(leaf.name)] not in leaf_names:
leaf_names[dictionnary[str(leaf.name)]] = 1
leaf.name = dictionnary[str(
leaf.name)] #+ ' (%s)' % my_accession2st[accession]
else:
leaf_names[dictionnary[str(leaf.name)]] += 1
leaf.name = dictionnary[str(
leaf.name
)] + '%s' % leaf_names[dictionnary[str(
leaf.name)]] #+ ' (%s)' % my_accession2st[accession]
except:
print("%s --> ?" % (leaf.name))
if write_corresp_table:
f.write("%s\t?\n" % (leaf.name))
pass
except:
from Bio import Phylo
tree = Phylo.read(tree_newick_name, tree_format)
leaves = tree.get_terminals()
leaf_names = {}
print(dictionnary)
for leaf in leaves:
try:
print("%s --> %s" % (leaf.name, dictionnary[str(leaf.name)]))
if write_corresp_table:
f.write("%s\t%s\n" %
(leaf.name, dictionnary[str(leaf.name)]))
print("%s --> %s" % (leaf.name, dictionnary[str(leaf.name)]))
if dictionnary[str(leaf.name)] not in leaf_names:
leaf_names[dictionnary[str(leaf.name)]] = 1
leaf.name = dictionnary[str(
leaf.name)] #+ ' (%s)' % my_accession2st[accession]
else:
leaf_names[dictionnary[str(leaf.name)]] += 1
leaf.name = dictionnary[str(
leaf.name
)] + '%s' % leaf_names[dictionnary[str(
leaf.name)]] #+ ' (%s)' % my_accession2st[accession]
except:
print("%s --> ?" % (leaf.name))
if write_corresp_table:
f.write("%s\t?\n" % (leaf.name))
print("%s --> ?" % (leaf.name))
pass
#species.name = dictionnary[str(species.name)] + ' (%s)' % 8
return tree
