with open(testclassfile) as tf:
target_tips = set(tf.read().splitlines())
for line in lines:
if line == "":
continue
else:
fields = line.split("\t")
hog = fields[1]
tree = fields[0]
try:
t = EvolTree(fields[2])
except:
continue
for node in t.traverse():
#UGLY!
istarget = node_in_class(node, t, target_tips)
brstat = node.dist
nname = node.name
if nname == "":
nname = "-".join(node.get_leaf_names())
try:
pname = node.up.name
except AttributeError:
pname = "root"
if pname == "":
pname = "-".join(node.up.get_leaf_names())
brname = pname + ":" + nname
print(hog,
tree,
tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')
print (tree)
print ('Tree and alignment loaded.')
input ('Tree will be mark in order to contrast Gorilla and Chimpanzee as foreground \nspecies.')
marks = ['1', '3', '7']
tree.mark_tree (marks, ['#1'] * 3)
print (tree.write ())
print ('we can easily colorize marked branches')
# display marked branches in orange
for node in tree.traverse ():
if not hasattr (node, 'mark'):
continue
if node.mark == '':
continue
node.img_style = NodeStyle ()
node.img_style ['bgcolor'] = '#ffaa00'
tree.show()
print ('''now running branch models
free branch models, 2 groups of branches, one with Gorilla and
chimp, the other with the rest of the phylogeny
''')
print ('running branch free...')
tree.run_model ('b_free.137')
print ('running branch neut...')
tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta')
print(tree)
print('Tree and alignment loaded.')
input(
'Tree will be mark in order to contrast Gorilla and Chimpanzee as foreground \nspecies.'
)
marks = ['1', 3, '7']
tree.mark_tree(marks, ['#1'] * 3)
print(tree.write())
# display marked branches in orange
for node in tree.traverse():
if not hasattr(node, 'mark'):
continue
if node.mark == '':
continue
node.img_style = NodeStyle()
node.img_style['bgcolor'] = '#ffaa00'
tree.show()
print('''now running branch-site models C and D that represents
the addition of one class of sites in on specific branch.
These models must be compared to null models M1 and M3.
if branch-site models are detected to be significantly better,
than, one class of site is evolving at different rate in the marked
clade.
''')
def load_parameters():
descendant_dict = defaultdict()
with open(input_file, 'r') as f:
all_lines = f.readlines()
aln_file = all_lines[0].strip()
if not os.path.exists(aln_file):
logger.error('Invalid cDNA alignment file: {0}'.format(aln_file))
sys.exit(1)
logger.info('Input cDNA alignment file: {0}'.format(aln_file))
seq_id_dict = defaultdict()
seq_id_list = []
for seq_record in AlignIO.read(aln_file, 'fasta'):
seq_id_dict[str(seq_record.id)] = 1
seq_id_list.append(str(seq_record.id))
tree_file = all_lines[1].strip()
if not os.path.exists(tree_file):
logger.error('Invalid tree file: {0}'.format(tree_file))
sys.exit(1)
logger.info('Input tree file: {0}'.format(tree_file))
tmp_t = Tree(tree_file, format=0)
node_id_dict = defaultdict()
for node in tmp_t:
node_id_dict[str(node.name)] = 1
if seq_id_dict != node_id_dict:
if len(seq_id_dict) < len(node_id_dict):
logger.warning('Sequences is less than tree nodes.')
logger.info('Trim input tree file.')
tree_file = trim_tree(tree_file, seq_id_list)
else:
logger.error('Sequences is falsely greater than tree nodes.')
sys.exit(1)
t = EvolTree(tree_file, format=1)
for descendant in t.iter_descendants():
descendant_dict[descendant.node_id] = str(descendant)
root = t.get_tree_root()
id_list = []
for leaf in t.traverse('preorder'):
id_list.append(leaf.node_id)
select_nodes = []
if len(all_lines) > 2:
for each_line in all_lines[2:]:
s = each_line.strip()
if s:
select_nodes.append(s)
if select_nodes:
nodes_line = ', '.join(select_nodes)
logger.info('Input nodes: {0}'.format(nodes_line))
for node in select_nodes:
if node not in t:
logger.error('Error node: {0}'.format(node))
sys.exit(1)
if not t.check_monophyly(values=select_nodes, target_attr='name'):
logger.error('Some nodes are not monophyletic.')
sys.exit(1)
common_ancestor = t.get_common_ancestor(select_nodes)
else:
common_ancestor = root
logger.info('No specific node')
run_list = []
for s in common_ancestor.iter_descendants():
run_list.append(s.node_id)
logger.info('These node ids will be checked: {0}'.format(
str(run_list)))
return run_list, aln_file, tree_file, descendant_dict
from ete3 import EvolTree
import sys
treepath=sys.argv[1]
treeout=sys.argv[2]
t = EvolTree(treepath)
ratites = {'aptHaa', 'aptRow', 'aptOwe', 'strCam', 'droNov', 'casCas', 'rheAme', 'rhePen'}
#annotate leaves
for leaf in t.traverse():
if leaf.is_leaf():
if leaf.name in ratites:
leaf.add_features(mark="{RatiteLeaf}")
else:
#internal node, get all leaf names and make sure all are in ratites
desc=set(leaf.get_leaf_names())
checkDesc=desc - ratites
if not checkDesc:
leaf.add_features(mark="{RatiteInternal}")
t.write(outfile=treeout)
# use the pruned tree saved in memory
if empty_seq_count >= 1:
if len(taxa_in_alignment) >= 1:
tree.prune(taxa_in_alignment, preserve_branch_length=True)
tree.unroot()
tree.write(outfile=out_tree_name, format=0)
tree = EvolTree(out_tree_name)
tree.link_to_alignment(alignment_file)
tree.workdir = os.getcwd()
# Record list of all node_ids in the tree for later retrieving omega from a
# background branch in the b_free model
list_of_node_ids = []
for node in tree.traverse('postorder'):
list_of_node_ids.append(node.node_id)
test_taxa = []
with open(test_taxa_file, 'r') as test_taxa_list:
for taxon in test_taxa_list:
taxon = taxon.rstrip()
test_taxa.append(taxon)
marked_taxon_ids = []
# Mark test taxa
for taxon in test_taxa:
taxon_node = tree & taxon # ete3 notation for finding a node within a tree
marked_taxon_id = taxon_node.node_id # mark_tree only takes node_ids, not
# labels
tree.mark_tree([marked_taxon_id])
with open(testclassfile) as tf:
target_tips=set(tf.read().splitlines())
for line in lines:
if line=="":
continue
else:
fields=line.split("\t")
hog=fields[1]
tree=fields[0]
try:
t=EvolTree(fields[2])
except:
continue
for node in t.traverse():
#UGLY!
istarget=node_in_class(node,t,target_tips)
brstat=node.dist
nname=node.name
if nname=="":
nname="-".join(node.get_leaf_names())
try:
pname=node.up.name
except AttributeError:
pname="root"
if pname=="":
pname="-".join(node.up.get_leaf_names())
brname=pname + ":" + nname
print(hog,tree,pname,nname,brname,brstat,istarget, sep=",", end="\n")
