def do_alnntree(pref, ndf, fasta, refs, congen, targetids, gaps=0.9, cpus=-1):
# TODO: add checkpoint to avoid repeating
to_phy = congen
for name, data in ndf.groupby('saccver'):
# mi = data.sstart.min()
# ma = data.send.max()
tx = data.staxid.iloc[0]
try:
seq = refs['>%s' % name].replace('\n', '').strip() # [mi-1:ma+1]
except KeyError:
name = name.split('|')[0]
seq = refs['>%s' % name].replace('\n', '').strip()
to_phy += '>%d.%s\n%s\n' % (tx, name, seq)
with shelve.open(fasta) as dic:
for h, s in dic.items():
if h.strip()[1:] in targetids:
print(h)
to_phy += '%s\n%s\n' % (h, s.strip().replace('\n', ''))
else:
print(h, 'not in')
aln, _ = stdin_run(['mafft', '--thread', str(cpus), '--auto', '-'], to_phy)
trm = trimaln(aln.decode('utf-8'), targetids, gaps=gaps)
tre, _ = stdin_run(['fasttreeMP', '-nt', '-gtr', '-gamma'], trm)
tre = tre.strip()[:-1].replace(b';', b'-').decode('utf-8') + ';'
t = PhyloTree(tre, sp_naming_function=lambda name: name.split('.')[0])
with open('%s.aln' % pref, 'w') as al, open('%s.treepickle' % pref, 'wb') \
as tp:
al.write(trm)
t.write(outfile='%s.tree' % pref)
dill.dump(t, tp)
tax2 = t.annotate_ncbi_taxa()
fix_species(t)
print(t)
return t, tax2
def test_species(self):
"""
tests if node.species and ncbi_query are working
"""
# test node.species
species_tree = PhyloTree(
"""(Felis_catus_1:1,
(Homo_sapiens_1:1, Pan_troglodytes_1:1),
Saccharomyces_cerevisiae_1:1);""",
format=1)
species_tree.set_species_naming_function(lambda n: n.name.split("_")[1] if "_" in n.name else '')
pattern0 = """('',
(' len(set(["sapiens","pygmaeus"]) & species(@))>0',
Pan_troglodytes_1)
);"""
pattern0 = TreePattern(pattern0)
root = species_tree.get_tree_root()
self.assertEqual(list(pattern0.find_match(species_tree)), [root])
# test ncbi taxonomy
ncbi = NCBITaxa()
taxonomy_tree = PhyloTree("((9598, 9606), 10090);", sp_naming_function=lambda name: name)
taxonomy_tree.annotate_ncbi_taxa()
root = taxonomy_tree.get_tree_root()
pattern1 = """ ' @.sci_name == "Euarchontoglires" ';"""
pattern2 = """
(( '@.sci_name=="H**o sapiens"' , '9526 in @.lineage ' )' @.rank=="subfamily" and @.taxid == 207598 ')
' @.sci_name == "Euarchontoglires" and "cellular organisms" in @.named_lineage';
"""
pattern1 = TreePattern(pattern1)
pattern2 = TreePattern(pattern2)
match1 = pattern1.find_match(taxonomy_tree)
match2 = pattern2.find_match(taxonomy_tree)
self.assertEqual(list(match1), [root])
self.assertEqual(list(match2), [root])
from ete3 import PhyloTree
from ete3 import NCBITaxa
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
input_tree = sys.argv[1]
input_fasta = sys.argv[2]
output_fasta_ordered_select = sys.argv[3]
output_fasta_ordered_all = sys.argv[4]
# There's a way to save these extra attributes, but it's a bit awkward (not supported by newick format)
# So we fetch them anew each time.
ncbi = NCBITaxa()
tree = PhyloTree(input_tree,
sp_naming_function=lambda name: name.split('.', 1)[0])
tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
print tree.get_ascii(attributes=["name", "sci_name", "taxid"])
record_dict = SeqIO.to_dict(SeqIO.parse(input_fasta, "fasta"))
# H**o sapiens
# Macaca mulatta
# Canis lupus familiaris
# Mus musculus
# Gallus gallus
# Anolis carolinensis
# Danio rerio
sorted_fasta_select = []
sorted_fasta_select.append(
SeqRecord(record_dict["9606.ENSP00000261448"].seq, "H**o sapiens", '', ''))
sorted_fasta_select.append(
def run(args):
from ete3 import Tree, PhyloTree
features = set()
for nw in args.src_tree_iterator:
if args.ncbi:
tree = PhyloTree(nw)
features.update([
"taxid", "name", "rank", "bgcolor", "sci_name",
"collapse_subspecies", "named_lineage", "lineage"
])
tree.annotate_ncbi_taxa(args.taxid_attr)
else:
tree = Tree(nw)
type2cast = {
"str": str,
"int": int,
"float": float,
"set": set,
"list": list
}
for annotation in args.feature:
aname, asource, amultiple, acast = None, None, False, str
for field in annotation:
try:
key, value = list(map(str.strip, field.split(":")))
except Exception:
raise ValueError("Invalid feature option [%s]" % field)
if key == "name":
aname = value
elif key == "source":
asource = value
elif key == "multiple":
#append
amultiple = value
elif key == "type":
try:
acast = type2cast[value]
except KeyError:
raise ValueError("Invalid feature type [%s]" % field)
else:
raise ValueError("Unknown feature option [%s]" % field)
if not aname and not asource:
ValueError(
'name and source are required when annotating a new feature [%s]'
% annotation)
features.add(aname)
for line in open(asource, 'rU'):
line = line.strip()
if not line or line.startswith('#'):
continue
nodenames, attr_value = list(map(str.strip, line.split('\t')))
nodenames = list(map(str.strip, nodenames.split(',')))
relaxed_grouping = True
if nodenames[0].startswith('!'):
relaxed_grouping = False
nodenames[0] = nodenames[0][1:]
if len(nodenames) > 1:
target_node = tree.get_common_ancestor(nodenames)
if not relaxed_grouping:
pass
# do something
else:
target_node = tree & nodenames[0]
if hasattr(target_node, aname):
log.warning('Overwriting annotation for node" [%s]"' %
nodenames)
else:
target_node.add_feature(aname, acast(attr_value))
dump(tree, features=features)
