def check(self, path, length):
input_records = SeqIO.to_dict(SeqIO.parse(path, "fasta"))
self.assertEqual(len(input_records), length)
# Any filesnames with spaces should get escaped with quotes
# automatically.
# Using keyword arguments here.
cline = _Fasttree.FastTreeCommandline(fasttree_exe, input=path, nt=True)
self.assertEqual(str(eval(repr(cline))), str(cline))
out, err = cline()
self.assertTrue(err.strip().startswith("FastTree"))
tree = Phylo.read(StringIO(out), "newick")
def lookup_by_names(tree):
names = {}
for clade in tree.find_clades():
if clade.name:
if clade.name in names:
raise ValueError("Duplicate key: %s" % clade.name)
names[clade.name] = clade
return names
names = lookup_by_names(tree)
self.assertGreater(len(names), 0)
def terminal_neighbor_dists(self):
"""Return a list of distances between adjacent terminals."""
def generate_pairs(self):
pairs = itertools.tee(self)
next(pairs[1]) # Advance second iterator one step
return zip(pairs[0], pairs[1])
return [self.distance(*i) for i in
generate_pairs(self.find_clades(terminal=True))]
for dist in terminal_neighbor_dists(tree):
self.assertGreater(dist, 0.0)
def phylogeny(self):
script_fname = sys.argv[0]
script_path = os.path.abspath(os.path.dirname(script_fname))
self.phylogenetic_tree = os.path.join(self.dir_path, "temp",
"%s_phylotree" % (self.time))
cmd = _Fasttree.FastTreeCommandline(
'fasttree',
input=os.path.abspath(self.multiple_sequence_alignment_2),
out=os.path.abspath(self.phylogenetic_tree))
self.qiime_phylo = os.path.join(self.qiime_out,
"%s_qiime_phylo.phy" % (self.time))
cmd()
copyfile(self.phylogenetic_tree, self.qiime_phylo)
#Create a temp fasta file with a space in the name
temp_filename_with_spaces = "Clustalw/temp horses.fasta"
handle = open(temp_filename_with_spaces, "w")
SeqIO.write(SeqIO.parse("Phylip/hennigian.phy", "phylip"), handle, "fasta")
handle.close()
for input_file in ["Quality/example.fasta", "Clustalw/temp horses.fasta"]:
input_records = SeqIO.to_dict(SeqIO.parse(input_file, "fasta"))
print("")
print("Calling fasttree on %s (with %i records)" \
% (repr(input_file), len(input_records)))
#Any filesnames with spaces should get escaped with quotes automatically.
#Using keyword arguments here.
cline = _Fasttree.FastTreeCommandline(fasttree_exe, input=input_file, nt=True)
assert str(eval(repr(cline)))==str(cline)
out, err = cline()
assert err.strip().startswith("FastTree")
print("")
print("Checking generation of tree terminals")
tree = Phylo.read(StringIO(out), 'newick')
def lookup_by_names(tree):
names = {}
for clade in tree.find_clades():
if clade.name:
if clade.name in names:
raise ValueError("Duplicate key: %s" % clade.name)
protein_tree_output = protein_tree_folder + "/" + cluster + ".tre"
nucleotide_tree_output = dna_tree_folder + "/" + cluster + ".tre"
unaligned_DNA.writeToFile(dna_unaligned_folder + "/" + cluster +
".fna",
format="fasta")
unaligned_AA.writeToFile(protein_unaligned_folder + "/" + cluster +
".faa",
format="fasta")
aligned_DNA.writeToFile(aligned_dna_file, format="fasta")
aligned_AA.writeToFile(aligned_aa_file, format="fasta")
#Make protein trees with FastTree
make_dna_tree = _Fasttree.FastTreeCommandline(
cmd='FastTree',
input=aligned_dna_file,
out=nucleotide_tree_output,
slow=True,
nt=True)
make_aa_tree = _Fasttree.FastTreeCommandline(cmd="FastTree",
input=aligned_aa_file,
out=protein_tree_output,
slow=True)
dna_out, dna_err = make_dna_tree()
aa_out, aa_err = make_aa_tree()
#Make protein trees using FastTree
#protein_tree = build_tree_fasttree(aligned_AA, PROTEIN, best_tree=True)
#protein_tree_output.write(protein_tree.getNewick(with_distances=True))
#protein_tree.writeToFile(protein_tree_output)
#protein_tree_output.close()
("Quality/example.fasta", "temp_test.tree"),
("Clustalw/temp horses.fasta", "temp_test.tree"),
]:
input_records = SeqIO.to_dict(SeqIO.parse(input_file, "fasta"),
lambda rec: rec.id)
if os.path.isfile(output_file):
os.remove(output_file)
print
print "Calling fasttree on %s (with %i records)" \
% (repr(input_file), len(input_records))
print "using output file %s" % repr(output_file)
#Any filesnames with spaces should get escaped with quotes automatically.
#Using keyword arguments here.
cline = _Fasttree.FastTreeCommandline(fasttree_exe,
input=input_file,
out=output_file)
assert str(eval(repr(cline))) == str(cline)
#print cline
out, err = cline()
assert err.strip().startswith("FastTree")
print
print "Checking generation of tree terminals"
tree = Phylo.read(output_file, 'newick')
def lookup_by_names(tree):
names = {}
for clade in tree.find_clades():
if clade.name:
