def test_build_tree_from_alignment(self):
tree = build_tree_from_alignment(self.seqs, DNA)
# test expected output for fasttree 1.1 and 2.0.1
try:
for o,e in zip(tree.traverse(), DndParser(exp_tree).traverse()):
self.assertEqual(o.Name,e.Name)
self.assertFloatEqual(o.Length,e.Length)
except AssertionError:
for o,e in zip(tree.traverse(), DndParser(exp_tree_201).traverse()):
self.assertEqual(o.Name,e.Name)
self.assertFloatEqual(o.Length,e.Length)
def main():
fdir = sys.argv[1]
odir = sys.argv[2]
mkdir_p(odir)
for fname in glob.iglob("{0}/*.fasta".format(fdir)):
groupName = fname.split( os.path.sep )[-1].rstrip(".fasta")
print("group {0}".format(groupName))
try:
seqs = cogent.LoadSeqs(fname, moltype=cogent.PROTEIN, aligned=False)
except Exception as e:
print(e)
exit(0)
aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
t = build_tree_from_alignment(aln, cogent.PROTEIN)
print("tree for group {0}".format( str(t) ) )
with open( os.path.sep.join( [ odir, groupName+".nwk" ] ), 'wb') as ofile:
ofile.write( str(t).replace("'","") )
def bootTree(i, aln_len, seqNames, seqs, outdir):
# stats
sys.stderr.write('Inferring bootstrap tree: {}\n'.format(i))
# bootstrap index
boot_idx = np.random.choice(range(aln_len), aln_len, replace=True)
# conversion back to aln object
aln_boot = seqs[:,boot_idx]
aln_boot = {name:''.join(seq) for name,seq in zip(seqNames, aln_boot)}
aln_boot = LoadSeqs(data=aln_boot, moltype=DNA)
# inferring tree
params = {'-boot' : 0}
tree = build_tree_from_alignment(aln_boot, moltype=DNA, params=params)
# writing out tree
outFile = os.path.join(outdir, 'boot{}.nwk'.format(i))
tree.writeToFile(outFile)
return(outFile)
def main():
fdir = sys.argv[1]
odir = sys.argv[2]
mkdir_p(odir)
for fname in glob.iglob("{0}/*.fasta".format(fdir)):
groupName = fname.split(os.path.sep)[-1].rstrip(".fasta")
print("group {0}".format(groupName))
try:
seqs = cogent.LoadSeqs(fname,
moltype=cogent.PROTEIN,
aligned=False)
except Exception as e:
print(e)
exit(0)
aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
t = build_tree_from_alignment(aln, cogent.PROTEIN)
print("tree for group {0}".format(str(t)))
with open(os.path.sep.join([odir, groupName + ".nwk"]), 'wb') as ofile:
ofile.write(str(t).replace("'", ""))
def bootTree(i, aln_len, seqNames, seqs, outdir):
# stats
sys.stderr.write('Inferring bootstrap tree: {}\n'.format(i))
# bootstrap index
boot_idx = np.random.choice(range(aln_len), aln_len, replace=True)
# conversion back to aln object
aln_boot = seqs[:, boot_idx]
aln_boot = {name: ''.join(seq) for name, seq in zip(seqNames, aln_boot)}
aln_boot = LoadSeqs(data=aln_boot, moltype=DNA)
# inferring tree
params = {'-boot': 0}
tree = build_tree_from_alignment(aln_boot, moltype=DNA, params=params)
# writing out tree
outFile = os.path.join(outdir, 'boot{}.nwk'.format(i))
tree.writeToFile(outFile)
return (outFile)
