def dnadist(seqs, output=None, verbose=True, force=False, args=None):
if args == None:
args = "y"
validate_seqs(seqs)
cwd = create_temp_dir()
util.tic("dnadist on %d of length %d" % (len(seqs), len(seqs.values()[0])))
# create input
labels = write_phylip_align(file("infile", "w"), seqs)
# run phylip
exec_phylip("dnadist", args, verbose)
util.toc()
# parse output
if output != None:
os.rename("outfile", "../" + output)
cleanup_temp_dir(cwd)
return labels
else:
name, mat = read_dist_matrix("outfile")
cleanup_temp_dir(cwd)
return labels, mat
def boot_neighbor(seqs,
iters=100,
seed=None,
output=None,
verbose=True,
force=False):
if seed == None:
seed = random.randInt(0, 1000) * 2 + 1
validate_seqs(seqs)
cwd = create_temp_dir()
util.tic("boot_neighbor on %d of length %d" %
(len(seqs), len(seqs.values()[0])))
# create input
labels = write_phylip_align(file("infile", "w"), seqs)
exec_phylip("seqboot", "r\n%d\ny\n%d" % (iters, seed), verbose)
os.rename("outfile", "infile")
exec_phylip("protdist", "m\nd\n%d\ny" % iters, verbose)
os.rename("outfile", "infile")
exec_phylip("neighbor", "m\n%d\n%d\ny" % (iters, seed), verbose)
util.toc()
# read tree samples
if output != None:
os.rename("outtree", "../" + output)
cleanup_temp_dir(cwd)
return labels
else:
trees = []
infile = file("outtree")
for i in xrange(iters):
tree = treelib.Tree()
tree.read_newick(infile)
rename_tree_with_name(tree, labels)
trees.append(tree)
infile.close()
cleanup_temp_dir(cwd)
return trees
def boot_proml(seqs,
iters=100,
seed=1,
jumble=5,
output=None,
verbose=True,
force=False):
validate_seqs(seqs)
cwd = create_temp_dir()
util.tic("bootProml on %d of length %d" %
(len(seqs), len(seqs.values()[0])))
# create input
labels = write_phylip_align(file("infile", "w"), seqs)
exec_phylip("seqboot", "y\n%d" % seed, verbose)
os.rename("outfile", "infile")
exec_phylip("proml", "m\nD\n%d\n%d\n%d\ny" % (iters, seed, jumble),
verbose)
util.toc()
# read tree samples
if output != None:
os.rename("outtree", "../" + output)
cleanup_temp_dir(cwd)
return labels
else:
trees = []
infile = file("outtree")
for i in xrange(iters):
tree = treelib.Tree()
tree.read_newick(infile)
rename_tree_with_names(tree, labels)
trees.append(tree)
infile.close()
cleanup_temp_dir(cwd)
return trees
def proml_treelk(aln, tree, verbose=True, force=False, args="u\ny"):
validate_seqs(aln)
cwd = create_temp_dir()
util.tic("proml on %d of length %d" % (len(aln), len(aln.values()[0])))
# create input
labels = write_phylip_align(file("infile", "w"), aln)
write_in_tree("intree", tree, labels)
# run phylip
exec_phylip("proml", args, verbose)
# parse logl
logl = read_logl("outfile")
# parse tree
tree = read_out_tree("outtree", labels)
cleanup_temp_dir(cwd)
util.toc()
return logl, tree
def align2tree(
prog,
seqs,
verbose=True,
force=False,
args=None,
usertree=None,
saveOutput="",
bootiter=1,
seed=1,
jumble=1,
):
validate_seqs(seqs)
cwd = create_temp_dir()
util.tic("%s on %d of length %d" %
(prog, len(seqs), len(seqs.values()[0])))
# create input
labels = write_phylip_align(file("infile", "w"), seqs)
util.write_list(file("labels", "w"), labels)
# initialize default arguments
if args == None:
args = "y"
# create user tree if given
if usertree != None:
write_in_tree("intree", usertree, labels)
args = "u\n" + args # add user tree option
# bootstrap alignment if needed
if bootiter > 1:
exec_phylip("seqboot", "r\n%d\ny\n%d" % (bootiter, seed), verbose)
os.rename("outfile", "infile")
# add bootstrap arguments
args = "m\nD\n%d\n%d\n%d\n%s" % (bootiter, seed, jumble, args)
# run phylip
exec_phylip(prog, args, verbose)
# check for PHYLIP GIVE UP
if is_phylip_give_up("outfile"):
tree = treelib.Tree()
tree.make_root()
# make star tree
for key in seqs:
tree.add_child(tree.root, treelib.TreeNode(key))
else:
# parse tree
if bootiter == 1:
tree = read_out_tree("outtree", labels, bootiter)
# parse likelihood
if prog in ["dnaml", "proml"]:
tree.data["logl"] = read_logl("outfile")
else:
trees = read_out_tree("outtree", labels, bootiter)
if saveOutput != "":
save_temp_dir(cwd, saveOutput)
else:
cleanup_temp_dir(cwd)
util.toc()
if bootiter == 1:
return tree
else:
return trees