def write_dlcoal_recon2(filename, coal_tree, extra,
exts={"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"locus_events": ".locus.events",
"daughters": ".daughters"
},
filenames={}):
"""Writes a reconciled gene tree to files"""
# coal
coal_tree.write(filenames.get("coal_tree", filename + exts["coal_tree"]),
rootData=True)
phylo.write_recon(
filenames.get("coal_recon", filename + exts["coal_recon"]),
extra["coal_recon"])
# locus
extra["locus_tree"].write(
filenames.get("locus_tree", filename + exts["locus_tree"]),
rootData=True)
phylo.write_recon(
filenames.get("locus_recon", filename + exts["locus_recon"]),
extra["locus_recon"])
phylo.write_events(
filenames.get("locus_events", filename + exts["locus_events"]),
extra["locus_events"])
util.write_list(
filenames.get("daughters", filename + exts["daughters"]),
[x.name for x in extra["daughters"]])
def write_dlcoal_recon(filename, coal_tree, extra,
exts={"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"daughters": ".daughters"
},
filenames={}):
"""Writes a reconciled gene tree to files"""
# coal
coal_tree.write(filenames.get("coal_tree", filename + exts["coal_tree"]),
rootData=True)
phylo.write_recon_events(
filenames.get("coal_recon", filename + exts["coal_recon"]),
extra["coal_recon"], noevent="none")
# locus
extra["locus_tree"].write(
filenames.get("locus_tree", filename + exts["locus_tree"]),
rootData=True)
phylo.write_recon_events(
filenames.get("locus_recon", filename + exts["locus_recon"]),
extra["locus_recon"], extra["locus_events"])
util.write_list(
filenames.get("daughters", filename + exts["daughters"]),
[x.name for x in extra["daughters"]])
def write(self, filename, coal_tree,
exts={"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"daughters": ".daughters"
},
filenames={}):
"""Writes a reconciled gene tree to files"""
assert coal_tree and self.coal_recon and \
self.locus_tree and self.locus_recon and self.locus_events and \
(self.daughters is not None)
# coal
coal_tree.write(
filenames.get("coal_tree", filename + exts["coal_tree"]),
rootData=True)
phylo.write_recon_events(
filenames.get("coal_recon", filename + exts["coal_recon"]),
self.coal_recon, noevent="none")
# locus
self.locus_tree.write(
filenames.get("locus_tree", filename + exts["locus_tree"]),
rootData=True)
phylo.write_recon_events(
filenames.get("locus_recon", filename + exts["locus_recon"]),
self.locus_recon, self.locus_events)
util.write_list(
filenames.get("daughters", filename + exts["daughters"]),
[x.name for x in self.daughters])
def write(
self,
filename,
coal_tree,
exts={
"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"daughters": ".daughters"
},
filenames={},
filestreams={}):
"""Writes a reconciled gene tree to files"""
assert coal_tree and self.coal_recon and \
self.locus_tree and self.locus_recon and self.locus_events and \
(self.daughters is not None)
# coal tree and recon
coal_tree.write(filestreams.get(
"coal_tree",
filenames.get("coal_tree", filename + exts["coal_tree"])),
rootData=True)
phylo.write_recon_events(filestreams.get(
"coal_recon",
filenames.get("coal_recon", filename + exts["coal_recon"])),
self.coal_recon,
noevent="none")
# locus tree and recon
self.locus_tree.write(filestreams.get(
"locus_tree",
filenames.get("locus_tree", filename + exts["locus_tree"])),
rootData=True)
phylo.write_recon_events(
filestreams.get(
"locus_recon",
filenames.get("locus_recon", filename + exts["locus_recon"])),
self.locus_recon, self.locus_events)
# daughters
util.write_list(
filestreams.get(
"daughters",
filenames.get("daughters", filename + exts["daughters"])),
[x.name for x in self.daughters])
def dndsMatrix(seqs, saveOutput="", verbose=False, safe=True):
if safe:
seqs = alignlib.mapalign(seqs, valfunc=removeStopCodons)
phylip.validate_seqs(seqs)
cwd = phylip.create_temp_dir()
util.tic("yn00 on %d of length %d" % (len(seqs), len(seqs.values()[0])))
# create input
labels = phylip.write_phylip_align(file("seqfile.phylip", "w"), seqs)
util.write_list(file("labels", "w"), labels)
# create control file
out = file("yn00.ctl", "w")
print >>out, "seqfile = seqfile.phylip"
print >>out, "outfile = outfile"
out.close()
# run yn00
if verbose:
os.system("yn00 yn00.ctl")
else:
os.system("yn00 yn00.ctl > /dev/null")
try:
dnmat = phylip.read_dist_matrix("2YN.dN")
dsmat = phylip.read_dist_matrix("2YN.dS")
except:
# could not make distance matrix
if safe:
# make dummy matrix
dnmat = labels, [[0] * len(labels)] * len(labels)
dsmat = labels, [[0] * len(labels)] * len(labels)
else:
raise Exception("could not read dn or ds matrices")
if saveOutput != "":
phylip.save_temp_dir(cwd, saveOutput)
else:
phylip.cleanup_temp_dir(cwd)
util.toc()
return dnmat, dsmat
def dndsMatrix(seqs, saveOutput="", verbose=False, safe=True):
if safe:
seqs = alignlib.mapalign(seqs, valfunc=removeStopCodons)
phylip.validate_seqs(seqs)
cwd = phylip.create_temp_dir()
util.tic("yn00 on %d of length %d" % (len(seqs), len(seqs.values()[0])))
# create input
labels = phylip.write_phylip_align(file("seqfile.phylip", "w"), seqs)
util.write_list(file("labels", "w"), labels)
# create control file
out = file("yn00.ctl", "w")
print >> out, "seqfile = seqfile.phylip"
print >> out, "outfile = outfile"
out.close()
# run yn00
if verbose:
os.system("yn00 yn00.ctl")
else:
os.system("yn00 yn00.ctl > /dev/null")
try:
dnmat = phylip.read_dist_matrix("2YN.dN")
dsmat = phylip.read_dist_matrix("2YN.dS")
except:
# could not make distance matrix
if safe:
# make dummy matrix
dnmat = labels, [[0] * len(labels)] * len(labels)
dsmat = labels, [[0] * len(labels)] * len(labels)
else:
raise Exception("could not read dn or ds matrices")
if saveOutput != "":
phylip.save_temp_dir(cwd, saveOutput)
else:
phylip.cleanup_temp_dir(cwd)
util.toc()
return dnmat, dsmat
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
def phyml(seqs, verbose=True, args=None,
usertree=None, seqtype="pep", saveOutput="", bootiter=0,
opttree=True, optbranches=True, nrates=4):
phylip.validate_seqs(seqs)
cwd = phylip.create_temp_dir()
util.tic("phyml on %d of length %d" % (len(seqs), len(seqs.values()[0])))
# create input
labels = phylip.write_phylip_align(file("infile", "w"), seqs)
util.write_list(file("labels", "w"), labels)
options = "y"
# only bootstrap when iterations are above 1
if bootiter == 1:
bootiter = 0
if usertree != None:
usertree = treelib.unroot(usertree)
phylip.write_in_tree("intree", usertree, labels)
treefile = "intree"
else:
treefile = "BIONJ"
optimize = ""
if opttree:
optimize += "y "
else:
optimize += "n "
if optbranches:
optimize += "y "
else:
optimize += "n "
if args == None:
if seqtype == "dna":
args = "infile 0 s 1 %d HKY e e %d e %s %s" % \
(bootiter, nrates, treefile, optimize)
elif seqtype == "pep":
args = "infile 1 s 1 %d JTT e %d e %s %s" % \
(bootiter, nrates, treefile, optimize)
else:
assert False, "unknown sequence type '%s'" % seqtype
phylip.exec_phylip("phyml %s" % args, options, verbose)
# parse tree
tree = phylip.read_out_tree("infile_phyml_tree.txt", labels)
# parse likelihood
tree.data["logl"] = float(file("infile_phyml_lk.txt").read())
if saveOutput != "":
phylip.save_temp_dir(cwd, saveOutput)
else:
phylip.cleanup_temp_dir(cwd)
util.toc()
return 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
def phyml(seqs,
verbose=True,
args=None,
usertree=None,
seqtype="pep",
saveOutput="",
bootiter=0,
opttree=True,
optbranches=True,
nrates=4):
phylip.validate_seqs(seqs)
cwd = phylip.create_temp_dir()
util.tic("phyml on %d of length %d" % (len(seqs), len(seqs.values()[0])))
# create input
labels = phylip.write_phylip_align(file("infile", "w"), seqs)
util.write_list(file("labels", "w"), labels)
options = "y"
# only bootstrap when iterations are above 1
if bootiter == 1:
bootiter = 0
if usertree != None:
usertree = treelib.unroot(usertree)
phylip.write_in_tree("intree", usertree, labels)
treefile = "intree"
else:
treefile = "BIONJ"
optimize = ""
if opttree:
optimize += "y "
else:
optimize += "n "
if optbranches:
optimize += "y "
else:
optimize += "n "
if args == None:
if seqtype == "dna":
args = "infile 0 s 1 %d HKY e e %d e %s %s" % \
(bootiter, nrates, treefile, optimize)
elif seqtype == "pep":
args = "infile 1 s 1 %d JTT e %d e %s %s" % \
(bootiter, nrates, treefile, optimize)
else:
assert False, "unknown sequence type '%s'" % seqtype
phylip.exec_phylip("phyml %s" % args, options, verbose)
# parse tree
tree = phylip.read_out_tree("infile_phyml_tree.txt", labels)
# parse likelihood
tree.data["logl"] = float(file("infile_phyml_lk.txt").read())
if saveOutput != "":
phylip.save_temp_dir(cwd, saveOutput)
else:
phylip.cleanup_temp_dir(cwd)
util.toc()
return tree
