def WriteTree(self, tree):
"""write tree to file.
"""
nexus = TreeTools.Newick2Nexus(tree)
t = nexus.trees[0]
TreeTools.MapTaxa(t, self.mMapOld2New)
outfile = open(self.mTempdir + "/" + self.mFilenameTree, "w")
outfile.write("%i 1\n" % self.mNumSequences)
outfile.write("%s\n" % TreeTools.Tree2Newick(t))
outfile.close()
def parseOutput(self, lines, out, err):
lines = re.sub("\s", "", "".join(lines))
lines = re.sub("\[[^\]]+\]", "", lines)
t = TreeTools.Newick2Nexus("".join(lines))
result = Result()
t = t.trees[0]
TreeTools.MapTaxa(t, self.mMapNew2Old)
result.mTree = t
result.mLog = out
result.mErr = err
return result
def run(self):
self.prepareRun()
if not self.mProgram:
raise UsageError("no program specified.")
s = subprocess.Popen("%s" % (self.mProgram),
shell=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.mTempdir,
close_fds=True)
(out, err) = s.communicate("\n".join(self.mOptions) + "\n")
if s.returncode != 0:
raise UsageError, "Error in running phylip.\n%s\n%s\nTemporary directory was %s" % (
out, err, self.mTempdir)
# Parse output files that might have been created:
result = PhylipResult()
# parse tree file
if os.path.exists("%s/outtree" % self.mTempdir):
nexus = TreeTools.Newick2Nexus(
open("%s/outtree" % self.mTempdir, "r"))
for tree in nexus.trees:
TreeTools.MapTaxa(tree, self.mMapPhylip2Input)
result.mNexus = nexus
if self.mLogLevel >= 1:
print "# received tree with %i taxa" % (len(
TreeTools.GetTaxa(nexus.trees[0])))
elif os.path.exists("%s/outfile" % self.mTempdir):
if self.mProgram in ("dnadist", "protdist"):
infile = open("%s/outfile" % self.mTempdir, "r")
result.mMatrix, row_headers, col_headers = MatlabTools.readMatrix(
infile, format="phylip")
result.mRowHeaders = []
for x in row_headers:
result.mRowHeaders.append(self.mMapPhylip2Input[x])
result.mColHeaders = result.mRowHeaders
elif self.mProgram == "contrast":
infile = open("%s/outfile" % self.mTempdir, "r")
result.parseContrasts(infile)
infile.close()
else:
raise "other return types not implemented"
if self.mLogLevel >= 2:
print out
if self.mLogLevel == 0:
shutil.rmtree(self.mTempdir)
return result
def prepareRun(self):
self.__reset()
self.mTempdir = tempfile.mkdtemp()
# self.mTempdir = "tmp"
if not os.path.exists(self.mTempdir):
os.mkdir(self.mTempdir)
if self.mInputMatrix and self.mInputData:
raise ValueError(
"please specify either input matrix or input data, but not both."
)
# prepare input matrix. Should already be in phylip like
# format, but long identifiers are shortened and tabs are
# replaced by spaces.
if self.mInputMatrix:
outfile = open(self.mTempdir + "/infile", "w")
identifiers = map(lambda x: re.split("\s+", x[:-1])[0],
self.mInputMatrix[1:])
self.updateMaps(identifiers)
outfile.write(self.mInputMatrix[0])
for line in self.mInputMatrix[1:]:
data = re.split("\s+", line[:-1])
new_line = self.mMapInput2Phylip[
data[0]] + " " + " ".join(data[1:])
outfile.write(new_line + "\n")
outfile.close()
if self.mLogLevel >= 1:
print "# written input matrix with %i taxa to %s" % (
len(identifiers), self.mTempdir + "/infile")
os.system("cat %s" % self.mTempdir + "/infile")
elif self.mInputData:
outfile = open(self.mTempdir + "/infile", "w")
outfile.write("%i %i\n" %
(len(self.mInputData), len(self.mInputData[0]) - 1))
identifiers = map(lambda x: x[0], self.mInputData)
self.updateMaps(identifiers)
for x in range(len(identifiers)):
outfile.write("%-10s %s\n" %
(self.mMapInput2Phylip[identifiers[x]], " ".join(
self.mInputData[x][1:])))
outfile.close()
if self.mLogLevel >= 1:
print "# written input matrix with %i taxa to %s" % (
len(identifiers), self.mTempdir + "/infile")
os.system("cat %s" % self.mTempdir + "/infile")
# prepare input tree or trees
self.mNInputTrees = 0
if self.mInputTree or self.mInputTrees:
outfile = open(self.mTempdir + "/intree", "w")
if self.mInputTree and self.mInputTrees:
raise UsageError(
"please supply either one or mupltiple trees, but not both."
)
if self.mInputTree:
trees = [self.mInputTree]
else:
trees = self.mInputTrees
for tree in trees:
if self.mPruneTree:
taxa = self.mMapInput2Phylip.keys()
TreeTools.PruneTree(tree, taxa)
taxa = TreeTools.GetTaxa(tree)
self.updateMaps(taxa)
TreeTools.MapTaxa(tree, self.mMapInput2Phylip)
# check if taxa are unique
taxa = tree.get_taxa()
staxa = set()
skip = False
for t in taxa:
if t in staxa:
if self.mLogLevel >= 1:
print "# skipping tree %s because of duplicate taxa." % (
tree.name)
skip = True
staxa.add(t)
if skip:
continue
outfile.write(TreeTools.Tree2Newick(tree) + "\n")
self.mNInputTrees += 1
if self.mLogLevel >= 1:
print "# written input tree with %i taxa to %s" % (len(
TreeTools.GetTaxa(tree)), self.mTempdir + "/intree")
print "#", TreeTools.Tree2Newick(tree)
outfile.close()
# prepare input multiple alignment
if self.mInputMali:
if self.mInputMatrix:
raise "both mali and matrix supplied - infile conflict."
outfile = open(self.mTempdir + "/infile", "w")
identifiers = self.mInputMali.getIdentifiers()
self.updateMaps(identifiers)
self.mInputMali.mapIdentifiers(self.mMapInput2Phylip)
self.mInputMali.writeToFile(outfile, format="phylip")
outfile.close()
if self.mLogLevel >= 1:
print "# written input multiple alignments with %i taxa and with %i to %s" %\
(self.mInputMali.getLength(),
self.mInputMali.getWidth(), self.mTempdir + "/intree")
