def RunPhyldogAnalysis(phyldogDir, ogs, speciesToUse, nParallel):
qRunSingley = True
Setup(phyldogDir, ogs, speciesToUse, qRunSingley)
start = time.time()
if qRunSingley:
nOGs = len(ogs)
cmds = [["mpirun -np 2 phyldog param=%s%s" % (phyldogDir, "GeneralOptions_OG%07d.opt" % i)] for i in xrange(nOGs)]
util.RunParallelCommands(nParallel, cmds, True)
else:
subprocess.call("mpirun -np %d phyldog param=GeneralOptions.opt" % nParallel, shell=True, cwd=phyldogDir, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stop = time.time()
print("%f seconds" % (stop-start))
return ProcessSpeciesTree(phyldogDir)
def DoTrees(self,
ogs,
idDict,
nProcesses,
qStopAfterSeqs,
qStopAfterAlignments,
nSwitchToMafft=500):
# 0
resultsDirsFullPath = []
for fn in [
self.GetFastaFilename, self.GetAlignmentFilename,
self.GetTreeFilename
]:
for qIDs in [True, False]:
d = os.path.split(fn(0, not qIDs))[0]
if not os.path.exists(d): os.mkdir(d)
if not qIDs: resultsDirsFullPath.append(d)
if qStopAfterSeqs: break
if qStopAfterAlignments and fn == self.GetAlignmentFilename: break
# 1.
fastaWriter = FastaWriter(self.ogsWorkingDir)
self.WriteFastaFiles(fastaWriter, ogs, idDict)
if qStopAfterSeqs: return resultsDirsFullPath
# 2
if qStopAfterAlignments:
util.PrintUnderline("Inferring multiple sequence alignments")
else:
util.PrintUnderline(
"Inferring multiple sequence alignments and gene trees")
# 3
alignCommands = self.GetAlignmentCommands(ogs, nSwitchToMafft)
if qStopAfterAlignments:
util.RunParallelCommands(nProcesses, alignCommands, qShell=True)
return resultsDirsFullPath[:2]
alignmentFilesToUse = [
self.GetAlignmentFilename(i) for i, _ in enumerate(alignCommands)
]
treeCommands = self.GetTreeCommands(alignmentFilesToUse, ogs)
commandsSet = []
for i in xrange(len(treeCommands)):
commandsSet.append([alignCommands[i], treeCommands[i]])
for i in xrange(len(treeCommands), len(alignCommands)):
commandsSet.append([alignCommands[i]])
util.RunParallelOrderedCommandLists(nProcesses, commandsSet)
# Convert ids to accessions
for i, alignFN in enumerate(alignmentFilesToUse):
with open(alignFN,
'rb') as infile, open(self.GetAlignmentFilename(i, True),
'wb') as outfile:
for line in infile:
if line.startswith(">"):
outfile.write(">" + idDict[line[1:].rstrip()] + "\n")
else:
outfile.write(line)
if os.path.exists(self.GetTreeFilename(i)):
util.RenameTreeTaxa(self.GetTreeFilename(i),
self.GetTreeFilename(i, True),
idDict,
qFixNegatives=True)
return resultsDirsFullPath[:2]