def runRaxmlNg(fastaFilePath, workingDir, outputPath, threads = 8):
# raxml-ng --msa prim.phy --model GTR+G --prefix T4 --threads 2 --seed 2 --tree pars{25},rand{25}
baseName = os.path.basename(outputPath).replace(".","")
raxmlFile = os.path.join(workingDir, "{}.raxml.bestTree".format(baseName))
seed = random.randint(1, 1000000)
args = [Configs.raxmlPath,
"--msa", fastaFilePath,
"--prefix", baseName,
"--threads", str(threads),
"--seed", str(seed)]
if Configs.inferDataType(fastaFilePath) == "protein":
args.extend(["--model", "LG+G"])
else:
args.extend(["--model", "GTR+G"])
args.extend(["--tree", "pars{{{}}}".format(1)])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {raxmlFile : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def runFastTree(fastaFilePath, workingDir, outputPath, mode = "normal", intree = None):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.fasttreePath]
if Configs.inferDataType(fastaFilePath) == "protein":
args.extend(["-lg"])
else:
args.extend(["-nt", "-gtr"])
if intree is not None:
args.extend(["-intree", intree])
if mode == "fast":
args.extend(["-fastest", "-nosupport"])
elif mode == "faster":
args.extend(["-fastest", "-nosupport", "-mlnni", "4" ])
elif mode == "noml":
args.extend(["-fastest", "-nosupport", "-noml"])
args.extend([fastaFilePath, ">", tempPath])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
