def DoTrees(self, ogs, idDict, nProcesses, nSwitchToMafft=500):
testFN = WriteTestFile(self.orthofinderWorkingDir)
if not orthofinder.CanRunCommand("mafft %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run mafft")
print("Please check MAFFT is installed and that the executables are in the system path\n")
return False
if not orthofinder.CanRunCommand("mafft %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run mafft")
print("Please check mafft is installed and that the executables are in the system path\n")
return False
if not orthofinder.CanRunCommand("FastTree %s" % testFN, qAllowStderr=True):
print("ERROR: Cannot run FastTree")
print("Please check FastTree is installed and that the executables are in the system path\n")
return False
os.remove(testFN)
# 0
dirs = ['Sequences', 'Alignments', 'Trees']
for d in dirs:
if not os.path.exists(self.baseOutputDir + d):
os.mkdir(self.baseOutputDir + d)
# 1.
fastaWriter = FastaWriter(self.orthofinderWorkingDir)
self.WriteFastaFiles(fastaWriter, ogs, idDict)
print("\nFasta files for orthogroups have been written to:\n %s" % self.baseOutputDir + "Sequences/")
# 2
IandOGs_toDo, nDone = self.OGsStillToDo(ogs)
if nDone != 0: print("\nAlignments and trees have already been generated for %d orthogroups" % nDone)
print("\nAlignments and trees will be generated for %d orthogroups" % len(IandOGs_toDo))
# 3
alignCommands = self.GetAlignmentCommands(IandOGs_toDo, nSwitchToMafft)
alignmentFilesToUse = [self.GetAlignmentFilename(i) for i, og in IandOGs_toDo]
treeCommands = self.GetTreeCommands(alignmentFilesToUse, IandOGs_toDo)
commandsSet = [(alignCmd, treeCms) for alignCmd, treeCms in zip(alignCommands, treeCommands)]
# 4
if len(commandsSet) > 0:
print("\nExample commands that will be run:")
for cmdSet in commandsSet[:10]:
for cmd in cmdSet:
print(cmd)
print("")
RunParallelCommandSets(nProcesses, commandsSet)
orthofinder.PrintCitation()
print("\nFasta files for orthogroups have been written to:\n %s\n" % (self.baseOutputDir + "Sequences/"))
print("Multiple sequences alignments have been written to:\n %s\n" % (self.baseOutputDir + "Alignments/"))
print("Gene trees have been written to:\n %s\n" % (self.baseOutputDir + "Trees/"))
def PrintHelp():
print("Usage")
print("-----")
print("python trees_for_orthogroups.py orthofinder_results_directory [-t max_number_of_threads]")
print("python trees_for_orthogroups.py -h")
print("\n")
print("Arguments")
print("---------")
print("""orthofinder_results_directory
Generate multiple sequence alignments and trees for the orthogroups in orthofinder_results_directory.\n""")
print("""-t max_number_of_threads, --threads max_number_of_threads
The maximum number of processes to be run simultaneously. The deafult is %d but this
should be increased by the user to the maximum number of cores available.\n""" % orthofinder.nThreadsDefault)
print("""-h, --help
Print this help text""")
orthofinder.PrintCitation()
def PrintHelp():
print("Usage")
print("-----")
print(
"get_orthologues.py orthofinder_results_directory [-t max_number_of_threads]"
)
print("get_orthologues.py -h")
print("\n")
print("Arguments")
print("---------")
print("""orthofinder_results_directory
Generate gene trees for the orthogroups, generated rooted species tree and infer ortholgues.\n"""
)
print("""-t max_number_of_threads, --threads max_number_of_threads
The maximum number of processes to be run simultaneously. The deafult is %d but this
should be increased by the user to the maximum number of cores available.\n"""
% orthofinder.nThreadsDefault)
print("""-h, --help
Print this help text""")
orthofinder.PrintCitation()
if arg == "-t" or arg == "--threads":
if len(args) == 0:
print("Missing option for command line argument -t")
orthofinder.Fail()
arg = args.pop(0)
try:
nProcesses = int(arg)
except:
print("Incorrect argument for number of threads: %s" % arg)
orthofinder.Fail()
else:
userDir = arg
# Check arguments
print("0. Getting Orthologues")
print("----------------------")
if nProcesses == None:
print(
"""\nNumber of parallel processes has not been specified, will use the default value.
Number of parallel processes can be specified using the -t option.""")
nProcesses = orthofinder.nThreadsDefault
print("Using %d threads for alignments and trees" % nProcesses)
orthofinderWorkingDir, orthofinderResultsDir, clustersFilename_pairs = tfo.GetOGsFile(
userDir)
resultsString = GetOrthologues(orthofinderWorkingDir,
orthofinderResultsDir,
clustersFilename_pairs, nProcesses)
print(resultsString)
orthofinder.PrintCitation()