def manage_folders_reads(self, args):
if (args.folders == None and args.reads == None and args.mreads == None):
eprint("error: Either folders or reads must be set!")
raise PSToolException("error: Either folders or reads must be set!")
if args.folders != None:
folders = args.folders
else:
folders = []
if args.mreads != None:
for mread in args.mreads:
folders.append(mread)
if args.reads != None:
for readfolder in args.reads:
# if downloads folder, then take the downloads folder + fail/pass plus any batch folder within
downloadpath = os.path.join(readfolder, "downloads")
if os.path.isdir(downloadpath):
for x in ['fail', 'skip', 'pass']:
if os.path.isdir(os.path.join(downloadpath, x)):
curfolder = os.path.join(downloadpath, x)
folders.append(curfolder)
all_subdirs = self._getsubdirs(curfolder)
for x in all_subdirs:
if x.startswith("batch"):
folders.append(os.path.join(curfolder, x))
else:
for x in os.walk(readfolder):
eprint("Adding path: " + x[0])
folders.append(x[0])
return folders
def exec(self):
iStart = time.time()
inputs = self.prepareInputs(self.args)
environment = self.prepareEnvironment(self.args)
ll = MapReduce(8)
result = ll.exec( inputs, self.execParallel, environment, self.chunkSize, self.joinParallel)
iEnd = time.time()
eprint("Making Results: " + str(time.strftime('%H:%M:%S [HH:MM:SS]', time.gmtime(iEnd - iStart))))
self.makeResults(result, environment, self.args)
iEnd = time.time()
eprint("Execution Time: " + str(time.strftime('%H:%M:%S [HH:MM:SS]', time.gmtime(iEnd-iStart))))
'alignment_stat'),
SimilarityAnalysisFactory(parser, subparsers, 'similarity'),
ReportFactory(parser, subparsers, 'summary'),
FoldChangeDistributionFactory(parser, subparsers, 'foldchange'),
FoldChangeFeatureCountsDistributionFactory(parser, subparsers,
'foldchange_fc'),
ReportFactory(parser, subparsers, 'timeline'),
FoldChangeSimilarityFactory(parser, subparsers, 'fcdist'),
FoldChangeTopRegulatedFactory(parser, subparsers, 'topreg'),
SecondaryAlignmentAnalysisFactory(parser, subparsers, 'sec_alignments')
]
for tool in allTools:
cmd2tool[tool.which] = tool
args = parser.parse_args()
if not 'func' in vars(args):
parser.print_help()
else:
try:
calcObj = args.func(args)
calcObj.exec()
except PSToolException as e:
eprint(e)
if args.which:
cmd2tool[args.which].print_usage()