def __init__(self, ctx):
super(Mapper, self).__init__(ctx)
self.ctx = ctx
jc = self.ctx.getJobConf()
self.__get_configuration(jc)
self.hit_counter = self.ctx.getCounter(self.COUNTER_CLASS,
"BLAST_HITS")
self.logger = logging.getLogger("mapper")
self.logger.setLevel(self.log_level)
self.input_file = "temp.in"
self.output_file = "temp.out"
engine_logger = logging.getLogger("blastall")
engine_logger.setLevel(self.log_level)
self.engine = Engine(exe_file=self.blastall_exe, logger=engine_logger)
try:
self.db_dir = jc.get("mapred.cache.archives").split(",")[0].split(
"#")[1]
except IndexError:
raise ValueError('bad format for "mapred.cache.archives"')
self.opts = {
"blastall.program": self.program,
"blastall.database": os.path.join(self.db_dir, self.db_name),
"blastall.out.tabular": True,
"blastall.input.file": self.input_file,
"blastall.output.file": self.output_file,
"blastall.evalue": self.evalue,
"blastall.gap.cost": self.gap_cost,
"blastall.word.size": self.word_size,
"blastall.filter": self.filter,
}
def main(argv):
logger = logging.getLogger("main")
logger.setLevel(logging.DEBUG)
parser = make_parser()
opt, args = parser.parse_args(argv)
try:
input_fn = args[1]
output_fn = args[2]
except IndexError:
parser.print_help()
sys.exit(2)
if opt.get_db:
get_db()
if opt.format_db:
retcode = format_db()
if retcode:
logging.warn("formatdb returned %d" % retcode)
OPTS["blastall.input.file"] = input_fn
OPTS["blastall.output.file"] = output_fn
engine = Engine(logger=logger)
engine.blastall(opts=OPTS)
