def get_results(self):
self.wait()
self.results_lock.acquire()
if self.result_alignment is not None:
self.results_lock.release()
return self.result_alignment
if self.killed:
raise RuntimeError("PastaAligner Job killed")
if self.align_job_list:
raise RuntimeError("hmm, this should be empty")
else:
j_list = self.merge_job_list
if j_list:
# These are merge jobs that need transitivity merging
if self.skip_merge:
r = self.multilocus_dataset.new_with_shared_meta()
r.append(j_list[0].get_results()[0]) #TODO: this should be changed to be multi-locus
for j in j_list[1:]:
r[0].merge_in(j.get_results()[0]) #TODO: this should be changed to be multi-locus
j.clear_results_object()
#assert all(x.is_aligned() for x in r)
else: # These are pairwise merges
r = self.multilocus_dataset.new_with_shared_meta()
for j in j_list:
a = CompactAlignment()
a.update_from_alignment(j.get_results())
r.append(a)
self.result_alignment = r
self.finished = True
else:
r = None # this can happen if jobs are killed
self.results_lock.release()
return r
parser.add_argument(
'-filterfragments',
metavar='N',
type=int,
help='sequences with less than N non-gap sequences will be removed')
parser.add_argument(
'-rename',
metavar='MappingFile',
type=argparse.FileType('r'),
help=
'Rename sequences, according to the mapping file generated by PASTA')
# parser.add_argument('actions', nargs='*',
# help='a list of actions (separated by space). Supported actions are: mask (see maskmin), rename (see namemap)')
args = parser.parse_args()
alg = CompactAlignment()
alg.read_file_object(args.infile, args.informat)
# if args.actions:
# print >>sys.stderr, "will perform the following actions: %s" %",".join(args.actions)
# else:
# print >>sys.stderr, "No actions will be taken. Input in %s will be written to output in %s." %(args.informat,args.outformat)
if args.masksites:
alg.mask_gapy_sites(args.masksites)
if args.filterfragments:
rem = []
for k, v in alg.items():
if len(v.seq) < args.filterfragments:
rem.append(k)
help='name of the output file (default: standard output)')
parser.add_argument('-informat', nargs='?', default="FASTA", choices = ["COMPACT3", "FASTA"],
help='format of the input file (default: FASTA)')
parser.add_argument('-outformat', nargs='?', default="FASTA", choices = ["COMPACT3", "FASTA", "PHYLIP"],
help='format of the output file (default: FASTA)')
parser.add_argument('-masksites', metavar='N', type=int,
help='sites with less than N non-gap characters will be masked out')
parser.add_argument('-filterfragments', metavar='N', type=int,
help='sequences with less than N non-gap sequences will be removed')
parser.add_argument('-rename', metavar='MappingFile', type=argparse.FileType('r'),
help='Rename sequences, according to the mapping file generated by PASTA')
# parser.add_argument('actions', nargs='*',
# help='a list of actions (separated by space). Supported actions are: mask (see maskmin), rename (see namemap)')
args = parser.parse_args()
alg = CompactAlignment()
alg.read_file_object(args.infile,args.informat)
# if args.actions:
# print >>sys.stderr, "will perform the following actions: %s" %",".join(args.actions)
# else:
# print >>sys.stderr, "No actions will be taken. Input in %s will be written to output in %s." %(args.informat,args.outformat)
if args.masksites:
alg.mask_gapy_sites(args.masksites)
if args.filterfragments:
rem = []
for k, v in alg.iteritems():
if len(v.seq) < args.filterfragments:
rem.append(k)
