def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
Query_collection=[]
rank_collection=[]
Query_dict=defaultdict(list)
temp_dir_name=tempfile.mkdtemp(prefix='root_')
level=0
for root,dirs,files in os.walk(opts.input_HMM_fp):
print root
#print ".................."
path_to_db=os.path.join(root,'db')
path_to_result=os.path.join(root,'result.out')
if level==0:
stdout,stderr,return_value = qcli_system_call('cmscan -E 1 '+path_to_db+' '+opts.input_query_fp+' > '+path_to_result)
if return_value != 0:
print 'Stdout:\n%s\nStderr:%s\n' % (stdout,stderr)
exit(1)
HMM_result=open(path_to_result,'U')
HMM_choice_list,HMM_Query_list,HMM_choice_list_with_ID=search_HMM(HMM_result)
create_temp_test_seq_file(temp_dir_name,HMM_choice_list_with_ID,open(opts.input_query_fp,'U'))
rank_collection.extend(HMM_choice_list)
Query_collection.extend(HMM_Query_list)
for Query_ID, rank in HMM_choice_list_with_ID:
Query_dict[Query_ID].append(rank)
else:
if os.path.basename(root) in rank_collection:
path_to_test_seq=os.path.join(temp_dir_name,os.path.basename(root)+'.fasta')
stdout,stderr,return_value = qcli_system_call('cmscan -E 1 '+path_to_db+' '+path_to_test_seq+' > '+path_to_result)
if return_value != 0:
print 'Stdout:\n%s\nStderr:%s\n' % (stdout,stderr)
exit(1)
HMM_result=open(path_to_result,'U')
HMM_choice_list,HMM_Query_list,HMM_choice_list_with_ID=search_HMM(HMM_result)
create_temp_test_seq_file(temp_dir_name,HMM_choice_list_with_ID,open(path_to_test_seq,'U'))
rank_collection.extend(HMM_choice_list)
for Query_ID, rank in HMM_choice_list_with_ID:
Query_dict[Query_ID].append(rank)
level+=1
shutil.rmtree(temp_dir_name)
taxonomy_assignment_to_query_seq(Query_dict,Query_collection,opts.output_fp)
def test_search_HMM(self):
expected_choice,expected_Query,expected_choice_ID=\
search_HMM(open('/scratch-lt/hhh34/taxonomy_by_infernal_slurm/cmscan_result.out','r'))
actual_Query = ['1000269','1001007']
actual_choice = ['k__Bacteria','k__Bacteria']
actual_choice_ID = [('1000269','k__Bacteria'),('1001007','k__Bacteria')]
self.assertEqual(actual_Query,expected_Query)
self.assertEqual(actual_choice,expected_choice)
self.assertEqual(actual_choice_ID,expected_choice_ID)
