def test_run_process_sff_gz_through_split_lib_FLX(self): """run_process_sff_through_pick_otus runs without error: Convert to \ FLX""" # remove generated mapping file moved_mapping_file = join(self.wf_out, split(self.fasting_mapping_fp)[-1]) self.files_to_remove.append(moved_mapping_file) run_process_sff_through_split_lib( 0, "Fasting_subset", sff_input_fp=self.sff_gz_fp, mapping_fp=self.fasting_mapping_fp, output_dir=self.wf_out, command_handler=call_commands_serially, params=self.params, qiime_config=self.qiime_config, convert_to_flx=True, write_to_all_fasta=False, status_update_callback=no_status_updates, ) # get the file basename input_file_basename = splitext(splitext(split(self.sff_fp)[1])[0])[0] # get the split-library sequence fpath split_lib_seqs_fp = join(self.wf_out, "split_libraries", "seqs.fna") sff_fp = join(self.wf_out, "Fasting_subset_FLX.sff") sff_seqs_fp = join(self.wf_out, "Fasting_subset_FLX.fna") sff_qual_fp = join(self.wf_out, "Fasting_subset_FLX.qual") sff_flow_fp = join(self.wf_out, "Fasting_subset_FLX.txt") new_map_fp = join(self.wf_out, "Fasting_subset_mapping.txt") # define files to remove self.files_to_remove.append(sff_fp) self.files_to_remove.append(sff_seqs_fp) self.files_to_remove.append(sff_qual_fp) self.files_to_remove.append(sff_flow_fp) # get the head of files split_lib_head = get_top_fastq_two_lines(open(split_lib_seqs_fp, "U")) raw_seq_head = get_top_fastq_two_lines(open(sff_seqs_fp, "U")) raw_qual_head = get_top_fastq_two_lines(open(sff_qual_fp, "U")) raw_flow_head = get_top_fastq_two_lines(open(sff_flow_fp, "U")) # check results self.assertEqual("".join(split_lib_head), exp_FLX_split_lib_head) self.assertEqual("".join(raw_seq_head), exp_FLX_raw_seq_head) self.assertEqual("".join(raw_qual_head), exp_FLX_raw_qual_head) self.assertEqual("".join(raw_flow_head), exp_Ti_raw_flow_head) # Check that the log file is created and has size > 0 log_fp = glob(join(self.wf_out, "log*.txt"))[0] self.assertTrue(getsize(log_fp) > 0)
def test_submit_processed_data_to_db(self): """run_process_sff_through_pick_otus runs without error""" run_process_sff_through_split_lib(0,'Fasting_subset', sff_input_fp=self.sff_fp, mapping_fp=self.fasting_mapping_fp, output_dir=self.wf_out, command_handler=call_commands_serially, params=self.params, qiime_config=self.qiime_config,convert_to_flx=False, write_to_all_fasta=False, status_update_callback=no_status_updates) input_file_basename = splitext(split(self.sff_fp)[1])[0] otu_fp = join(self.wf_out,'picked_otus','seqs_otus.txt') split_lib_seqs_fp = join(self.wf_out,'split_libraries',\ 'seqs.fna') run_chain_pick_otus(split_lib_seqs_fp, output_dir=self.gg_out, command_handler=call_commands_serially, params=self.params, qiime_config=self.qiime_config,parallel=False, status_update_callback=no_status_updates) input_fname = splitext(split(self.sff_fp)[-1])[0] db_input_fp = join(self.wf_out,input_fname) analysis_id=submit_sff_and_split_lib(data_access,\ db_input_fp+'.fna',0) load_otu_mapping(data_access,self.wf_out,analysis_id) print 'Analysis ID is: %s' % str(analysis_id) print 'Testing the FLOW_DATA loading!' exp_sff_md5='314f4000857668d45a413d2e94a755fc' exp_num_seqs=22 exp_read_id='FLP3FBN01ELBSX' exp_instr_code='GS FLX' exp_sff_fname='Fasting_subset' con = data_access.getSFFDatabaseConnection() cur = con.cursor() seq_run_info="""select j.seq_run_id,f.sff_filename,f.number_of_reads,f.md5_checksum, h.instrument_code from analysis j inner join seq_run_to_sff_file s on j.seq_run_id=s.seq_run_id inner join sff_file f on f.sff_file_id=s.sff_file_id inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id inner join sequencing_run h on h.seq_run_id=s.seq_run_id""" seq_run_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_1\'" % (str(analysis_id)) results = cur.execute(seq_run_info) #print 'Calling getTestFlowData...' for data in results: obs_seq_run_id,obs_sff_filename,obs_num_of_reads,obs_sff_md5,\ obs_instrument_code = data self.assertEqual(obs_sff_filename,exp_sff_fname) self.assertEqual(obs_num_of_reads,exp_num_seqs) self.assertEqual(obs_sff_md5,exp_sff_md5) self.assertEqual(obs_instrument_code,exp_instr_code) ''' print 'After getTestFlowData...' #print 'Calling getTestFlowData...' obs_seq_run_id,obs_sff_filename,obs_num_of_reads,obs_sff_md5,\ obs_instrument_code,obs_read_id,obs_read_seq,obs_flow_string,\ obs_qual_string = data_access.getTestFlowData(True,analysis_id, 'test.PCx634_1') #print 'After getTestFlowData...' self.assertEqual(obs_sff_filename,exp_sff_fname) self.assertEqual(obs_num_of_reads,exp_num_seqs) self.assertEqual(obs_sff_md5,exp_sff_md5) self.assertEqual(obs_instrument_code,exp_instr_code) self.assertEqual(obs_read_id,exp_read_id) self.assertEqual(obs_read_seq,exp_read_seq) self.assertEqual(str(obs_flow_string),exp_flow_string) self.assertEqual(str(obs_qual_string),exp_qual_string) print 'Done testing Flow_Data!' ''' print 'Testing Split-Library Data' exp_split_lib_seq='CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG' exp_split_lib_md5='2c67e0acf745bef73e26c36f0b3bd00a' exp_split_lib_seq_md5='008918f7469f8e33d5dd6e01075d5194' split_lib_info="""select distinct j.seq_run_id,slrm.ssu_sequence_id,l.command,l.md5_checksum, s.sequence_string,s.md5_checksum from analysis j inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id and j.split_library_run_id=slrm.split_library_run_id inner join ssu_sequence s on slrm.ssu_sequence_id=s.ssu_sequence_id inner join split_library_run l on j.split_library_run_id=l.split_library_run_id""" split_lib_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_1\'" % (str(analysis_id)) results = cur.execute(split_lib_info) #print 'Calling getTestFlowData...' for data in results: obs_seq_run_id,obs_ssu_seq_id,obs_split_lib_cmd,obs_split_lib_md5,\ obs_split_lib_seq,obs_split_lib_seq_md5 = data self.assertEqual(obs_split_lib_md5,exp_split_lib_md5) self.assertEqual(obs_split_lib_seq,exp_split_lib_seq) self.assertEqual(obs_split_lib_seq_md5,exp_split_lib_seq_md5) ''' obs_seq_run_id,obs_ssu_seq_id,obs_split_lib_cmd,obs_split_lib_md5,\ obs_split_lib_seq,obs_split_lib_seq_md5 = \ data_access.getTestSplitLibData(True,analysis_id, 'test.PCx634_1') self.assertEqual(obs_split_lib_md5,exp_split_lib_md5) self.assertEqual(obs_split_lib_seq,exp_split_lib_seq) self.assertEqual(obs_split_lib_seq_md5,exp_split_lib_seq_md5) ''' print 'Testing OTU Data!' #exp_prokmsa=83669 exp_otu_md5='0b8edcf8a4275730001877496b41cf55' exp_threshold=97 otu_info="""select distinct j.seq_run_id,slrm.ssu_sequence_id,ot.reference_id,gr.ssu_sequence_id, ot.reference_id,j.otu_picking_run_id,p.command,p.md5_sum_input_file, p.threshold from analysis j inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id and j.split_library_run_id=slrm.split_library_run_id inner join otu_table ot on j.otu_run_set_id=ot.otu_run_set_id inner join gg_plus_denovo_reference gr on ot.reference_id=gr.reference_id inner join otu_picking_run p on j.otu_picking_run_id=p.otu_picking_run_id""" otu_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_2\'" % (str(analysis_id)) results = cur.execute(otu_info) for data in results: obs_seq_run_id,obs_ssu_seq_id,obs_otu_id,obs_otu_ssu_id,\ obs_prokmsa,obs_otu_picking_run_id,obs_pick_otu_cmd,\ obs_otu_md5,obs_threshold = data ''' obs_seq_run_id,obs_ssu_seq_id,obs_otu_id,obs_otu_ssu_id,\ obs_prokmsa,obs_otu_picking_run_id,obs_pick_otu_cmd,\ obs_otu_md5,obs_threshold = \ data_access.getTestOTUData(True,analysis_id, 'test.PCx634_2') ''' #self.assertEqual(obs_prokmsa,exp_prokmsa) self.assertEqual(obs_otu_md5,exp_otu_md5) self.assertEqual(obs_threshold,exp_threshold) otu_fail_info="""select distinct j.seq_run_id,f.ssu_sequence_id from analysis j inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id inner join otu_picking_failures f on slrm.ssu_sequence_id=f.ssu_sequence_id""" otu_fail_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_14\'" % (str(analysis_id)) results = cur.execute(otu_fail_info) for data in results: obs_seq_run_id,obs_ssu_id= data ''' obs_seq_run_id,obs_ssu_id = \ data_access.getTestOTUFailureData(True,analysis_id, 'test.PCx634_14') ''' self.failIfEqual(obs_seq_run_id,0) self.failIfEqual(obs_ssu_id,0) valid=data_access.deleteTestAnalysis(True,analysis_id) if not valid: print "Error: Could not delete data from DB!"
def test_make_study_sffs(self): """Runs the original SFF through split-lib, then runs the filtered one one through split-lib and verifies they are the same.""" #Run original SFF throught split-lib run_process_sff_through_split_lib(0,'Fasting_subset',\ sff_input_fp=self.sff_fp,\ mapping_fp=self.fasting_mapping_fp,\ output_dir=self.wf_out, \ command_handler=call_commands_serially,\ params=self.params,\ qiime_config=self.qiime_config,\ convert_to_flx=False,\ write_to_all_fasta=False,\ status_update_callback=no_status_updates) #Create a per study SFF per_library_output=join(self.wf_out,'per_study_sff') create_dir(per_library_output) make_study_sffs(per_library_output,609) #Run the new SFF through split-lib new_map_fp=join(per_library_output, 'study_609_run_Fasting_subset_mapping.txt') new_sff_fp=join(per_library_output,'filtered_sffs', 'study_609_Fasting_subset.sff') new_processed_output=join(self.wf_out,'filtered_wf_da') create_dir(new_processed_output) run_process_sff_through_split_lib(0,'Fasting_subset',\ sff_input_fp=new_sff_fp,\ mapping_fp=new_map_fp,\ output_dir=new_processed_output, \ command_handler=call_commands_serially,\ params=self.params,\ qiime_config=self.qiime_config,\ convert_to_flx=False,\ write_to_all_fasta=False,\ status_update_callback=no_status_updates) #parse the split-library fasta files old_split_lib_seqs=MinimalFastaParser(open(join(self.wf_out, 'split_libraries','seqs.fna')),'U') new_split_lib_seqs=MinimalFastaParser(open(join(new_processed_output, 'split_libraries','seqs.fna')),'U') #Convert original SFF split-lib fasta into a Dictionary for easy lookup old_seqs={} for key,val in old_split_lib_seqs: new_key_head=key.split(' ') new_key_head[0]=new_key_head[0].split('_')[0] old_seqs[' '.join(new_key_head)]=val #Convert new SFF split-lib fasta into a Dictionary for easy lookup new_seqs={} for key,val in new_split_lib_seqs: new_key_head=key.split(' ') new_key_head[0]=new_key_head[0].split('_')[0].split('.')[1] new_seqs[' '.join(new_key_head)]=val #Check that the seqs and headers match for key in old_seqs: self.assertTrue(old_seqs[key]==new_seqs[key]) #Check that the output histograms are equal old_histogram=open(join(self.wf_out,'split_libraries', 'histograms.txt')).readlines() new_histogram=open(join(new_processed_output,'split_libraries', 'histograms.txt')).readlines() self.assertEqual(old_histogram,new_histogram) #Check that the output log files are equal old_log=open(join(self.wf_out,'split_libraries', 'split_library_log.txt')).readlines() new_log=open(join(new_processed_output,'split_libraries', 'split_library_log.txt')).readlines() self.assertEqual(old_log[:23],new_log[:23])
def test_submit_processed_data_to_db(self): """run_process_sff_through_pick_otus runs without error""" self.files_to_remove.append(join(self.wf_out,'Fasting_subset.fna')) self.files_to_remove.append(join(self.wf_out,'Fasting_subset.qual')) self.files_to_remove.append(join(self.wf_out,'Fasting_subset.txt')) # remove generated mapping file moved_mapping_file=join(self.wf_out,split(self.fasting_mapping_fp)[-1]) self.files_to_remove.append(moved_mapping_file) # process the sequence data first before loading run_process_sff_through_split_lib(0,'Fasting_subset', sff_input_fp=self.sff_fp, mapping_fp=self.fasting_mapping_fp, output_dir=self.wf_out, command_handler=call_commands_serially, params=self.params, qiime_config=self.qiime_config,convert_to_flx=False, write_to_all_fasta=False, status_update_callback=no_status_updates) # get the file basename input_file_basename = splitext(split(self.sff_fp)[1])[0] # get key filepaths otu_fp = join(self.wf_out,'picked_otus','seqs_otus.txt') split_lib_seqs_fp = join(self.wf_out,'split_libraries',\ 'seqs.fna') # run chained OTU-picking run_chain_pick_otus(split_lib_seqs_fp, output_dir=self.gg_out, command_handler=call_commands_serially, params=self.params, qiime_config=self.qiime_config,parallel=False, status_update_callback=no_status_updates) input_fname = splitext(split(self.sff_fp)[-1])[0] db_input_fp = join(self.wf_out,input_fname) # submit the data analysis_id, input_dir, seq_run_id, split_lib_input_md5sum = \ submit_sff_and_split_lib(data_access,db_input_fp+'.fna', self.study_id) # load OTU picking load_otu_mapping(data_access,self.wf_out,analysis_id) # load split-lib sequences split_library_id=load_split_lib_sequences(data_access,input_dir, analysis_id, seq_run_id, split_lib_input_md5sum) ### TEST raw sequence data load # expected results print 'Analysis ID is: %s' % str(analysis_id) print 'Testing the FLOW_DATA loading!' exp_sff_md5='314f4000857668d45a413d2e94a755fc' exp_num_seqs=22 exp_read_id='FLP3FBN01ELBSX' exp_instr_code='GS FLX' exp_sff_fname='Fasting_subset' # define the query to pull data from DB con = data_access.getSFFDatabaseConnection() cur = con.cursor() seq_run_info="""select j.seq_run_id,f.sff_filename,f.number_of_reads,f.md5_checksum, h.instrument_code from analysis j inner join seq_run_to_sff_file s on j.seq_run_id=s.seq_run_id inner join sff_file f on f.sff_file_id=s.sff_file_id inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id inner join sequencing_run h on h.seq_run_id=s.seq_run_id""" seq_run_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_1\'" % (str(analysis_id)) results = cur.execute(seq_run_info) # get observed values for data in results: obs_seq_run_id,obs_sff_filename,obs_num_of_reads,obs_sff_md5,\ obs_instrument_code = data # check results self.assertEqual(obs_sff_filename,exp_sff_fname) self.assertEqual(obs_num_of_reads,exp_num_seqs) self.assertEqual(obs_sff_md5,exp_sff_md5) self.assertEqual(obs_instrument_code,exp_instr_code) # TEST split-library data load # expected results print 'Testing Split-Library Data' exp_split_lib_seq='CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG' exp_split_lib_md5='2c67e0acf745bef73e26c36f0b3bd00a' exp_split_lib_seq_md5='008918f7469f8e33d5dd6e01075d5194' # define the query to pull data from DB split_lib_info="""select distinct j.seq_run_id,slrm.ssu_sequence_id,l.command,l.md5_checksum, s.sequence_string,s.md5_checksum from analysis j inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id and j.split_library_run_id=slrm.split_library_run_id inner join ssu_sequence s on slrm.ssu_sequence_id=s.ssu_sequence_id inner join split_library_run l on j.split_library_run_id=l.split_library_run_id""" split_lib_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_1\'" % (str(analysis_id)) results = cur.execute(split_lib_info) # get observed values for data in results: obs_seq_run_id,obs_ssu_seq_id,obs_split_lib_cmd,obs_split_lib_md5,\ obs_split_lib_seq,obs_split_lib_seq_md5 = data # check results self.assertEqual(obs_split_lib_md5,exp_split_lib_md5) self.assertEqual(obs_split_lib_seq,exp_split_lib_seq) self.assertEqual(obs_split_lib_seq_md5,exp_split_lib_seq_md5) # TEST OTU-table data load # expected results print 'Testing OTU Data!' exp_otu_md5='0b8edcf8a4275730001877496b41cf55' exp_threshold=97 # define the query to pull data from DB otu_info="""select distinct j.seq_run_id,slrm.ssu_sequence_id,ot.reference_id,gr.ssu_sequence_id, ot.reference_id,j.otu_picking_run_id,p.command,p.md5_sum_input_file, p.threshold from analysis j inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id and j.split_library_run_id=slrm.split_library_run_id inner join otu_table ot on j.otu_run_set_id=ot.otu_run_set_id inner join gg_plus_denovo_reference gr on ot.reference_id=gr.reference_id inner join otu_picking_run p on j.otu_picking_run_id=p.otu_picking_run_id""" otu_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_2\'" % (str(analysis_id)) results = cur.execute(otu_info) # get observed values for data in results: obs_seq_run_id,obs_ssu_seq_id,obs_otu_id,obs_otu_ssu_id,\ obs_prokmsa,obs_otu_picking_run_id,obs_pick_otu_cmd,\ obs_otu_md5,obs_threshold = data # check results self.assertEqual(obs_otu_md5,exp_otu_md5) self.assertEqual(obs_threshold,exp_threshold) # TEST OTU-failures data load # define the query to pull data from DB otu_fail_info="""select distinct j.seq_run_id,f.ssu_sequence_id from analysis j inner join split_library_read_map slrm on j.seq_run_id=slrm.seq_run_id inner join otu_picking_failures f on slrm.ssu_sequence_id=f.ssu_sequence_id""" otu_fail_info+=" where j.analysis_id=%s and slrm.sequence_name=\'test.PCx634_14\'" % (str(analysis_id)) results = cur.execute(otu_fail_info) # get observed values for data in results: obs_seq_run_id,obs_ssu_id= data # check results self.failIfEqual(obs_seq_run_id,0) self.failIfEqual(obs_ssu_id,0) # delete the loaded data valid=data_access.deleteTestAnalysis(True,analysis_id) if not valid: print "Error: Could not delete data from DB!"