def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
try:
from data_access_connections import data_access_factory
from enums import ServerConfig
import cx_Oracle
if opts.submit_to_test_db:
data_access = data_access_factory(DataAccessType.qiime_test)
else:
data_access = data_access_factory(ServerConfig.data_access_type)
except ImportError:
print "NOT IMPORTING QIIMEDATAACCESS"
pass
input_dir=opts.input_otu_dir
load_otu_mapping(data_access,input_dir)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
submit_to_test_db=opts.submit_to_test_db
fasta_file_paths=opts.fasta_file_paths
study_id=opts.study_id
output_dir=opts.output_dir
platform=opts.platform
user_id=opts.user_id
if submit_to_test_db == 'False':
# Load the data into the database
data_access = data_access_factory(ServerConfig.data_access_type)
else:
# Load the data into the database
data_access = data_access_factory(DataAccessType.qiime_test)
# Get all of the fasta files
if (platform=='FLX' or platform=='TITANIUM'):
print 'Submitting SFF data to database...'
analysis_id = submit_sff_and_split_lib(data_access, fasta_file_paths, study_id)
elif platform=='ILLUMINA':
print 'Submitting Illumina data to database...'
analysis_id = submit_illumina_and_split_lib(data_access, fasta_file_paths, study_id,output_dir)
elif platform=='FASTA':
print 'Submitting FASTA data to database...'
analysis_id = submit_fasta_and_split_lib(data_access, fasta_file_paths, study_id, output_dir)
study_info=data_access.getStudyInfo(study_id,user_id)
if study_info['investigation_type'].lower() == 'metagenome':
# skip OTU loading
pass
else:
print 'Submitting OTU data to database...'
load_otu_mapping(data_access, output_dir, analysis_id)
print 'Completed database loading.'
def test_submit_processed_data_to_db_fasta(self):
"""submit_processed_data_to_db_fasta runs without error"""
run_process_fasta_through_split_lib(0,'Fasting_subset',\
input_fp=','.join(self.fasta_fps),\
mapping_fp=self.fasta_map_fp,\
output_dir=self.wf_out, \
command_handler=call_commands_serially,\
params=self.params,\
qiime_config=self.qiime_config,\
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=True,
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_fasta_and_split_lib(data_access,
','.join(self.fasta_fps),
0, self.wf_out)
load_otu_mapping(data_access,self.wf_out,analysis_id)
print 'Analysis ID is: %s' % str(analysis_id)
print 'Testing the SEQ_RUN loading!'
exp_sff_md5=['412eee0be168a285415d9e4db3dbbf2f']
exp_num_seqs=22
exp_instr_code='FASTA'
exp_sff_fname=['test_split_lib_seqs']
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.sample_name=\'test.PCx354.281526\'" % (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
print 'After getTestSeqRunData...'
self.assertTrue(obs_sff_filename in exp_sff_fname)
self.assertEqual(obs_num_of_reads,exp_num_seqs)
self.assertTrue(obs_sff_md5 in exp_sff_md5)
self.assertEqual(obs_instrument_code,exp_instr_code)
print 'Done testing SEQ_RUN!'
print 'Testing Split-Library Data'
exp_split_lib_seq='TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG'
exp_split_lib_md5='412eee0be168a285415d9e4db3dbbf2f'
exp_split_lib_seq_md5='59843d3394983f2caa26f583014a3389'
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.sample_name=\'test.PCx354.281526\'" % (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)
print 'Testing OTU Data!'
#exp_prokmsa=97550
exp_otu_md5='cec9b6c184ffdb12d9de4450034ab775'
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.sample_name=\'test.PCx354.281526\'" % (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
#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.sample_name=\'test.PCx635.281531\'" % (str(analysis_id))
results = cur.execute(otu_fail_info)
for data in results:
obs_seq_run_id,obs_ssu_id= data
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_submit_processed_data_to_db_illumina(self):
"""run_process_illumina_through_pick_otus runs without error"""
run_process_illumina_through_split_lib(0,'Fasting_subset',\
input_fp=','.join(self.illumina_fps),\
mapping_fp=self.illumina_map_fp,\
output_dir=self.wf_out, \
command_handler=call_commands_serially,\
params=self.params,\
qiime_config=self.qiime_config,\
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=True,
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_illumina_and_split_lib(data_access,
','.join(self.illumina_fps),
0,
self.wf_out)
load_otu_mapping(data_access,self.wf_out,analysis_id)
print 'Analysis ID is: %s' % str(analysis_id)
print 'Testing the SEQ_RUN loading!'
exp_sff_md5=['2b14442f7df4d06ac1e241816bf3ce4a','53181ca3427e5b4ce28a6b13cb3b98dd']
exp_num_seqs=100
exp_instr_code='ILLUMINA'
exp_sff_fname=['s_8_2_sequence_100_records','s_8_1_sequence_100_records']
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.sample_name=\'HKE08Aug07\'" % (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
print 'After getTestSeqRunData...'
self.assertTrue(obs_sff_filename in exp_sff_fname)
self.assertEqual(obs_num_of_reads,exp_num_seqs)
self.assertTrue(obs_sff_md5 in exp_sff_md5)
self.assertEqual(obs_instrument_code,exp_instr_code)
print 'Done testing SEQ_RUN!'
print 'Testing Split-Library Data'
exp_split_lib_seq='TACGAAGGGAGCTAGCGTTATTCGGAATGATTGGGTGTAAAGAGTTTGTAGATTGCAAAATTTTTGTTATTAGTAAAAAATTGAATTTATTATTTAAAGATGCTTTTAATACAATTTTGCTTGAGTATAGTAGAGGAAAAT'
exp_split_lib_md5='1443e25614090e660b003c5774ed4cba'
exp_split_lib_seq_md5='7e8278ef1f5561d997cad48eabe40847'
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.sample_name=\'HKE08Aug07\'" % (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)
print 'Testing OTU Data!'
#exp_prokmsa=97550
exp_otu_md5='56222e11026575d9850009768c0b8885'
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.sample_name=\'SSBH05July07\'" % (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
#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.sample_name=\'HKE08Aug07\'" % (str(analysis_id))
results = cur.execute(otu_fail_info)
for data in results:
obs_seq_run_id,obs_ssu_id= data
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_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!"
