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!"
