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])
