args['strip'], is_enum=args['enumerate'])
dsb_baseline = DomainSetBuilder(cons_baseline, args['win'], args['max_g'],
args['strip'], is_enum=args['enumerate'])
# dsb_baseline = DomainSetBuilder(win=args['win'], max_gap=args['max_g'],
# is_enum=args['enumerate'], consensus=cons_baseline,
# is_strip=args['strip'])
domains_query = dsb_query.build() # build abundance counts
domains_baseline = dsb_baseline.build()
status_message('Identifying domains', 'OK')
db = DomainAbundanceBuilder(query=domains_query, baseline=domains_baseline)
domains = db.build() # build contingency matrices
dpp = DomainPrettyPrinter(domains = domains, pval = args['p'],
out=args['o'])
dpp.display() # pretty-print domains
status_message('Domain over-representation computation complete ', 'OK')
else:
args.update({'f':args['query'],'f2':args['baseline'],'a':None})
input_state = InputWrapperState(args)
#input_state.assign_matrix() # parse in-built or custom matrix
targets = input_state.parse_fasta(input_state.fname)
baselines = input_state.parse_fasta(input_state.fname2)
if not args['overlap']:
target_names = list([target.name for target in targets])
baselines = list([baseline for baseline in baselines if baseline.name not in target_names])
extract_and_analyze_domains(targets,baselines,input_state)
status_message('Domain analysis via multiple runs complete ', 'OK')
except (IOError, KeyboardInterrupt, IndexError) as e:
print(str(e))
consensus_object = msa_driver.build_consensus(args['thresh'],args['type'])
# Write MSA and consensus to file
consensus_fact = ConsensusFilterFactory(msa_driver,consensus_object)
consensus_fact.write(fname=args['build'])
#consensus_fact = ConsensusFilterFactory(driver.alns, driver.composite, args['thresh'], args['type'])
#consensus_fact.build_consensus()
#consensus_fact.write(fname=args['build']) # write analysis
if __name__ == '__main__':
try:
args = AlignmentCommandParser().parse_args()
AlignmentArgumentValidator(args) # test all arguments are correct
print('spaghetti - v.' + str(version) + '\n=================')
input_state = InputWrapperState(args)
input_state.assign_matrix() # parse in-built or custom matrix
targets = input_state.parse_fasta(input_state.fname) # next, parse fasta file
if input_state.fname2 is None:
queries = targets
else:
queries = input_state.parse_fasta(input_state.fname2)
if args['mode'] == 'local':
run_local(targets, queries, input_state)
elif args['mode'] == 'msa': # start multiple-sequence alignment (MSA)
run_msa(queries, input_state)
except (IOError, KeyboardInterrupt, IndexError) as e:
print(str(e)+'\n')