stats_dir = sys.argv[4]
log.info("I got the input file!")
# ---------------------- Initialize Solver --------------------- #
greedySolver = GreedySolver()
taxonomySolver = SimpleTaxonomySolver()
solver = Solver(determine_host, greedySolver, taxonomySolver)
# ---------------------- Run Solver --------------------- #
start_total = time.time()
solver.generateSolutionXML(aln_file, dataset_xml_file, solution_xml_output_file, stats_dir)
log.info("Successfully initialized solver!")
end_total = time.time()
elapsed_time_total = end_total - start_total
print ("TOTAL - \t\telapsed time: %.2f" % elapsed_time_total)
# fill_containers (aln_file)
# -------------------- Test stats methods ----------------------- #
'''
read_container = ReadContainer.Instance()
cds_aln_container = CdsAlnContainer.Instance()
no_alns = stats.num_reads_with_no_alignments(read_container)
dataset_xml_file = sys.argv[2]
solution_xml_output_file = sys.argv[3]
stats_dir = sys.argv[4]
log.info("I got the input file!")
# ---------------------- Initialize Solver --------------------- #
greedySolver = GreedySolver()
taxonomySolver = SimpleTaxonomySolver()
solver = Solver(determine_host, greedySolver, taxonomySolver)
# ---------------------- Run Solver --------------------- #
start_total = time.time()
solver.generateSolutionXML(aln_file, dataset_xml_file,
solution_xml_output_file, stats_dir)
log.info("Successfully initialized solver!")
end_total = time.time()
elapsed_time_total = end_total - start_total
print("TOTAL - \t\telapsed time: %.2f" % elapsed_time_total)
# fill_containers (aln_file)
# -------------------- Test stats methods ----------------------- #
'''
read_container = ReadContainer.Instance()
cds_aln_container = CdsAlnContainer.Instance()
no_alns = stats.num_reads_with_no_alignments(read_container)
# cdsAlnCont = CdsAlnContainer.Instance()
# readCont.populate_from_aln_file(aln_file)
# print "passed container initialization!"
# ---------------------- Initialize Solver --------------------- #
greedySolver = GreedySolver()
taxonomySolver = SimpleJoinTaxonomySolver()
solver = Solver(determine_host, greedySolver, taxonomySolver)
# ---------------------- Run Solver --------------------- #
solver.generateSolutionXML(aln_file)
print "Successfully initialized solver!"
# fill_containers (aln_file)
# -------------------- Test stats methods ----------------------- #
'''
read_container = ReadContainer.Instance()
cds_aln_container = CdsAlnContainer.Instance()
no_alns = stats.num_reads_with_no_alignments(read_container)
print "Reads with no alignments: %d" % no_alns
print "Number of reads: %d" % stats.num_reads(read_container)
print "Number of reads with no aligned cdss: %d" % \
read_container = ReadContainer()
read_container.populate_from_aln_file(read_alignment_file=args.input)
elapsed_time = timing.end(start)
log.info("Populate read container - elapsed time: %s",
timing.humanize(elapsed_time))
# Populate record container
# The record container type can now be determine from the input parameters
# and injected into the Solver
start = timing.start()
record_container = RecordContainer()
record_container.set_db_access(db_access)
# Extract all records from database
record_container.populate(read_container.fetch_all_reads_versions())
elapsed_time = timing.end(start)
log.info("Populate record container - elapsed time: %s",
timing.humanize(elapsed_time))
solver.generateSolutionXML(read_container=read_container,
record_container=record_container,
dataset_xml_file=args.descr,
output_solution_filename=args.output,
stats_dir=args.stats_dir,
solution_file=args.solution_file)
processing_delta = timing.end(processing_start)
log.info("Processing done in %s",
timing.humanize(processing_delta))
log.info("Finished.")
start = timing.start()
read_container = ReadContainer()
read_container.populate_from_aln_file(read_alignment_file=args.input)
elapsed_time = timing.end(start)
log.info("Populate read container - elapsed time: %s",
timing.humanize(elapsed_time))
# Populate record container
# The record container type can now be determine from the input parameters
# and injected into the Solver
start = timing.start()
record_container = RecordContainer()
record_container.set_db_access(db_access)
# Extract all records from database
record_container.populate(read_container.fetch_all_reads_versions())
elapsed_time = timing.end(start)
log.info("Populate record container - elapsed time: %s",
timing.humanize(elapsed_time))
solver.generateSolutionXML(read_container=read_container,
record_container=record_container,
dataset_xml_file=args.descr,
output_solution_filename=args.output,
stats_dir=args.stats_dir,
solution_file=args.solution_file)
processing_delta = timing.end(processing_start)
log.info("Processing done in %s", timing.humanize(processing_delta))
log.info("Finished.")