sys.stderr.write("############# PATHS\n")
_print_paths(blastn_app_path, gmap_app_path, gmapl_app_path,
hsblastn_app_path, blastn_dbs_path, gmap_dbs_path,
hsblastn_dbs_path, split_blast_path, genmap_path,
tmp_files_path)
sys.stderr.write("\n")
############################ Databases configuration #################################
######################################################################################
############### Configured databases
###############
sys.stderr.write("############# DATABASES\n\n")
databases_conf_file = __app_path + DATABASES_CONF
databases_config = DatabasesConfig(databases_conf_file, verbose=False)
for database_id in databases_config.get_databases():
database_name = databases_config.get_database_name(database_id)
database_type = databases_config.get_database_type(database_id)
sys.stderr.write("DB: " + database_name + " --> ID: " + database_id +
", type: " + database_type + "\n")
sys.stderr.write("\n")
############## External databases
##############
# In blastn DBs path
databases_ids = databases_config.get_databases_ids() # set(databases_ids)
other_dbs = set()
num_found = 0
#####
if verbose_param:
_print_parameters(query_fasta_path, maps_names, aligner_list,
threshold_id, threshold_cov, n_threads, sort_param,
multiple_param, best_score, show_anchored,
show_genes, show_markers, extend_window,
show_unmapped, collapsed_view)
############### MAIN
if verbose_param: sys.stderr.write("\n")
############# ALIGNMENTS - REFERENCES
# Databases
databases_conf_file = __app_path + DATABASES_CONF
databases_config = DatabasesConfig(databases_conf_file, verbose_param)
#facade = AlignmentFacade(split_blast_path, blastn_app_path, gmap_app_path, hsblastn_app_path,
# blastn_dbs_path, gmap_dbs_path, hsblastn_dbs_path, gmapl_app_path,
# tmp_files_path, databases_config, verbose = verbose_param)
alignment_facade = AlignmentFacade(paths_config, verbose=verbose_param)
############ Pre-loading of some objects
############
# DatasetsFacade
# Datasets config
datasets_conf_file = __app_path + DATASETS_CONF
datasets_config = DatasetsConfig(datasets_conf_file)
datasets_ids = datasets_config.get_datasets_list(
) #datasets_config.get_datasets().keys()
# Num threads
if options.n_threads: n_threads = int(options.n_threads)
else: n_threads = DEFAULT_N_THREADS
# Hierarchical
if options.search_type: search_type = options.search_type
else: search_type = DEFAULT_HIERARCHICAL
# ref_type
if options.ref_type: ref_type_param = options.ref_type
else: ref_type_param = DEFAULT_REF_TYPE
# Databases
databases_conf_file = __app_path+DATABASES_CONF
databases_config = DatabasesConfig(databases_conf_file, verbose_param)
if options.databases_param: # or "all databases in conf"
databases_names = options.databases_param
databases_ids = databases_config.get_databases_ids(databases_names.strip().split(","))
elif options.databases_ids_param:
databases_ids = options.databases_ids_param.strip().split(",")
databases_names = ",".join(databases_config.get_databases_names(databases_ids))
else:
databases_ids = databases_config.get_databases().keys()
databases_names = ",".join(databases_config.get_databases_names(databases_ids))
if len(databases_ids)<=0 or len(databases_names)<=0:
raise Exception("No valid databases were found. Please, check your --databases parameter or your conf/databases.conf file.")
sys.stderr.write("\n")
sys.stderr.write("############# PATHS\n")
_print_paths(blastn_app_path, gmap_app_path, gmapl_app_path, hsblastn_app_path,
blastn_dbs_path, gmap_dbs_path, hsblastn_dbs_path,
split_blast_path, genmap_path, tmp_files_path)
sys.stderr.write("\n")
############################ Databases configuration #################################
######################################################################################
############### Configured databases
###############
sys.stderr.write("############# DATABASES\n\n")
databases_conf_file = __app_path+DATABASES_CONF
databases_config = DatabasesConfig(databases_conf_file, verbose = False)
for database_id in databases_config.get_databases():
database_name = databases_config.get_database_name(database_id)
database_type = databases_config.get_database_type(database_id)
sys.stderr.write("DB: "+database_name+" --> ID: "+database_id+", type: "+database_type+"\n")
sys.stderr.write("\n")
############## External databases
##############
# In blastn DBs path
databases_ids = databases_config.get_databases_ids() # set(databases_ids)
other_dbs = set()
num_found = 0
first = True
# Num threads
if options.n_threads: n_threads = int(options.n_threads)
else: n_threads = DEFAULT_N_THREADS
# Hierarchical
if options.search_type: search_type = options.search_type
else: search_type = DEFAULT_HIERARCHICAL
# ref_type
if options.ref_type: ref_type_param = options.ref_type
else: ref_type_param = DEFAULT_REF_TYPE
# Databases
databases_conf_file = __app_path+DATABASES_CONF
databases_config = DatabasesConfig(databases_conf_file, verbose_param)
if options.databases_param: # or "all databases in conf"
databases_names = options.databases_param
databases_ids = databases_config.get_databases_ids(databases_names.strip().split(","))
elif options.databases_ids_param:
databases_ids = options.databases_ids_param.strip().split(",")
databases_names = ",".join(databases_config.get_databases_names(databases_ids))
else:
databases_ids = databases_config.get_databases().keys()
databases_names = ",".join(databases_config.get_databases_names(databases_ids))
if len(databases_ids)<=0 or len(databases_names)<=0:
raise Exception("No valid databases were found. Please, check your --databases parameter or your conf/databases.conf file.")