def load_exon_configuration (ref_protein_id, ref_species_dict, exon_type):
'''
Load exons of a particular type for all available species
@param ref_protein_id: referent protein id
@param exon_type: exon_type: ensembl, genewise, blatn, tblastn, sw_gene, sw_exon
'''
dc = DescriptionParser()
exon_container = ExonContainer.Instance()
ens_exon_container = EnsemblExonContainer.Instance()
logger = Logger.Instance()
containers_logger = logger.get_logger('containers')
if exon_type == "ensembl" or exon_type == "genewise":
if not check_status_file_no_alignment(ref_protein_id):
containers_logger.info ("{0},exon_type:{1},check status file -> failed".format(ref_protein_id, exon_type))
return False
else:
if not check_status_file(ref_protein_id):
containers_logger.info ("{0},exon_type:{1},check status file -> failed".format(ref_protein_id, exon_type))
return False
if not ref_species_dict:
ref_species_dict = FileUtilities.get_reference_species_dictionary()
(known_species, abinitio_species) = dc.get_separated_species(ref_protein_id)
for species in known_species:
ref_species = ref_species_dict[species]
if exon_type != "genewise":
if exon_type == "ensembl":
exons = EnsemblExons ((ref_protein_id, species), ref_species)
try:
exon_dict = exons.load_exons()
except Exception, e:
containers_logger.error("{0},{1},{2},error loading exons".format(ref_protein_id, species, exon_type))
continue
else:
exons = Exons((ref_protein_id, species), ref_species, exon_type)
try:
exon_dict = exons.load_exons()
except Exception, e:
containers_logger.error("{0},{1},{2},error loading exons".format(ref_protein_id, species, exon_type))
continue
if not exon_dict:
continue
if (exon_type != "ensembl"):
exons.set_exon_ordinals()
data_map_key = [ref_protein_id, species]
exon_container.add(exon_type, data_map_key, exons)
def get_species_list(protein_id, path):
'''
@param path: returns the list of species in the .status file, if the file doesn't exist, it returns the list parsed from protein
description file.
'''
desc_parser = DescriptionParser()
species_list = []
if (os.path.isfile("{0}/.status".format(path))):
for species in open('{0}/.status'.format(path), 'r').readlines():
species_list.append(species.strip())
else:
species_list = desc_parser.get_species(protein_id)
return species_list