def generate_SW_exon_alignments2 (protein_id, species_list = None, referenced_species = "Homo_sapiens"):
# utilities
alignment_generator = AlignmentTargetGenerator()
crawler = DirectoryCrawler()
command_generator = CommandGenerator()
logger = Logger.Instance()
alignment_logger = logger.get_logger('alignment')
exon_container = ExonContainer.Instance()
tmp_fasta_target_path = "tmp_target.fa"
ref_exons_fasta = "%s/%s.fa" % (crawler.get_database_path(protein_id), referenced_species)
#ref_exons = exon_container.get((protein_id, referenced_species, "ensembl"))
#ref_exons.export_coding_exons_to_fasta(tmp_ref_exons_fasta_path)
failed_species_list = []
if (not species_list):
species_list = alignment_generator.get_SW_exon_targets(protein_id)
try:
(proteins_known, proteins_abinitio) = DescriptionParser().parse_descr_file(protein_id)
except IOError, e:
alignment_logger.error("{0}, , SW cDNA_EXONS, {2}".format(protein_id, e))
return False
