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