def generate_fasta(logger,internal_services,token,ref,output_dir,obj_name): try: ga = GenomeAnnotationAPI(internal_services, token=token, ref= "{}/{}".format(ref,obj_name)) except Exception as e: raise Exception("Unable to Call GenomeAnnotationAPI : {0}: {1}".format(e)) logger.info("Generating FASTA file from Assembly for {}/{}".format(ref,obj_name)) fasta_start = datetime.datetime.utcnow() output_file = os.path.join(output_dir,'{}.fasta'.format(obj_name)) with open(output_file, 'w') as fasta_file: ga.get_assembly().get_fasta().to_file(fasta_file) fasta_file.close() fasta_end = datetime.datetime.utcnow() logger.info("Generating FASTA for {} took {}".format(obj_name, fasta_end - fasta_start)) return output_file
def generate_fasta(logger, internal_services, token, ref, output_dir, obj_name): try: ga = GenomeAnnotationAPI(internal_services, token=token, ref="{}/{}".format(ref, obj_name)) except Exception as e: raise Exception( "Unable to Call GenomeAnnotationAPI : {0}: {1}".format(e)) logger.info("Generating FASTA file from Assembly for {}/{}".format( ref, obj_name)) fasta_start = datetime.datetime.utcnow() output_file = os.path.join(output_dir, '{}.fasta'.format(obj_name)) with open(output_file, 'w') as fasta_file: ga.get_assembly().get_fasta().to_file(fasta_file) fasta_file.close() fasta_end = datetime.datetime.utcnow() logger.info("Generating FASTA for {} took {}".format( obj_name, fasta_end - fasta_start)) return output_file
def generate_fasta(logger,internal_services,token,ref,output_dir,obj_name): try: ga = GenomeAnnotationAPI(internal_services, token=token, ref= ref) except Exception as e: raise Exception("Unable to Call GenomeAnnotationAPI : {0}".format("".join(traceback.format_exc()))) logger.info("Generating FASTA file from Assembly for {}".format(obj_name)) fasta_start = datetime.datetime.utcnow() output_file = os.path.join(output_dir,'{}.fasta'.format(obj_name)) fasta_file= io.open(output_file, 'wb') try: ga.get_assembly().get_fasta().to_file(fasta_file) except Exception as e: #raise Exception("Unable to Create FASTA file from Genome Annotation : {0}".format(obj_name)) raise Exception("Unable to Create FASTA file from Genome Annotation : {0}".format("".join(traceback.format_exc()))) finally: fasta_file.close() fasta_end = datetime.datetime.utcnow() logger.info("Generating FASTA for {} took {}".format(obj_name, fasta_end - fasta_start)) return output_file
def get_assembly(self, ctx, ref): """ Retrieve the Assembly associated with this GenomeAnnotation. @return Reference to AssemblyAPI object :param ref: instance of type "ObjectReference" :returns: instance of type "ObjectReference" """ # ctx is the context object # return variables are: returnVal #BEGIN get_assembly ga = GenomeAnnotationAPI_local(self.services, ctx['token'], ref) returnVal = ga.get_assembly(ref_only=True) #END get_assembly # At some point might do deeper type checking... if not isinstance(returnVal, basestring): raise ValueError('Method get_assembly return value ' + 'returnVal is not type basestring as required.') # return the results return [returnVal]
gto['domain'] = taxon.get_domain() except Exception, e: success = 0 try: gto['genetic_code'] = taxon.get_genetic_code() except Exception, e: success = 0 try: gto['taxonomy'] = ",".join(taxon.get_scientific_lineage()) except Exception, e: success = 0 assemb = {}; success = 0; try: assemb = ga.get_assembly(); success = 1; except Exception, e: success = 0 if success == 1: gto['contigobj'] = { 'id' : sys.argv[6], 'name' : sys.argv[6], 'source' : 'KBase', 'source_id' : sys.argv[6], 'md5' : "", 'type' : "Genome", 'contigs' : [] };