def generate_gff(logger,internal_services,token,ref,output_dir,obj_name,output_file): try: ga = GenomeAnnotationAPI(internal_services, token=token, ref= "{}/{}".format(ref,obj_name)) except: raise Exception("Unable to Call GenomeAnnotationAPI : {0}".format(e)) logger.info("Requesting GenomeAnnotation GFF for {}/{}".format(ref,obj_name)) gff_start = datetime.datetime.utcnow() #output_file = os.path.join(output_dir,'{}.gff'.format(obj_name)) with open(output_file, 'w') as gff_file: ga.get_gff().to_file(gff_file) gff_file.close() gff_end = datetime.datetime.utcnow() logger.info("Generating GFF for {} took {}".format(obj_name, gff_end - gff_start))
def generate_gff(logger, internal_services, token, ref, output_dir, obj_name, output_file): try: ga = GenomeAnnotationAPI(internal_services, token=token, ref="{}/{}".format(ref, obj_name)) except: raise Exception("Unable to Call GenomeAnnotationAPI : {0}".format(e)) logger.info("Requesting GenomeAnnotation GFF for {}/{}".format( ref, obj_name)) gff_start = datetime.datetime.utcnow() #output_file = os.path.join(output_dir,'{}.gff'.format(obj_name)) with open(output_file, 'w') as gff_file: ga.get_gff().to_file(gff_file) gff_file.close() gff_end = datetime.datetime.utcnow() logger.info("Generating GFF for {} took {}".format(obj_name, gff_end - gff_start))
def generate_gff(logger,internal_services,token,ref,output_dir,obj_name,output_file): try: ga = GenomeAnnotationAPI(internal_services, token=token, ref= ref) except: raise Exception("Unable to Call GenomeAnnotationAPI : {0}".format(("".join(traceback.format_exc())))) logger.info("Requesting GenomeAnnotation GFF for {}".format(obj_name)) gff_start = datetime.datetime.utcnow() gff_file= io.open(output_file, 'wb') #output_file = os.path.join(output_dir,'{}.gff'.format(obj_name)) try: ga.get_gff().to_file(gff_file) except Exception as e: #raise Exception("Unable to Create GFF file from Genome Annotation : {0}: {1}".format(obj_name,e)) raise Exception("Unable to Create GFF file from Genome Annotation : {0}: {1}".format(obj_name,"".join(traceback.format_exc()))) finally: gff_file.close() gff_end = datetime.datetime.utcnow() logger.info("Generating GFF for {} took {}".format(obj_name, gff_end - gff_start))