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))
