def gast(runobj):
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
# Should return a list not a string
idx_keys = get_keys(runobj)
# get GAST object
mygast = Gast(runobj, idx_keys)
# Check for unique files and create them if not there
result_code = mygast.check_for_uniques_files(idx_keys)
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code[0] == "ERROR":
logger.error("uniques not found failed")
sys.exit("uniques not found failed")
sleep(5)
# CLUSTERGAST
result_code = mygast.clustergast()
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code[0] == "ERROR":
logger.error("clutergast failed")
sys.exit("clustergast failed")
sleep(5)
# GAST_CLEANUP
result_code = mygast.gast_cleanup()
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code[0] == "ERROR":
logger.error("gast_cleanup failed")
sys.exit("gast_cleanup failed")
sleep(5)
# GAST2TAX
result_code = mygast.gast2tax()
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code[0] == "ERROR":
logger.error("gast2tax failed")
sys.exit("gast2tax failed")
def run_gast2tax(args):
#sys.path.append("/xraid2-2/vampsweb/"+args.site+"/")
#from pipeline.utils import *
from pipeline.gast import Gast
import pipeline.constants as C
if os.path.exists(args.names_file) and os.path.getsize(args.names_file) > 0:
class expando(object):pass
runobj = expando()
runobj.output_dir = ''
runobj.use_cluster = True
runobj.user = ''
runobj.run = ''
# for vamps this has to be True and empty list
print 'VUU ',args.vamps_user_upload
runobj.vamps_user_upload = args.vamps_user_upload
runobj.platform = args.platform
runobj.site = args.site
key = args.key
runobj.datasets = []
mygast = Gast(run_object = runobj)
( refdb, taxdb ) = mygast.get_reference_databases(args.dna_region)
#print tax_file
max_gast_distance = C.max_gast_distance['default']
if args.dna_region in C.max_gast_distance:
max_gast_distance = C.max_gast_distance[args.dna_region]
ref_taxa = mygast.load_reftaxa(taxdb)
mygast.assign_taxonomy(key, args.gast_dir, args.dna_region, args.names_file, ref_taxa)
def run_gast2tax(args):
#sys.path.append("/xraid2-2/vampsweb/"+args.site+"/")
#from pipeline.utils import *
from pipeline.gast import Gast
import pipeline.constants as C
if os.path.exists(
args.names_file) and os.path.getsize(args.names_file) > 0:
class expando(object):
pass
runobj = expando()
runobj.output_dir = ''
runobj.use_cluster = True
runobj.user = ''
runobj.run = ''
# for vamps this has to be True and empty list
print 'VUU ', args.vamps_user_upload
runobj.vamps_user_upload = args.vamps_user_upload
runobj.platform = args.platform
runobj.site = args.site
key = args.key
runobj.datasets = []
mygast = Gast(run_object=runobj)
(refdb, taxdb) = mygast.get_reference_databases(args.dna_region)
#print tax_file
max_gast_distance = C.max_gast_distance['default']
if args.dna_region in C.max_gast_distance:
max_gast_distance = C.max_gast_distance[args.dna_region]
ref_taxa = mygast.load_reftaxa(taxdb)
mygast.assign_taxonomy(key, args.gast_dir, args.dna_region,
args.names_file, ref_taxa)
def gast(runobj):
logger.info("STARTING GAST()")
# logger.info("vsearch version: " % utils.get_vsearch_version)
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
# Should return a list not a string
idx_keys = get_keys(runobj)
# get GAST object
mygast = Gast(runobj, idx_keys)
# Check for unique files and create them if not there
result_code = mygast.check_for_unique_files(idx_keys)
runobj.run_status_file_h.write(json.dumps(result_code)+"\n")
if result_code['status'] == 'ERROR':
logger.error("uniques not found failed")
sys.exit("uniques not found failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, "GAST ERROR", "uniques file not found - failed" )
elif runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, result_code['status'], result_code['message'] )
sleep(5)
# CLUSTERGAST
result_code = mygast.clustergast()
runobj.run_status_file_h.write(json.dumps(result_code)+"\n")
if result_code['status'] == 'ERROR':
logger.error("clutergast failed")
sys.exit("clustergast failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, "GAST ERROR", "clustergast failed" )
elif runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, result_code['status'], result_code['message'] )
sleep(5)
# GAST_CLEANUP
result_code = mygast.gast_cleanup()
runobj.run_status_file_h.write(json.dumps(result_code)+"\n")
if result_code['status'] == 'ERROR':
logger.error("gast_cleanup failed")
sys.exit("gast_cleanup failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, "GAST ERROR", "gast_cleanup failed" )
elif runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, result_code['status'], result_code['message'] )
sleep(5)
# GAST2TAX
result_code = mygast.gast2tax()
runobj.run_status_file_h.write(json.dumps(result_code)+"\n")
if result_code['status'] == 'ERROR':
logger.error("gast2tax failed")
sys.exit("gast2tax failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, "GAST ERROR", "gast2tax failed" )
elif runobj.vamps_user_upload:
write_status_to_vamps_db( runobj.site, runobj.run, result_code['status'], result_code['message'] )
def gast(runobj):
logger.info("STARTING GAST()")
# logger.info("vsearch version: " % utils.get_vsearch_version)
# for vamps 'new_lane_keys' will be prefix
# of the uniques and names file
# that was just created in vamps_gast.py
# or we can get the 'lane_keys' directly from the config_file
# for illumina:
# a unique idx_key is a concatenation of barcode_index and run_key
# Should return a list not a string
idx_keys = get_keys(runobj)
# get GAST object
mygast = Gast(runobj, idx_keys)
# Check for unique files and create them if not there
result_code = mygast.check_for_unique_files(idx_keys)
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code['status'] == 'ERROR':
logger.error("uniques not found failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run, "GAST ERROR",
"uniques file not found - failed")
sys.exit("uniques not found failed")
elif runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run,
result_code['status'], result_code['message'])
sleep(5)
# CLUSTERGAST
result_code = mygast.clustergast()
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code['status'] == 'ERROR':
logger.error("clutergast failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run, "GAST ERROR",
"clustergast failed")
sys.exit("clustergast failed")
elif runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run,
result_code['status'], result_code['message'])
sleep(5)
# GAST_CLEANUP
result_code = mygast.gast_cleanup()
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code['status'] == 'ERROR':
logger.error("gast_cleanup failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run, "GAST ERROR",
"gast_cleanup failed")
sys.exit("gast_cleanup failed")
elif runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run,
result_code['status'], result_code['message'])
sleep(5)
# GAST2TAX
result_code = mygast.gast2tax()
runobj.run_status_file_h.write(json.dumps(result_code) + "\n")
if result_code['status'] == 'ERROR':
logger.error("gast2tax failed")
if runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run, "GAST ERROR",
"gast2tax failed")
sys.exit("gast2tax failed")
elif runobj.vamps_user_upload:
write_status_to_vamps_db(runobj.site, runobj.run,
result_code['status'], result_code['message'])