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mostly data dir
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@jodyphelan
jodyphelan committed Jan 19, 2025
1 parent f8a5070 commit e5ca3ee
Showing 1 changed file with 38 additions and 7 deletions.
45 changes: 38 additions & 7 deletions tb-profiler
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ discovered_plugins = {


__softwarename__ = 'tbprofiler'
__default_db_dir__ = f'{sys.base_prefix}/share/{__softwarename__}'

@atexit.register
def cleanup():
Expand Down Expand Up @@ -117,6 +118,7 @@ def plugin_decorator(func):
for plugin in tbp.ProfilePlugin.__subclasses__():
logging.debug(f"Running pre process for {plugin}")
plugin().pre_process(args)
print(plugin)
func(args)
for plugin in tbp.ProfilePlugin.__subclasses__():
logging.debug(f"Running post process for {plugin}")
Expand All @@ -137,6 +139,8 @@ def main_profile(args):
tbp.process_tb_profiler_args(args)

variants_profile = pp.run_profiler(args)
for plugin in tbp.ProfilePlugin.__subclasses__():
plugin().process_variants(args,variants_profile)

notes = set()
if 'rules' in args.conf:
Expand Down Expand Up @@ -187,8 +191,7 @@ def main_profile(args):
tbp.run_snp_dists(args,result)
tbp.update_neighbour_snp_dist_output(args,result)

for plugin in tbp.ProfilePlugin.__subclasses__():
plugin().run(args)



### Create folders for results if they don't exist ###
Expand Down Expand Up @@ -291,9 +294,30 @@ def main_create_db(args):
pp.create_db(args,extra_files=extra_files)

def main_load_library(args):
variables_file = "%(prefix)s.variables.json" % vars(args)
source_dir = os.path.realpath(args.dir)
pp.load_db(variables_file,args.software_name,source_dir=source_dir)
with TempFolder() as tmpfolder:
if args.prefix.endswith(".tar.gz") or args.prefix.endswith(".zip"):
if args.prefix.endswith(".tar.gz"):
import tarfile
with tarfile.open(args.prefix, 'r:gz') as tar_ref:
tar_ref.extractall(tmpfolder)
elif args.prefix.endswith(".zip"):
import zipfile
with zipfile.ZipFile(args.prefix, 'r') as zip_ref:
zip_ref.extractall(tmpfolder)

variables_files = glob.glob(f"{tmpfolder}/*.variables.json")
if len(variables_files)!=1:
pp.errorlog("Archive must contain only one variables file")
sys.exit()
variables_file = variables_files[0]
args.prefix = "{}/{}".format(tmpfolder,variables_file.split("/")[-1].replace(".variables.json",""))
source_dir = os.path.realpath(tmpfolder)



variables_file = "%(prefix)s.variables.json" % vars(args)
pp.load_db(variables_file,args.software_name,source_dir=source_dir)



Expand Down Expand Up @@ -459,12 +483,14 @@ for cls in tbp.ProfilePlugin.__subclasses__():
plugins.add_argument(*a['args'],**a['kwargs'])

other=parser_sub.add_argument_group("Other options")
other.add_argument('--snpeff_config','--snpeff-config',type=str,help='Set the config filed used by snpEff')
other.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
other.add_argument('--debug',action='store_true',help=argparse.SUPPRESS)
other.add_argument('--delly_vcf','--delly-vcf',help=argparse.SUPPRESS)
other.add_argument('--supplementary_bam','--supplementary-bam',help=argparse.SUPPRESS)
other.add_argument('--low_dp_mask','--low-dp-mask',help=argparse.SUPPRESS)
other.add_argument('--save_low_dp_mask','--save-low-dp-mask',action='store_true',help=argparse.SUPPRESS)
other.add_argument('--db_dir',default=__default_db_dir__,help='Database directory')
other.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
other.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
other.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
Expand All @@ -488,6 +514,7 @@ parser_sub.add_argument('--threads','-t',default=1,help='Threads to use',type=in
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--db_dir',default=__default_db_dir__,help='Database directory')
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.add_argument('--debug',action='store_true',help=argparse.SUPPRESS)
Expand All @@ -513,6 +540,7 @@ parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argp
parser_sub.add_argument('--threads','-t',default=1,help='Threads to use',type=int)
parser_sub.add_argument('--ram',default=2,type=int_2_or_more,help='Maximum memory to use in Gb')
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--db_dir',default=__default_db_dir__,help='Database directory')
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.add_argument('--debug',action='store_true',help=argparse.SUPPRESS)
Expand All @@ -531,6 +559,7 @@ parser_sub.add_argument('--external_db','--external-db',type=str,help='Path to d
parser_sub.add_argument('--dir','-d',nargs="+",default=["results"],help='Storage directory')
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--db_dir',default=__default_db_dir__,help='Database directory')
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.add_argument('--debug',action='store_true',help=argparse.SUPPRESS)
Expand All @@ -551,6 +580,7 @@ parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--suspect',action="store_true",help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--db_dir',default=__default_db_dir__,help='Database directory')
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level')
parser_sub.add_argument('--debug',action='store_true',help=argparse.SUPPRESS)
Expand All @@ -576,6 +606,7 @@ parser_sub.add_argument('--include_original_mutation','--include-original-mutati
parser_sub.add_argument('--load',action="store_true", help='Automaticaly load database')
parser_sub.add_argument('--no_overwrite','--no-overwrite',action="store_true", help="Don't load if existing database with prefix exists")
parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')
parser_sub.add_argument('--db_dir',default=__default_db_dir__,help='Database directory')
parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS)
parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".")
parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__)
Expand Down Expand Up @@ -659,13 +690,13 @@ if hasattr(args, 'func'):
args.dir = os.path.abspath(args.dir)

if hasattr(args, 'db'):
if args.db=="tbdb" and not args.external_db and pp.nofile(sys.base_prefix+"/share/tbprofiler/tbdb.fasta"):
if args.db=="tbdb" and not args.external_db and pp.nofile(f"{args.db_dir}/tbdb.fasta"):
logging.error("Can't find the tbdb file at %s. Please run 'tb-profiler update_tbdb' to load the default library or specify another using the '--external_db' flag" % sys.base_prefix)
raise SystemExit
if args.external_db:
args.conf = pp.get_db(args.software_name,args.external_db)
args.conf = pp.get_db(args.db_dir,args.external_db)
else:
args.conf = pp.get_db(args.software_name,args.db)
args.conf = pp.get_db(args.db_dir,args.db)
if args.conf is None:
logging.error("Can't find the database %s. Please run 'tb-profiler create_db' to create the database or specify another using the '--external_db' flag" % args.db)
raise SystemExit
Expand Down

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