def set_localdir():
"""Set the local database directory from the enviornmental variable
GCN_DATA_DIR"""
local = lib_config.gcn_path('GCN_DATA_DIR')
if local is not None:
global _LOCALDIR
_LOCALDIR = local
def main():
"""to generate Clinvitae VCF file"""
desc = 'Generating Clinvitae VCF file'
parser = argparse.ArgumentParser(description=desc)
parser.add_argument('--preprocess', action='store_const', dest='preprocess',\
required=False, default=False, const=True, help='download Clinvitae')
parser.add_argument('-g', dest='mutalyzer_fn', required=False,\
default=None, help='a file generated from https://mutalyzer.nl/position-converter')
parser.add_argument('-o', '--out_dir', dest='out_dir', required=False,\
type=str, default = lib_config.gcn_path('GCN_DATA_DIR'),\
help='output directory')
args = parser.parse_args()
if args.preprocess:
clinvt = lib_clinvitae.ClinVitae(args.out_dir)
clinvt.download()
_ = clinvt.extract_cDNA()
elif args.mutalyzer_fn:
clinvt = lib_clinvitae.ClinVitae(args.out_dir)
if os.path.exists(clinvt.tsv) and os.path.exists(args.mutalyzer_fn):
clinvt.gdna_to_vcf(args.mutalyzer_fn)
else:
raise RuntimeError('check if both [%s] and [%s] exists'%\
(clinvt.tsv,args.mutalyzer_fn))
else:
raise RuntimeError('it does not do anything!')
def __init__(self):
self.location = lib_config.gcn_path('GCN')
self.liftover = os.path.join(self.location, \
'gcn/bin/hgConvert/liftOver_exe', \
'liftOver')
self.chaindata = os.path.join(self.location, 'gcn/bin/hgConvert', \
'chainData')
self.tmpdir = os.path.join(self.location, 'gcn/bin/hgConvert', 'temp')
if not os.path.exists(self.tmpdir):
os.system('mkdir %s' % (self.tmpdir))
def _check_env(self):
flag = 0
envs = ['GCN', 'GCN_DATA_DIR', 'GCN_DB_DIR']
for env in envs:
loc = lib_config.gcn_path(env)
if loc:
if not os.path.exists(loc):
self.logger.error('Path set to %s environment does not '
'exist..' % env)
flag = 1
else:
self.logger.error('%s environment variable is not set..' % env)
flag = 1
return flag
'GENCODE':
os.path.join(_LOCALDIR, 'gencode', 'wgEncodeGencodeBasicV19.txt'),
'FUNSIM':
os.path.join(_LOCALDIR, 'geneontology', 'uprot20160505_funsim.tsv'),
'GOA':
os.path.join(_LOCALDIR, 'geneontology', 'gene_association.goa_human'),
'GOBO':
os.path.join(_LOCALDIR, 'geneontology', 'go.obo'),
'MIRNA':
os.path.join(_LOCALDIR, 'mirna', 'human_predictions_S_C_aug2010.txt'),
'UTRDB':
os.path.join(_LOCALDIR, 'utrdb', ''),
'CLNPHESNP':
os.path.join(_LOCALDIR, 'clnphesnp', ''),
'LOGFILE':
lib_config.gcn_path('GCN_LOGFILE'),
'UNIPROT':
os.path.join(_LOCALDIR, 'uniprot', 'uniprot_sprot_human.dat'),
'OMIM':
os.path.join(_LOCALDIR, 'omim', 'uniprot_sprot_human.dat'),
'NSFP':
os.path.join(_LOCALDIR, 'dbnsfp', ''),
'GERP':
os.path.join(_LOCALDIR, 'gerp', '*.txt'),
'REFGENOME':
os.path.join(_LOCALDIR, 'refgenome', 'human_g1k_v37.fasta'),
'REFGENOME_UCSC':
os.path.join(_LOCALDIR, 'refgenome', 'hg19.fasta'),
'REGULOME':
os.path.join(_LOCALDIR, 'regulome', ''),
'SeqCapEZ_Exome':