def run(self):
self.warning('Storing file: %s' % self.param_required('filename'))
# First, rename the file
fileO = File(path=self.param_required('filename'),
type=self.param_required('type'))
layout_dict = self.param_required('layout_dict')
newlayout = self.param_required('newlayout').split(",")
newbits = [layout_dict[i] for i in newlayout]
newname = ".".join(newbits)
compression = None
if self.param('compression'):
compression = self.param('compression')
add_date = False
if self.param('add_date'):
add_date = True
fileO.rename(newname=newname,
extension=self.param_required('extension'),
add_date=add_date,
compression=compression)
new_f = File(path=self.param_required('filename'),
type=self.param_required('type'))
new_f.move(self.param('final_dir') + "/" + fileO.name)
if self.param_is_defined('store'):
hostname = self.param_required('hostname')
username = self.param_required('username')
db = self.param_required('db')
port = self.param_required('port')
pwd = self.param_required('pwd')
reseqdb = ReseqTrackDB(host=hostname,
user=username,
port=port,
pwd=pwd,
db=db)
new_f.store(reseqdb, do_md5=True, dry=False)
self.param('stored_file', new_f.path)
def fetch_input(self):
filename = self.param_required('filename')
fileO = None
if self.param_is_defined('hostname') and self.param_is_defined('username'):
hostname = self.param('hostname')
username = self.param('username')
db = self.param('db')
port = self.param('port')
pwd = self.param('pwd')
reseqdb = ReseqTrackDB(host=hostname,
user=username,
port=port,
pwd=pwd,
db=db)
fileO = reseqdb.fetch_file_by_filename(filename)
else:
fileO = File(
path=filename,
type='PHASED_VCF',
)
self.param('file_object', fileO)
args = parser.parse_args()
reseqdb = ReseqTrackDB(host=args.hostname,
user=args.username,
port=args.port,
pwd=args.pwd,
db=args.db)
dry = None
if args.dry == "True":
dry = True
elif args.dry == "False":
dry = False
else:
raise Exception("I do not recognize this args.dry option:{0}".format(
args.dry))
with open(args.f) as f:
for line in f:
line = line.rstrip('\n')
bits = line.split('\t')
f = File(path=bits[0],
type=bits[2],
size=bits[3],
md5=bits[1],
host_id=bits[4],
withdrawn=bits[5],
created=bits[6])
f.store(reseqdb, dry=dry)
log_filename = "subset_vcf_%s.log" % outprefix
logger = logging.getLogger("subset_vcf")
logger.setLevel(logging.INFO)
# create the logging file handler
fh = logging.FileHandler(log_filename)
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
fh.setFormatter(formatter)
# add handler to logger object
logger.addHandler(fh)
logger.info("Program started")
vcfQC = VcfQC(vcf=file.path,
bgzip_folder=args.bgzip_folder,
vcftools_folder=args.vcftools_folder)
vcffile = vcfQC.subset_vcf(bed=args.bed,
outprefix=outprefix,
outdir=args.outdir,
create_index=True)
f = File(path=vcffile, type=args.type, host_id=1, withdrawn=0)
f.store(reseqdb, do_md5=True)
logger.info("Done!.")
hostname=args.hostname
username=args.username
db=args.db
port=args.port
pwd=args.pwd
reseqdb = ReseqTrackDB(host=hostname,user=username,port=port,pwd=pwd,db=db)
file=reseqdb.fetch_file_by_filename(args.filename)
l=os.path.basename(file.path).split('.')
l.remove('vcf')
l.remove('gz')
outprefix='.'.join(l)
vcfQC = VcfQC(vcf=file.path,bcftools_folder=args.bcftools_folder)
stats=vcfQC.stats(outprefix=outprefix,outdir=args.outdir)
#store attributes
for attr,value in stats.summary_numbers.items():
Attribute(table_name="file",other_id=file.dbID,name="STATS_"+attr,value=value).store(reseqdb)
Attribute(table_name="file",other_id=file.dbID,name="STATS_ts_tv",value=stats.ts_tv).store(reseqdb)
Attribute(table_name="file",other_id=file.dbID,name="STATS_ts_tv_1stalt",value=stats.ts_tv_1stalt).store(reseqdb)
Attribute(table_name="file",other_id=file.dbID,name="STATS_no_singleton_snps",value=stats.no_singleton_snps).store(reseqdb)
#store file
stats_f=File(path=stats.filename,type=file.type+"_STATS",host_id=1,withdrawn=0)
stats_f.store(reseqdb,do_md5=True)
logger.info("Done!.")