def fetch_input(self):
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)
self.param('reseqdb', reseqdb)
def reseqtrackdb_object():
'''Returns an object'''
hostname = pytest.config.getoption("--hostname")
username = pytest.config.getoption("--username")
port = pytest.config.getoption("--port")
pwd = pytest.config.getoption("--pwd")
db = pytest.config.getoption("--db")
reseqtrackdb_object = ReseqTrackDB(host=hostname,
user=username,
port=port,
pwd=pwd,
db=db)
return reseqtrackdb_object
fh.setFormatter(formatter)
# add handler to logger object
logger.addHandler(fh)
logger.info("Program started")
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)
with open(args.ifile) as f:
for p in f:
p = p.rstrip("\n")
filename = os.path.basename(p)
logger.info("Changing file type for %s" % filename)
fileO = reseqdb.fetch_file_by_filename(filename)
old_type = fileO.type
newtype = ""
if old_type == "LC_BAM" or old_type == "EX_BAM":
newtype = args.newtype
#RESEQTRACK DB conn params
parser.add_argument('--hostname', type=str, required=True, help='Hostname for ReseqTrack DB' )
parser.add_argument('--username', type=str, required=True, help='User for ReseqTrack DB' )
parser.add_argument('--port', type=int, required=True, help='Port number in the ReseqTrack DB' )
parser.add_argument('--pwd', type=str, help='PWD for the ReseqTrack DB' )
parser.add_argument('--db', type=str, required=True, help='DB name in the ReseqTrack DB' )
#files that will be analyzed
parser.add_argument('-vcfl','--vcflist', nargs='+', help='<Required> List of VCFs to analyze', required=True)
parser.add_argument('-cnames','--columnames', nargs='+', help='<Required> List of columns used in the .csv and .png files', required=True)
parser.add_argument('--chros_f', type=str, required=True, help='File with chros' )
parser.add_argument('--outprefix', type=str, required=True, help='Prefix for output files' )
args = parser.parse_args()
reseqtrackdb_object=ReseqTrackDB(host=args.hostname,user=args.username,port=args.port,pwd=args.pwd,db=args.db)
def get_annotation(attr_list,dict_str,pattern):
patt = re.compile( pattern )
patt1 = re.compile('^STATS_.*(chr.+)_filt' )
for a in attr_list:
match = patt.match( a.name )
match1 = patt1.match( a.name )
if match:
if match1:
dict_str[match1.group(1)].append(a.value)
else:
raise Exception("Error matching the attribute name")
return dict_str
fh.setFormatter(formatter)
# add handler to logger object
logger.addHandler(fh)
logger.info("Program started")
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)
l1 = get_files_by_type(reseqdb, args.ftype_1)
l2 = get_files_by_type(reseqdb, args.ftype_2)
l3 = []
if args.ftype_3:
l3 = get_files_by_type(reseqdb, args.ftype_3)
others_ids = list(set(l1 + l2 + l3))
new_c = Collection(name=args.collection_name,
type=args.collection_type,
others_dbIDs=others_ids,
parser.add_argument('--size',
type=str,
required=True,
help='Size for font in plots. i.e. 50')
args = parser.parse_args()
hostname = args.hostname
username = args.username
db = args.db
port = args.port
pwd = args.pwd
reseqtrackdb_object = ReseqTrackDB(host=hostname,
user=username,
port=port,
pwd=pwd,
db=db)
vcf_f = reseqtrackdb_object.fetch_file_by_url(args.ifile)
attrbs = reseqtrackdb_object.fetch_attributes_by_other_id(vcf_f.dbID)
def rec_dd():
return defaultdict(rec_dd)
#valid attributes, edit it to modify the order of columns
valid_attrb = ['VAR_SENSITIVITY', 'VAR_SPECIFICITY', 'GENOTYPE_CONCORDANCE']
x = rec_dd()