diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rw-r--r-- | wqflask/base/data_set.py | 22 |
1 files changed, 16 insertions, 6 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index e1d7e2f9..41c5d8ba 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ from db import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import locate, locate_ignore_error +from utility.tools import locate, locate_ignore_error, flat_files from maintenance import get_group_samplelists @@ -53,7 +53,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists from utility.logger import getLogger logger = getLogger(__name__ ) @@ -226,7 +226,7 @@ class Markers(object): class HumanMarkers(Markers): def __init__(self, name, specified_markers = []): - marker_data_fh = open(locate('genotype') + '/' + name + '.bim') + marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() @@ -299,11 +299,21 @@ class DatasetGroup(object): self.markers = HumanMarkers(self.name, markers) def get_markers(self): - #logger.debug("self.species is:", self.species) - if self.species == "human": + logger.debug("self.species is:", self.species) + + def check_plink_gemma(): + if flat_file_exists("mapping"): + MAPPING_PATH = flat_files("mapping")+"/" + if (os.path.isfile(MAPPING_PATH+self.name+".bed") and + (os.path.isfile(MAPPING_PATH+self.name+".map") or + os.path.isfile(MAPPING_PATH+self.name+".bim"))): + return True + return False + + if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers self.markers = marker_class(self.name) |