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authorzsloan2017-01-26 16:26:16 +0000
committerzsloan2017-01-26 16:26:16 +0000
commite63c4014e7bc34b440707be19af3779b72102fdb (patch)
tree6692f7145db3b620a4e316f4d5289c6809ec9250 /wqflask/base/data_set.py
parent2fe052c10bc1e6468da277a6afbb51468e447c47 (diff)
downloadgenenetwork2-e63c4014e7bc34b440707be19af3779b72102fdb.tar.gz
GEMMA now works with CFW data (had to update where it looks for the input files and how it writes the phenotype file)
Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results
Diffstat (limited to 'wqflask/base/data_set.py')
-rw-r--r--wqflask/base/data_set.py22
1 files changed, 16 insertions, 6 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 06e02b02..94b38e13 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)