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-rwxr-xr-xwqflask/base/data_set.py50
1 files changed, 44 insertions, 6 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 30221503..cf219fda 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -16,8 +16,6 @@
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
-#we
-#
# This module is used by GeneNetwork project (www.genenetwork.org)
from __future__ import absolute_import, print_function, division
@@ -27,6 +25,7 @@ import string
import collections
import json
+import gzip
import cPickle as pickle
import itertools
@@ -52,8 +51,6 @@ from pprint import pformat as pf
DS_NAME_MAP = {}
def create_dataset(dataset_name, dataset_type = None):
-
- print("dataset_type:", dataset_type)
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
#dataset_type = get_dataset_type_from_json(dataset_name)
@@ -129,7 +126,7 @@ def create_datasets_list():
for result in g.db.execute(query).fetchall():
#The query at the beginning of this function isn't necessary here, but still would
#rather just reuse it
- print("type: {}\tname: {}".format(dataset_type, result.Name))
+ #print("type: {}\tname: {}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
@@ -261,6 +258,36 @@ class DatasetGroup(object):
if maternal and paternal:
self.parlist = [maternal, paternal]
+ def get_sample_list(self):
+ genofilename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
+ genofile = open(genofilename, "r")
+ for line in genofile:
+ line = line.strip()
+ if line.startswith(("#", "@")):
+ continue
+ headline = line
+ break
+ headers = headline.split("\t")
+ if headers[3] == "Mb":
+ self.samplelist = headers[4:]
+ else:
+ self.samplelist = headers[3:]
+
+ #if genotype_1.type == "group" and self.parlist:
+ # genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)
+ #else:
+ # genotype_2 = genotype_1
+
+ #determine default genotype object
+ #if self.incparentsf1 and genotype_1.type != "intercross":
+ # genotype = genotype_2
+ #else:
+ # self.incparentsf1 = 0
+ # genotype = genotype_1
+
+ #self.samplelist = list(genotype.prgy)
+
+
def read_genotype_file(self):
'''Read genotype from .geno file instead of database'''
#if self.group == 'BXD300':
@@ -275,7 +302,18 @@ class DatasetGroup(object):
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
- genotype_1.read(full_filename)
+ if os.path.isfile(full_filename):
+ print("Reading file: ", full_filename)
+ genotype_1.read(full_filename)
+ print("File read")
+ else:
+ try:
+ full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno'))
+ #print("Reading file")
+ genotype_1.read(full_filename)
+ #print("File read")
+ except IOError:
+ print("File doesn't exist!")
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)