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authorzsloan2019-05-24 11:35:12 -0500
committerzsloan2019-05-24 11:35:12 -0500
commite304c2cfdf1b38da483efa607a2acd72b66ad0de (patch)
tree90197932aa4f867bd710afaefe6e59082689279c /wqflask/base/data_set.py
parent338521197f5de79bafa8f230c692d3efab0da9c1 (diff)
downloadgenenetwork2-e304c2cfdf1b38da483efa607a2acd72b66ad0de.tar.gz
Replaced qtlreaper Dataset object with python object
Diffstat (limited to 'wqflask/base/data_set.py')
-rw-r--r--wqflask/base/data_set.py7
1 files changed, 5 insertions, 2 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index beb2a8a2..b324ac74 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -43,6 +43,7 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility.benchmark import Bench
from utility import chunks
+from utility import gen_geno_ob
from utility.tools import locate, locate_ignore_error, flat_files
from maintenance import get_group_samplelists
@@ -388,14 +389,16 @@ class DatasetGroup(object):
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
- genotype_1 = reaper.Dataset()
+ #genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
- genotype_1.read(full_filename)
+ #genotype_1.read(full_filename)
+
+ genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)