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authorzsloan2019-06-05 13:01:36 -0500
committerzsloan2019-06-05 13:01:36 -0500
commit66c6bbfcbbd5fb23145ec09956f4809e5f701bec (patch)
treec01cfdc476e6d49be06978e15ec0cac9aca69ccc /wqflask/base
parent319cb6f8a9f3b57137cb13855eb84545a08399e8 (diff)
downloadgenenetwork2-66c6bbfcbbd5fb23145ec09956f4809e5f701bec.tar.gz
Fixed issue that caused interval mapping to not work because the python implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper)
Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/data_set.py9
1 files changed, 6 insertions, 3 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b324ac74..1fd1792e 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -384,7 +384,7 @@ class DatasetGroup(object):
[result.extend(l) for l in lists if l]
return result
- def read_genotype_file(self):
+ def read_genotype_file(self, use_reaper=False):
'''Read genotype from .geno file instead of database'''
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
@@ -396,9 +396,12 @@ class DatasetGroup(object):
full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
- #genotype_1.read(full_filename)
- genotype_1 = gen_geno_ob.genotype(full_filename)
+ if use_reaper:
+ genotype_1 = reaper.Dataset()
+ genotype_1.read(full_filename)
+ else:
+ 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)