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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py7
1 files changed, 4 insertions, 3 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 65b989a8..48a931c5 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -143,6 +143,7 @@ def run_human(pheno_vector,
timestamp = datetime.datetime.utcnow().isoformat()
+ # Pickle chunks of input SNPs (from Plink interator) and compress them
#print("Starting adding loop")
for part, result in enumerate(results):
#data = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
@@ -517,7 +518,7 @@ class LMM:
Kve = []
self.nonmissing = x
- print("this K is:", pf(K))
+ print("this K is:", K.shape, pf(K))
if len(Kva) == 0 or len(Kve) == 0:
if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
@@ -529,8 +530,8 @@ class LMM:
self.K = K
self.Kva = Kva
self.Kve = Kve
- print("self.Kva is: ", pf(self.Kva))
- print("self.Kve is: ", pf(self.Kve))
+ print("self.Kva is: ", self.Kva.shape, pf(self.Kva))
+ print("self.Kve is: ", self.Kve.shape, pf(self.Kve))
self.Y = Y
self.X0 = X0
self.N = self.K.shape[0]