From 2c6d1fcba1138415ecb3ca447e09d06d660af0db Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 14 Mar 2015 12:14:53 +0300
Subject: Working on kinship: GN2 and simple matrix multiplicatino agree

---
 wqflask/wqflask/my_pylmm/pyLMM/genotype.py |  2 +-
 wqflask/wqflask/my_pylmm/pyLMM/kinship.py  |  4 ++++
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py      |  4 ++--
 wqflask/wqflask/my_pylmm/pyLMM/runlmm.py   | 23 +++++++++++------------
 4 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/genotype.py b/wqflask/wqflask/my_pylmm/pyLMM/genotype.py
index f5d9ee8c..315fd824 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/genotype.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/genotype.py
@@ -23,7 +23,7 @@ import operator
 def replace_missing_with_MAF(snp_g):
     """
     Replace the missing genotype with the minor allele frequency (MAF)
-    in the snp row
+    in the snp row. It is rather slow!
     """
     cnt = Counter(snp_g)
     tuples = sorted(cnt.items(), key=operator.itemgetter(1))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index 61da68fc..c1750e1d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -61,6 +61,10 @@ def f_init(q):
 
 def kinship_full(G,options):
     print G.shape
+    m = G.shape[0] # snps
+    n = G.shape[1] # inds
+    sys.stderr.write(str(m)+" SNPs\n")
+    assert m>n, "n should be larger than m (snps>inds)"
     m = np.dot(G.T,G)
     m = m/G.shape[0]
     return m
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 36c3602f..7bf77be5 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -340,8 +340,8 @@ def calculate_kinship(genotype_matrix, temp_data=None, is_testing=False):
     print("genotype 2D matrix m (snps) is:", m)
     keep = []
     for counter in range(m):
-        if is_testing and counter>8:
-            break
+        # if is_testing and counter>8:
+        #     break
         #print("type of genotype_matrix[:,counter]:", pf(genotype_matrix[:,counter]))
         #Checks if any values in column are not numbers
         not_number = np.isnan(genotype_matrix[:,counter])
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 0b8830d4..80478368 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -116,28 +116,27 @@ if cmd == 'redis':
 elif cmd == 'kinship':
     G = g
     print "Original G",G.shape, "\n", G
+    if y:
+        gnt = np.array(gn).T
+        Y,g = phenotype.remove_missing(y,g.T,options.verbose)
+        G = g.T
+        print "Removed missing phenotypes",G.shape, "\n", G
     if options.maf_normalization:
         G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g )
         print "MAF replacements: \n",G
     if not options.skip_genotype_normalization:
         G = np.apply_along_axis( genotype.normalize, axis=1, arr=G)
             
-    print G.shape, "\n", G
     K = kinship_full(G,options)
+    print "Genotype",G.shape, "\n", G
     print "first Kinship method",K.shape,"\n",K
-    K2 = calculate_kinship(np.copy(G.T),None,options)
+    K2 = calculate_kinship(np.copy(G.T),temp_data=None,is_testing=options.testing)
+    print "Genotype",G.shape, "\n", G
     print "GN2 Kinship method",K2.shape,"\n",K2
-    K3 = kinship(G,options)
+
+    print "Genotype",G.shape, "\n", G
+    K3 = kinship(np.copy(G),options)
     print "third Kinship method",K3.shape,"\n",K3
-    sys.exit(1)
-    gnt = np.array(gn).T
-    Y,g = remove_missing_phenotypes(y,gnt,options.verbose)
-    G = g
-    print G.shape,G
-    K = calculate_kinship(np.copy(G),temp_data=None,is_testing=options.testing)
-    print G.shape,G
-    print "first Kinship method",K.shape,K
-    K = kinship(G.T,options)
     assert(K[0][0]==1.28)
 else:
     print "Doing nothing"
-- 
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