Make the new version of genotype normalization default

4 files changed, 20 insertions, 9 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
index f30cf1e6..7bceb089 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
@@ -45,15 +45,20 @@ def mprint(msg,data):
     m = np.array(data)
     print(msg,m.shape,"=\n",m)
 
+def fatal(msg):
+    logger.critical(msg)
+    raise Exception(msg)
+
 def callbacks():
     return dict(
         write = sys.stdout.write,
         writeln = print,
-        debug = logging.debug,
-        info = logging.info,
-        warning = logging.warning,
-        error = logging.error,
-        critical = logging.critical,
+        debug = logger.debug,
+        info = logger.info,
+        warning = logger.warning,
+        error = logger.error,
+        critical = logger.critical,
+        fatal = fatal,
         progress = progress,
         mprint = mprint
     )
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 035f31e8..8be3fc6f 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -66,7 +66,7 @@ except ImportError:
     sys.stderr.write("WARNING: LMM standalone version missing the Genenetwork2 environment\n")
     pass
 
-progress,mprint,debug,info = uses('progress','mprint','debug','info')
+progress,mprint,debug,info,fatal = uses('progress','mprint','debug','info','fatal')
 
 #np.seterr('raise')
 
@@ -278,7 +278,7 @@ def run_other_old(pheno_vector,
     print("Running the original LMM engine in run_other (old)")
     print("REML=",restricted_max_likelihood," REFIT=",refit)
     with Bench("Calculate Kinship"):
-        kinship_matrix,genotype_matrix = calculate_kinship_old(genotype_matrix, tempdata)
+        kinship_matrix,genotype_matrix = calculate_kinship_new(genotype_matrix, tempdata)
     
     print("kinship_matrix: ", pf(kinship_matrix))
     print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
@@ -408,6 +408,7 @@ def calculate_kinship_old(genotype_matrix, temp_data=None):
     
     """
     info("call calculate_kinship_old")
+    fatal("THE FUNCTION calculate_kinship_old IS OBSOLETE, use calculate_kinship_new instead - see Genotype Normalization Problem on Pjotr's blog")
     n = genotype_matrix.shape[0]
     m = genotype_matrix.shape[1]
     info("genotype 2D matrix n (inds) is: %d" % (n))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index fc7a4b9d..ef0bdd7e 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -21,7 +21,7 @@ from optparse import OptionParser
 import sys
 import tsvreader
 import numpy as np
-from lmm import gn2_load_redis, calculate_kinship_old
+from lmm import gn2_load_redis, calculate_kinship_new
 from kinship import kinship, kinship_full
 import genotype
 import phenotype
@@ -190,7 +190,7 @@ elif cmd == 'kinship':
         print "Genotype",G.shape, "\n", G
         print "first Kinship method",K.shape,"\n",K
         k1 = round(K[0][0],4)
-        K2,G = calculate_kinship_old(np.copy(G).T,temp_data=None)
+        K2,G = calculate_kinship_new(np.copy(G).T,temp_data=None)
         print "Genotype",G.shape, "\n", G
         print "GN2 Kinship method",K2.shape,"\n",K2
         k2 = round(K2[0][0],4)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
index 36bf8fd5..40b2021d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
@@ -57,6 +57,10 @@ def mprint(msg,data):
               m[-2][0:3]," ... ",m[-2][-3:],"\n ",
               m[-1][0:3]," ... ",m[-1][-3:],"]")
 
+def fatal(msg):
+    logger.critical(msg)
+    raise Exception(msg)
+
 def callbacks():
     return dict(
         write = sys.stdout.write,
@@ -66,6 +70,7 @@ def callbacks():
         warning = logger.warning,
         error = logger.error,
         critical = logger.critical,
+        fatal = fatal,
         progress = progress,
         mprint = mprint
     )