diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/gn2.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/standalone.py | 5 |
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temp_data=None): """ info("call calculate_kinship_old") + fatal("THE FUNCTION calculate_kinship_old IS OBSOLETE, use calculate_kinship_new instead - see Genotype Normalization Problem on Pjotr's blog") n = genotype_matrix.shape[0] m = genotype_matrix.shape[1]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 ) |