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-rwxr-xr-xwqflask/runserver.py6
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py23
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/gn2.py8
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py53
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm2.py18
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py3
6 files changed, 72 insertions, 39 deletions
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 9d5686a9..fadae6bf 100755
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -20,9 +20,9 @@ from wqflask import app
import logging
#from themodule import TheHandlerYouWant
-file_handler = logging.FileHandler("/tmp/flask_gn_log_danny_unsecure")
-file_handler.setLevel(logging.DEBUG)
-app.logger.addHandler(file_handler)
+# file_handler = logging.FileHandler("/tmp/flask_gn_log_danny_unsecure")
+# file_handler.setLevel(logging.DEBUG)
+# app.logger.addHandler(file_handler)
import logging_tree
logging_tree.printout()
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 7708356b..fba34b99 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -40,6 +40,7 @@ from utility import temp_data
from utility.benchmark import Bench
+PYLMM_COMMAND= 'python /home/pjotr/izip/git/opensource/python/gn2/wqflask/wqflask/my_pylmm/pyLMM/lmm.py'
class MarkerRegression(object):
@@ -126,8 +127,9 @@ class MarkerRegression(object):
#Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
self.qtl_results = []
- for qtl in self.filtered_markers:
- print("lod score is:", qtl['lod_score'])
+ for index,qtl in enumerate(self.filtered_markers):
+ if index<40:
+ print("lod score is:", qtl['lod_score'])
if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
print("changing to X")
self.json_data['chr'].append("X")
@@ -144,7 +146,7 @@ class MarkerRegression(object):
self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
- print("json_data:", self.json_data)
+ # print("json_data:", self.json_data)
self.js_data = dict(
@@ -272,7 +274,7 @@ class MarkerRegression(object):
""")
def run_rqtl_geno(self):
- print("Calling R/qtl from python")
+ print("Calling R/qtl")
self.geno_to_rqtl_function()
@@ -655,8 +657,7 @@ class MarkerRegression(object):
Redis.set(key, json_params)
Redis.expire(key, 60*60)
- command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
- "other")
+ command = PYLMM_COMMAND+' --key {} --species {}'.format(key,"other")
os.system(command)
@@ -713,8 +714,8 @@ class MarkerRegression(object):
# "refit": False,
# "temp_data": tempdata}
- print("genotype_matrix:", str(genotype_matrix.tolist()))
- print("pheno_vector:", str(pheno_vector.tolist()))
+ # print("genotype_matrix:", str(genotype_matrix.tolist()))
+ # print("pheno_vector:", str(pheno_vector.tolist()))
params = dict(pheno_vector = pheno_vector.tolist(),
genotype_matrix = genotype_matrix.tolist(),
@@ -732,7 +733,7 @@ class MarkerRegression(object):
Redis.expire(key, 60*60)
print("before printing command")
- command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
+ command = PYLMM_COMMAND + ' --key {} --species {}'.format(key,
"other")
print("command is:", command)
print("after printing command")
@@ -745,7 +746,7 @@ class MarkerRegression(object):
json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
results = json.loads(json_results[1])
p_values = [float(result) for result in results['p_values']]
- print("p_values:", p_values)
+ print("p_values:", p_values[:10])
#p_values = self.trim_results(p_values)
t_stats = results['t_stats']
@@ -806,7 +807,7 @@ class MarkerRegression(object):
print("Before creating the command")
- command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
+ command = PYLMM_COMMAND+' --key {} --species {}'.format(key,
"human")
print("command is:", command)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
index 40b2021d..821195c8 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
@@ -17,7 +17,7 @@ logger = logging.getLogger('lmm2')
logging.basicConfig(level=logging.DEBUG)
np.set_printoptions(precision=3,suppress=True)
-progress_location = None
+progress_location = None
progress_current = None
progress_prev_perc = None
@@ -25,17 +25,17 @@ def progress_default_func(location,count,total):
global progress_current
value = round(count*100.0/total)
progress_current = value
-
+
progress_func = progress_default_func
def progress_set_func(func):
global progress_func
progress_func = func
-
+
def progress(location, count, total):
global progress_location
global progress_prev_perc
-
+
perc = round(count*100.0/total)
if perc != progress_prev_perc and (location != progress_location or perc > 98 or perc > progress_prev_perc + 5):
progress_func(location, count, total)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 98bbead8..5b06c9ae 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -42,25 +42,27 @@ from redis import Redis
Redis = Redis()
import sys
-sys.path.append("/home/zas1024/gene/wqflask/")
-
-has_gn2=True
from utility.benchmark import Bench
from utility import temp_data
-sys.path.append("/home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/")
-
from kinship import kinship, kinship_full, kvakve
import genotype
import phenotype
import gwas
+has_gn2=True
+sys.stderr.write("INFO: pylmm system path is "+":".join(sys.path)+"\n")
+sys.stderr.write("INFO: pylmm file is "+__file__+"\n")
+
# ---- A trick to decide on the environment:
try:
- from wqflask.my_pylmm.pyLMM import chunks
+ sys.stderr.write("INFO: trying loading module\n")
+ import utility.formatting # this is never used, just to check the environment
+ sys.stderr.write("INFO: This is a genenetwork2 environment\n")
from gn2 import uses, progress_set_func
except ImportError:
+ # Failed to load gn2
has_gn2=False
import standalone as handlers
from standalone import uses, progress_set_func
@@ -852,30 +854,49 @@ def gwas_with_redis(key,species,new_code=True):
debug("Updating REDIS percent_complete=%d" % (round(i*100.0/total)))
progress_set_func(update_tempdata)
- def narray(key):
- print(key)
- v = params[key]
+ def narray(t):
+ info("Type is "+t)
+ v = params.get(t)
if v is not None:
- v = np.array(v).astype(np.float)
+ # Note input values can be array of string or float
+ v1 = [x if x != 'NA' else 'nan' for x in v]
+ v = np.array(v1).astype(np.float)
return v
- def narrayT(key):
- m = narray(key)
+ def marray(t):
+ info("Type is "+t)
+ v = params.get(t)
+ if v is not None:
+ m = []
+ for r in v:
+ # Note input values can be array of string or float
+ r1 = [x if x != 'NA' else 'nan' for x in r]
+ m.append(np.array(r1).astype(np.float))
+ return np.array(m)
+ return np.array(v)
+
+ def marrayT(t):
+ m = marray(t)
if m is not None:
return m.T
return m
# We are transposing before we enter run_gwas - this should happen on the webserver
# side (or when reading data from file)
- k = narray('kinship_matrix')
- g = narrayT('genotype_matrix')
+ k = marray('kinship_matrix')
+ g = marrayT('genotype_matrix')
+ mprint("geno",g)
y = narray('pheno_vector')
n = len(y)
- m = params['num_genotypes']
- ps,ts = run_gwas(species,n,m,k,y,g,narray('covariate_matrix'),params['restricted_max_likelihood'],params['refit'],params['input_file_name'],new_code)
+ m = params.get('num_genotypes')
+ if m is None:
+ m = g.shape[0]
+ info("m=%d,n=%d" % (m,n))
+ ps,ts = run_gwas(species,n,m,k,y,g,narray('covariate_matrix'),params['restricted_max_likelihood'],params['refit'],params.get('input_file_name'),new_code)
results_key = "pylmm:results:" + params['temp_uuid']
+ # fatal(results_key)
json_results = json.dumps(dict(p_values = ps,
t_stats = ts))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
index 358bf27e..c65843ec 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
@@ -24,14 +24,24 @@ from scipy import optimize
from optmatrix import matrixMult
import kinship
+sys.stderr.write("INFO: pylmm (lmm2) system path is "+":".join(sys.path)+"\n")
+sys.stderr.write("INFO: pylmm (lmm2) file is "+__file__+"\n")
+
# ---- A trick to decide on the environment:
try:
- from wqflask.my_pylmm.pyLMM import chunks
- from gn2 import uses
+ sys.stderr.write("INFO: trying loading module\n")
+ import utility.formatting # this is never used, just to check the environment
+ sys.stderr.write("INFO: This is a genenetwork2 environment (lmm2)\n")
+ from gn2 import uses, progress_set_func
except ImportError:
- sys.stderr.write("WARNING: LMM2 standalone version missing the Genenetwork2 environment\n")
+ # Failed to load gn2
has_gn2=False
- from standalone import uses
+ import standalone as handlers
+ from standalone import uses, progress_set_func
+ sys.stderr.write("WARNING: LMM2 standalone version missing the Genenetwork2 environment\n")
+
+progress,mprint,debug,info,fatal = uses('progress','mprint','debug','info','fatal')
+
def calculateKinship(W,center=False):
"""
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py b/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py
index 27daf43f..66b34ee2 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py
@@ -56,7 +56,8 @@ def geno(fn):
print fn
with open(fn,'r') as tsvin:
- assert(tsvin.readline().strip() == "# Genotype format version 1.0")
+ line = tsvin.readline().strip()
+ assert line == "# Genotype format version 1.0", line
tsvin.readline()
tsvin.readline()
tsvin.readline()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 21:29:13 +0000