diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/runserver.py | 6 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 23 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/gn2.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 53 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm2.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py | 3 |
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() |