diff options
| -rw-r--r-- | wqflask/utility/tools.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/auwerx/phewas_analysis.py | 45 |
2 files changed, 30 insertions, 21 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index d71a9cef..4d213f4c 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -153,6 +153,9 @@ def locate(name, subdir=None): if subdir: sys.stderr.write(subdir) raise Exception("Can not locate "+name+" in "+base) +def locate_phewas(name, subdir=None): + return locate(name,'/phewas/'+subdir) + def locate_ignore_error(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -217,6 +220,7 @@ USE_REDIS = get_setting_bool('USE_REDIS') USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') GENENETWORK_FILES = get_setting('GENENETWORK_FILES') +PHEWAS_FILES = get_setting('GENENETWORK_FILES')+"/phewas" # TEMP_TRAITS = get_setting('TEMP_TRAITS') PYLMM_COMMAND = pylmm_command() @@ -242,7 +246,7 @@ if os.environ.get('WQFLASK_OVERRIDES'): OVERRIDES[k] = cmd logger.debug(OVERRIDES) -assert_file(get_setting("GENENETWORK_FILES")+"/auwerx/PheWAS_pval_EMMA_norm.RData") +assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") assert_dir(get_setting("JS_BIODALLIANCE")) assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") diff --git a/wqflask/wqflask/auwerx/phewas_analysis.py b/wqflask/wqflask/auwerx/phewas_analysis.py index e9455fba..31f6ac5d 100644 --- a/wqflask/wqflask/auwerx/phewas_analysis.py +++ b/wqflask/wqflask/auwerx/phewas_analysis.py @@ -21,7 +21,10 @@ from base import trait as TRAIT from base.trait import GeneralTrait from utility import helper_functions -from utility.tools import locate +from utility.tools import locate, locate_phewas + +import utility.logger +logger = utility.logger.getLogger(__name__ ) r_library = ro.r["library"] # Map the library function r_options = ro.r["options"] # Map the options function @@ -36,20 +39,20 @@ r_seq = ro.r["seq"] # Map the rep (repeat) function class PheWAS(object): def __init__(self): - print("Initialization of PheWAS") + ("Initialization of PheWAS") # TODO: Loading the package should only be done once, since it is quite expensive - print(r_library("auwerx")) # Load the auwerx package + logger.info(r_library("auwerx")) # Load the auwerx package self.r_create_Pheno_aligner = ro.r["create.Pheno_aligner"] # Map the create.Pheno_aligner function self.r_calculate_all_pvalue_parallel = ro.r["calculate.all.pvalue.parallel"] # Map the calculate.all.pvalue.parallel function self.r_PheWASManhattan = ro.r["PheWASManhattan"] # Map the PheWASManhattan function self.r_Stop = ro.r["throwStopError"] # Map the PheWASManhattan function self.r_PyLoadData = ro.r["PyLoadData"] # Map the load function - print("Initialization of PheWAS done !") + logger.info("Initialization of PheWAS done !") def run_analysis(self, requestform): - print("Starting PheWAS analysis on dataset") + logger.info("Starting PheWAS analysis on dataset") genofilelocation = locate("BXD.geno", "genotype") # Get the location of the BXD genotypes - precompfile = locate("PheWAS_pval_EMMA_norm.RData", "auwerx") # Get the location of the pre-computed EMMA results + precompfile = locate_phewas("PheWAS_pval_EMMA_norm.RData", "auwerx") # Get the location of the pre-computed EMMA results # Get user parameters, trait_id and dataset, and store/update them in self self.trait_id = requestform["trait_id"] @@ -58,21 +61,21 @@ class PheWAS(object): self.region = int(requestform["num_region"]) self.mtadjust = str(requestform["sel_mtadjust"]) - # Print some debug - print "self.trait_id:" + self.trait_id + "\n" - print "self.datasetname:" + self.datasetname + "\n" - print "self.dataset.type:" + self.dataset.type + "\n" + # Logger.Info some debug + logger.info("self.trait_id:" + self.trait_id + "\n") + logger.info("self.datasetname:" + self.datasetname + "\n") + logger.info("self.dataset.type:" + self.dataset.type + "\n") # GN Magic ? - self.this_trait = GeneralTrait(dataset=self.dataset, name = self.trait_id, get_qtl_info = False, get_sample_info=False) - pprint(vars(self.this_trait)) + self.this_trait = GeneralTrait(dataset=self.dataset, name = self.trait_id, get_qtl_info = False, get_sample_info=False) + logger.info(vars(self.this_trait)) # Set the values we need self.chr = str(self.this_trait.chr); self.mb = int(self.this_trait.mb); - # print some debug - print "location:" + self.chr + ":" + str(self.mb) + "+/-" + str(self.region) + "\n" + # logger.info some debug + logger.info("location:" + self.chr + ":" + str(self.mb) + "+/-" + str(self.region) + "\n") # Load in the genotypes file *sigh* to make the markermap parser = genofile_parser.ConvertGenoFile(genofilelocation) @@ -94,10 +97,13 @@ class PheWAS(object): self.results['imgurl1'] = webqtlUtil.genRandStr("phewas_") + ".png" self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1'] self.results['mtadjust'] = self.mtadjust - print("IMAGE AT:", self.results['imgurl1'] ) - print("IMAGE AT:", self.results['imgloc1'] ) + logger.info("IMAGE AT:", self.results['imgurl1'] ) + logger.info("IMAGE AT:", self.results['imgloc1'] ) # Create the PheWAS plot (The gene/probe name, chromosome and gene/probe positions should come from the user input) # TODO: generate the PDF in the temp folder, with a unique name + assert(precompfile) + assert(phenoaligner) + assert(snpaligner) phewasres = self.r_PheWASManhattan("Test", precompfile, phenoaligner, snpaligner, "None", self.chr, self.mb, self.region, self.results['imgloc1'] , self.mtadjust) self.results['phewas1'] = phewasres[0] self.results['phewas2'] = phewasres[1] @@ -107,10 +113,10 @@ class PheWAS(object): #self.r_PheWASManhattan(allpvalues) #self.r_Stop() - print("Initialization of PheWAS done !") + logger.info("Initialization of PheWAS done !") def loadImage(self, path, name): - print("pre-loading imgage results:", self.results[path]) + logger.info("pre-loading imgage results:", self.results[path]) imgfile = open(self.results[path], 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") @@ -121,7 +127,7 @@ class PheWAS(object): self.loadImage("imgloc1", "imgdata1") def process_results(self, results): - print("Processing PheWAS output") + logger.info("Processing PheWAS output") # TODO: get the PDF in the temp folder, and display it to the user template_vars = {} template_vars["results"] = self.results @@ -129,4 +135,3 @@ class PheWAS(object): template_vars["R_debuglog"] = self.results['R_debuglog'] return(dict(template_vars)) - |