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| author | DannyArends | 2017-02-17 21:30:41 +0100 |
|---|---|---|
| committer | DannyArends | 2017-02-17 21:30:41 +0100 |
| commit | c465eb3e4b17a3cd3c9ce20d330295c5d1d44567 (patch) | |
| tree | bc339bebd66590447579b94e05019449e8ac77a1 | |
| parent | f9d0de7cbc69eb1205e0f1f7c261efa34ed0bb42 (diff) | |
| download | genenetwork2-c465eb3e4b17a3cd3c9ce20d330295c5d1d44567.tar.gz | |
Connecting p.adjust parameters, and updating the region size parameter
| -rw-r--r-- | wqflask/wqflask/auwerx/phewas_analysis.py | 7 |
1 files changed, 5 insertions, 2 deletions
diff --git a/wqflask/wqflask/auwerx/phewas_analysis.py b/wqflask/wqflask/auwerx/phewas_analysis.py index ed2df01f..b9789404 100644 --- a/wqflask/wqflask/auwerx/phewas_analysis.py +++ b/wqflask/wqflask/auwerx/phewas_analysis.py @@ -55,6 +55,8 @@ class PheWAS(object): self.trait_id = requestform["trait_id"] self.datasetname = requestform["dataset"] self.dataset = data_set.create_dataset(self.datasetname) + self.region = int(requestform["num_region"]) + self.mtadjust = str(requestform["sel_mtadjust"]) # Print some debug print "self.trait_id:" + self.trait_id + "\n" @@ -70,7 +72,7 @@ class PheWAS(object): self.mb = int(self.this_trait.mb); # print some debug - print "location:" + self.chr + ":" + str(self.mb) + "\n" + print "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) @@ -92,11 +94,12 @@ class PheWAS(object): self.results = {} 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'] ) # 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 - phewasres = self.r_PheWASManhattan("Test", precompfile, phenoaligner, snpaligner, "None", self.chr, self.mb, self.mb, self.results['imgloc1'] ) + 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] self.results['tabulardata'] = phewasres[2] |