diff options
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 26 |
1 files changed, 19 insertions, 7 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 8fb1d841..af441489 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -69,7 +69,7 @@ class MarkerRegression(object): self.maf = start_vars['maf'] # Minor allele frequency self.suggestive = "" self.significant = "" - #print("self.maf:", self.maf) + self.pair_scan = False # Initializing this since it is checked in views to determine which template to use self.dataset.group.get_markers() if self.mapping_method == "gemma": @@ -86,11 +86,8 @@ class MarkerRegression(object): self.method = start_vars['mapmethod_rqtl_geno'] self.model = start_vars['mapmodel_rqtl_geno'] - if start_vars['pair_scan'] == "true": self.pair_scan = True - else: - self.pair_scan = False print("pair scan:", self.pair_scan) print("DOING RQTL GENO") @@ -283,6 +280,10 @@ class MarkerRegression(object): r_library = ro.r["library"] # Map the library function r_c = ro.r["c"] # Map the c function r_sum = ro.r["sum"] # Map the sum function + plot = ro.r["plot"] # Map the plot function + postscript = ro.r["postscript"] # Map the postscript function + png = ro.r["png"] # Map the png function + dev_off = ro.r["dev.off"] # Map the device off function print(r_library("qtl")) # Load R/qtl @@ -315,13 +316,19 @@ class MarkerRegression(object): if self.pair_scan: if(r_sum(covar)[0] > 0): # If sum(covar) > 0 we have a covariate matrix - print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar) + print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method, n_cluster = 16) else: - print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno") + print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=self.model, method=self.method, n_cluster = 16) print("Pair scan results:", result_data_frame) + + self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + png(file=webqtlConfig.IMGDIR+self.pair_scan_filename+".png") + plot(result_data_frame) + dev_off() + + return self.process_pair_scan_results(result_data_frame) - return 0 else: if(r_sum(covar)[0] > 0): print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method) @@ -373,6 +380,11 @@ class MarkerRegression(object): pheno_as_string += ")" return pheno_as_string + def process_pair_scan_results(self, result): + results = [] + + return results + def process_rqtl_results(self, result): # TODO: how to make this a one liner and not copy the stuff in a loop qtl_results = [] |