diff options
| -rw-r--r-- | wqflask/wqflask/auwerx/ephewas_analysis.py | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/wqflask/wqflask/auwerx/ephewas_analysis.py b/wqflask/wqflask/auwerx/ephewas_analysis.py index edfb2801..2f6d6061 100644 --- a/wqflask/wqflask/auwerx/ephewas_analysis.py +++ b/wqflask/wqflask/auwerx/ephewas_analysis.py @@ -24,13 +24,56 @@ from utility.tools import locate from rpy2.robjects.packages import importr utils = importr("utils") +r_library = ro.r["library"] # Map the library function +r_options = ro.r["options"] # Map the options function +r_write_table = ro.r["write.table"] # Map the write.table function +r_head = ro.r["head"] # Map the head function +r_load = ro.r["load"] # Map the head function +r_colnames = ro.r["colnames"] # Map the colnames function +r_list = ro.r["list"] # Map the list function +r_c = ro.r["c"] # Map the c (combine) function +r_print = ro.r["print"] # Map the print function +r_seq = ro.r["seq"] # Map the rep (repeat) function + class EPheWAS(object): def __init__(self): print("Initialization of ePheWAS") + print(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_data_gatherer = ro.r["data.gatherer"] # Map the data.gatherer function print("Initialization of ePheWAS done !") def run_analysis(self, requestform): print("Starting ePheWAS analysis on dataset") + genofilelocation = locate("BXD.geno", "genotype") # Get the location of the BXD genotypes + tissuealignerloc = locate("Tissue_color_aligner.csv", "auwerx") # Get the location of the Tissue_color_aligner + + # Get user parameters, trait_id and dataset, and store/update them in self + self.trait_id = requestform["trait_id"] + self.datasetname = requestform["dataset"] + self.dataset = data_set.create_dataset(self.datasetname) + + # 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" + + # Load in the genotypes file *sigh* to make the markermap + parser = genofile_parser.ConvertGenoFile(genofilelocation) + parser.process_csv() + snpinfo = [] + for marker in parser.markers: + snpinfo.append(marker["name"]); + snpinfo.append(marker["chr"]); + snpinfo.append(marker["Mb"]); + + rnames = r_seq(1, len(parser.markers)) + # Create the snp aligner object out of the BXD genotypes + snpaligner = ro.r.matrix(snpinfo, nrow=len(parser.markers), dimnames = r_list(rnames, r_c("SNP", "Chr", "Pos")), ncol = 3, byrow=True) + + # Create the phenotype aligner object using R + phenoaligner = self.r_create_Pheno_aligner() + print("Initialization of ePheWAS done !") def process_results(self, results): |