Starting integration of the ePheWas tool

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):