Example #1
0
 def copyinputs(self, copier):
     if not self.num_pcs == 0:
         for i in xrange(self.chrom_count):
             pc_fn = PrecomputeLocoPcs.create_out_fn(self.pc_prefix, i)
             copier.input(pc_fn)
     copier.input(self.pheno_fn)
     copier.input(self.snp_reader)
Example #2
0
 def copyinputs(self, copier):
     if not self.num_pcs == 0:
         for i in xrange(self.chrom_count):
             pc_fn = PrecomputeLocoPcs.create_out_fn(self.pc_prefix, i)
             copier.input(pc_fn)
     copier.input(self.pheno_fn)
     copier.input(self.snp_reader)
Example #3
0
    def dowork(self, i, train_snp_idx, test_snp_idx, result, G, y):
        logging.info("{0}, {1}".format(len(train_snp_idx), len(test_snp_idx)))

        # intersect selected SNPs with train snps
        if not self.selected_snps is None:
            # intersect snp names
            logging.info("intersecting train snps with selected snps for LOCO")
            int_snp_idx = argintersect_left(self.snp_reader.rs[train_snp_idx],
                                            self.selected_snps)
            sim_keeper_idx = np.array(train_snp_idx)[int_snp_idx]

        else:
            sim_keeper_idx = train_snp_idx

        # subset data

        # fast indexing (needs to be C-order)
        assert np.isfortran(G) == False
        #G_train = G.take(train_snp_idx, axis=1)
        G_sim = G.take(sim_keeper_idx, axis=1)
        G_test = G.take(test_snp_idx, axis=1)

        t0 = time.time()

        if self.num_pcs == 0:
            pcs = None
        else:
            if not self.pc_prefix is None:
                out_fn = PrecomputeLocoPcs.create_out_fn(self.pc_prefix, i)
                logging.info("loading pc from file: %s" % out_fn)
                pcs = load(out_fn)[:, 0:self.num_pcs]
                logging.info("..done")

            else:
                assert False, "please precompute PCs"

                logging.info("done after %.4f seconds" % (time.time() - t0))

        # only use PCs
        if self.pcs_only:
            G_sim = None
            logging.info("Using PCs only in LocoGWAS")
        gwas = FastGwas(G_sim,
                        G_test,
                        y,
                        self.delta,
                        train_pcs=pcs,
                        mixing=self.mixing)
        gwas.run_gwas()

        assert len(gwas.p_values) == len(test_snp_idx)

        # wrap up results
        return test_snp_idx, gwas.p_values, result
Example #4
0
    def dowork(self, i, train_snp_idx, test_snp_idx, result, G, y):
        logging.info("{0}, {1}".format(len(train_snp_idx), len(test_snp_idx)))
        
        # intersect selected SNPs with train snps
        if not self.selected_snps is None:
            # intersect snp names
            logging.info("intersecting train snps with selected snps for LOCO")
            int_snp_idx = argintersect_left(self.snp_reader.rs[train_snp_idx], self.selected_snps)
            sim_keeper_idx = np.array(train_snp_idx)[int_snp_idx]

        else:
            sim_keeper_idx = train_snp_idx

        # subset data
            
        # fast indexing (needs to be C-order)
        assert np.isfortran(G) == False
        #G_train = G.take(train_snp_idx, axis=1)
        G_sim = G.take(sim_keeper_idx, axis=1)
        G_test = G.take(test_snp_idx, axis=1)

        t0 = time.time()

        if self.num_pcs == 0:
            pcs = None
        else:
            if not self.pc_prefix is None:
                out_fn = PrecomputeLocoPcs.create_out_fn(self.pc_prefix, i)
                logging.info("loading pc from file: %s" % out_fn)
                pcs = load(out_fn)[:,0:self.num_pcs]
                logging.info("..done")

            else:
                assert False, "please precompute PCs"

                logging.info("done after %.4f seconds" % (time.time() - t0))

        # only use PCs
        if self.pcs_only:
            G_sim = None
            logging.info("Using PCs only in LocoGWAS")
        gwas = FastGwas(G_sim, G_test, y, self.delta, train_pcs=pcs, mixing=self.mixing)
        gwas.run_gwas()

        assert len(gwas.p_values) == len(test_snp_idx)

        # wrap up results
        return test_snp_idx, gwas.p_values, result