def run_scr2(lamP, lamR, lamS, outf, subi, subt): #(ba,tf, genes, tfs) = load_bacteria('B_subtilis.csv','tfNames.txt',range(250)) (ba,tf, genes, tfs) = load_B_anthracis(subi, subt) (BC_priors, sign) = ([], []) #(BC_priors, sign) = load_priors('gsSDnamesWithActivitySign082213','B_subtilis') orth = [] print ba.shape organisms = ['B_subtilis'] gene_ls = [genes] tf_ls = [tfs] Xs = [tf] Ys = [ba] priors = BC_priors Bs = fl.solve_ortho_direct(organisms, gene_ls, tf_ls, Xs, Ys, orth, priors, lamP, lamR, lamS) Bs_str_l = [] Bs_str_l.append('\t'.join(tfs)) for gi in range(len(genes)): gene = genes[gi] regulators = Bs[0][:, gi] Bs_str_l.append(gene +'\t'+ '\t'.join(map(str, regulators))) f = file(outf, 'w') f.write('\n'.join(Bs_str_l)) f.close()
def run_both_adjust(lamP, lamR, lamS, outf, sub_s, sub_i, sub_t): (bs_e, bs_t , bs_genes, bs_tfs) = load_B_subtilis(sub_s) (BS_priors, sign) = load_priors('gsSDnamesWithActivitySign082213','B_subtilis') (ba_e, ba_t, ba_genes, ba_tfs) = load_B_anthracis(sub_i, sub_t) (BA_priors, sign) = ([], []) Xs = [bs_t, ba_t] Ys = [bs_e, ba_e] priors = BS_priors + BA_priors orth = load_orth('bs_ba_ortho_804',['B_anthracis','B_subtilis']) #orth = load_orth('',['B_subtilis']) organisms = ['B_subtilis','B_anthracis'] #ortht = random_orth(bs_tfs, ba_tfs, organisms, 250) #orthg = random_orth(bs_genes, ba_genes, organisms, 2500) #orth = ortht+orthg #print orth #return gene_ls = [bs_genes, ba_genes] tf_ls = [bs_tfs, ba_tfs] Bs = fl.solve_ortho_direct(organisms, gene_ls, tf_ls, Xs, Ys, orth, priors, 'yes', lamP, lamR, lamS) write_bs(bs_genes, bs_tfs, Bs[0], outf+'_subtilis') write_bs(ba_genes, ba_tfs, Bs[1], outf+'_anthracis')