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')
