示例#1
0
文件: netsvd.py 项目: bh0085/compbio
def net_ggsvd(name=nu.default_name, reset=0):
    hardcopy = False
    try:
        if reset:
            raise Exception("compute")
        return nw.readnet(name, hardcopy=hardcopy)

    except Exception as e:
        if e.args[0] != "compute":
            raise Exception()
        nw.claim_reset()
        ggn = nu.net_genegene_norm(reset=mod(reset, 2))

        U, S, Vh = lin.svd(ggn)
        V = Vh.T
        dosave = (U, S, V)
        nw.writenet(name, dosave, hardcopy=hardcopy)

        print """
Ran ggsvd.

No hardcopies have been saved yet"""
        if reset:
            net_ggsvd_U(reset=2)
            net_ggsvd_V(reset=2)
            net_ggsvd_S(reset=2)
            print """
...saved hardcopies of U,S,V
"""
        return dosave
示例#2
0
文件: netsvd.py 项目: bh0085/compbio
def net_square_svd(name=nu.default_name, reset=0):
    hardcopy = False
    try:
        if reset:
            raise Exception("compute")
        return nw.readnet(name, hardcopy=hardcopy)

    except Exception as e:
        if e.args[0] != "compute":
            raise Exception()
        nw.claim_reset()
        sqa = nu.net_square_affinity(reset=mod(reset, 2))

        U, S, Vh = lin.svd(sqa)
        V = Vh.T
        uvecs = U[:, : len(S)]
        vvecs = V
        dosave = (sqa[1], (uvecs, S, vvecs))
        nw.writenet(name, dosave, hardcopy=hardcopy)
        print """
Ran net square svd for the current values.

Nothing has yet been saved to HD.

"""
        if reset:
            net_square_svd_U(reset=2)
            net_square_svd_V(reset=2)
            net_square_svd_S(reset=2)

            print """
...saved hardcopies of U,S,V
"""
        return dosave
示例#3
0
def get_net(name = 'unsup' , reset = 0):
    hardcopy = True

    try:
        if reset: raise Exception('compute')
        return nw.readnet(name, hardcopy = hardcopy)
    except Exception, e:
        if e.args[0] != 'compute': raise Exception()
        nw.claim_reset()
        net = parse_name(name)
        nw.writenet(name, net, hardcopy = hardcopy)
        return net
示例#4
0
def net_cluster_ggsvdV(k = k,reset = 0):
    hardcopy = True
    try:
        if reset: raise Exception('compute')
        out,sxs =  nw.rn2(name, hardcopy = hardcopy)
        if not sxs: raise Exception()

    except Exception as e:
        if e.args[0] != 'compute': raise Exception()
        nw.claim_reset()
        gg = ns.net_ggsvd_V().T
        kmeans = mlpy.Kmeans(k)
        clustered = kmeans.compute(gg[0:maxgenes,:])
        means = kmeans.means
        nw.wn2(name, (clustered, means) ,hardcopy = hardcopy) 
    return out
示例#5
0
def net_cluster_genes_by_tf(k= k, reset = 0):
    hardcopy = True
    try:
        if reset: raise Exception('compute')
        out,sxs =  nw.rn2(name, hardcopy = hardcopy)
        if not sxs: raise Exception()

    except Exception as e:
        if e.args[0] != 'compute': raise Exception()
        nw.claim_reset()    
        gg = nu.net_affinity(reset = mod(reset,2))
        kmeans = mlpy.Kmeans(k)
        clustered = kmeans.compute(gg[0:maxgenes,:])
        means = kmeans.means
        out = (clustered,means)
        nw.wn2(name, (clustered, means) ,hardcopy = hardcopy) 
    return out
示例#6
0
文件: netsvd.py 项目: bh0085/compbio
def net_svd(name=nu.default_name, reset=0):
    hardcopy = True
    try:
        if reset:
            raise Exception("compute")
        return nw.readnet(name=nu.default_name, hardcopy=hardcopy)
    except Exception as e:
        if e.args[0] != "compute":
            raise Exception()
        nw.claim_reset()
        a = nu.net_affinity(reset=mod(reset, 2))[0]
        N = a[0]
        U, S, Vh = lin.svd(N)
        V = Vh.T
        U = U[:, len(S)]
        dosave = (a[1], (U, S, V))
        nw.writenet(name, dosave, hardcopy=hardcopy)
        return dosave