gennet_launch_Gene_networks_RefGene.py

import os
os.chdir("/data/public/GenNet")
import sys
import glob
import numpy as np
import pandas as pd
#sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import matplotlib
matplotlib.use('agg')
import tensorflow as tf
import tensorflow.keras as K
import scipy
import tables

tf.keras.backend.set_epsilon(0.0000001)
tf_version = tf.__version__  # ToDo use packaging.version
if tf_version <= '1.13.1':
    from GenNet_utils.LocallyDirectedConnected import LocallyDirected1D
    print('= or less then 1.13.1: tensorflow version is', tf_version)
elif tf_version >= '2.0':
    from GenNet_utils.LocallyDirectedConnected_tf2 import LocallyDirected1D
    print('= or more then 2.0: tensorflow version is', tf_version)
else:
    print("unexpected tensorflow version")
    from GenNet_utils.LocallyDirectedConnected_tf2 import LocallyDirected1D

studyname = 'test_GN_ref'

def layer_block(model, mask, i, regression):
    
    if regression:
        activation_type="relu"
    else:
        activation_type="tanh"
    
    model = LocallyDirected1D(mask=mask, filters=1, input_shape=(mask.shape[0], 1),
                              name="LocallyDirected_" + str(i))(model)
    model = K.layers.Flatten()(model)

    model = K.layers.Activation(activation_type)(model)
    model = K.layers.BatchNormalization(center=False, scale=False)(model)
    return model


def add_covariates(model, input_cov, num_covariates, regression, negative_values_ytrain, mean_ytrain):
    if num_covariates > 0:
        model = activation_layer(model, regression, negative_values_ytrain)
        model = K.layers.concatenate([model, input_cov], axis=1)
        model = K.layers.BatchNormalization(center=False, scale=False)(model)
        model = K.layers.Dense(units=1, bias_initializer= tf.keras.initializers.Constant(mean_ytrain))(model)
    return model


def activation_layer(model, regression, negative_values_ytrain):
   
    if regression: 
        if negative_values_ytrain:
            model = K.layers.Activation("linear")(model)
            print('using a linear activation function')
        else:
            model = K.layers.Activation("relu")(model)
            print('using a relu activation function')
    else:
        model = K.layers.Activation("sigmoid")(model)
        
    return model

def create_network_from_npz(datapath,
                            inputsize,
                            genotype_path,
                            l1_value=0.01,
                            regression=False,
                            num_covariates=0,
                            mask_order = []):
    print("Creating networks from npz masks")
    print("regression", regression)
    if regression:
        mean_ytrain, negative_values_ytrain = regression_properties(datapath)
    else:
        mean_ytrain = 0
        negative_values_ytrain = False

    masks = []
    mask_shapes_x = []
    mask_shapes_y = []

    print(mask_order)

    if len(mask_order) > 0:  # if mask_order is defined we use this order
        for mask in mask_order:
            mask = scipy.sparse.load_npz(datapath + '/'+str(mask)+'.npz')
            masks.append(mask)
            mask_shapes_x.append(mask.shape[0])
            mask_shapes_y.append(mask.shape[1])

        for x in range(len(masks) - 1):  # check that the masks fit eachother
            assert mask_shapes_y[x] == mask_shapes_x[x + 1]
    else:
        # if mask order is not defined we can sort the mask by the size
        for npz_path in glob.glob(datapath + '/*.npz'):
            mask = scipy.sparse.load_npz(npz_path)
            masks.append(mask)
            mask_shapes_x.append(mask.shape[0])
            mask_shapes_y.append(mask.shape[1])

        for i in range(len(masks)):  # sort all the masks in the correct order
            argsort_x = np.argsort(mask_shapes_x)[::-1]
            argsort_y = np.argsort(mask_shapes_y)[::-1]

            mask_shapes_x = np.array(mask_shapes_x)
            mask_shapes_y = np.array(mask_shapes_y)
            assert all(argsort_x == argsort_y)  # check that both dimensions have the same order

            masks = [masks[i] for i in argsort_y]  # sort masks
            mask_shapes_x = mask_shapes_x[argsort_x]
            mask_shapes_y = mask_shapes_y[argsort_y]

            for x in range(len(masks) - 1):  # check that the masks fit eachother
                assert mask_shapes_y[x] == mask_shapes_x[x + 1]
    print('mask_shapes_x[0]', mask_shapes_x[0])
    assert mask_shapes_x[0] == inputsize
    print('mask_shapes_y[-1]', mask_shapes_y[-1])
    if mask_shapes_y[-1] == 1:  # should we end with a dense layer?
        all_masks_available = True
    else:
        all_masks_available = False

    input_layer = K.Input((inputsize,), name='input_layer')
    input_cov = K.Input((num_covariates,), name='inputs_cov')

    model = K.layers.Reshape(input_shape=(inputsize,), target_shape=(inputsize, 1))(input_layer)
    
    for i in range(len(masks)):
        mask = masks[i]
        model = layer_block(model, mask, i, regression)

    model = K.layers.Flatten()(model)

    if all_masks_available:
        model = LocallyDirected1D(mask=masks[-1], filters=1, input_shape=(mask.shape[0], 1),
                                  name="output_layer")(model)
    else:
        model = K.layers.Dense(units=1, name="output_layer",
                               kernel_regularizer=tf.keras.regularizers.l1(l=l1_value)
                               )(model)

    model = add_covariates(model, input_cov, num_covariates, regression, negative_values_ytrain, mean_ytrain)

    output_layer = activation_layer(model, regression, negative_values_ytrain)
    model = K.Model(inputs=[input_layer, input_cov], outputs=output_layer)

    print(model.summary())

    return model, masks

def get_testdata(datapath):
    # ytest = pd.read_csv(datapath + "ytest_"+studyname+".csv")
    h5file = tables.open_file(datapath  + studyname + '_genotype_processed.h5', "r")
    # ybatch = ytest["labels"]
    # xbatchid = np.array(ytest["tot_index"].values, dtype=np.int64)
    xbatch = h5file.root.data[:]
    # ybatch = np.reshape(np.array(ybatch), (-1, 1))
    h5file.close()
    return xbatch

def predict():
    xtest = get_testdata(datapath)
    pred = model.predict(xtest)
    print('model prediction: ', pred)

datapath = '/data/public/GenNet/processed_data/'
inputsize = 6986636
num_covariates = 0
genotype_path = datapath
l1_value = 0.001
model, masks = create_network_from_npz(datapath=datapath, inputsize=inputsize, genotype_path=genotype_path,mask_order=['UKBB_sparse_connection_mask_refseq_alligned'],
                                               l1_value=l1_value, regression=False, num_covariates=num_covariates,)
model.load_weights(datapath + 'bestweight_job_diabetes.h5')
print('weights have been loaded')
predict()