def test_map_sequence_to_gene_expression_chry(self): gene_expression_manager = GeneExpressionManager() gene_expression_manager.load_gene_expression_data() # retrieve first row as expected row expected_row = gene_expression_manager.iso_gene_expression_data[1][None, :] # pass expected row sequence no to function sequence_no = expected_row[0][0] result_row = gene_expression_manager.map_sequence_to_gene_expression(sequence_no) self.assertEqual(expected_row.tolist(), result_row.tolist())
def test_load_gene_expression_data_ehux(self): gene_expression_manager = GeneExpressionManager() gene_expression_manager.load_gene_expression_data() ehux_result_count = len(gene_expression_manager.ehux_gene_expression_data) expected_count = 24203 self.assertEqual(ehux_result_count, expected_count)
def test_load_gene_expression_data_for_geph(self): gene_expression_manager = GeneExpressionManager() gene_expression_manager.load_gene_expression_data() geph_result_count = len(gene_expression_manager.geph_gene_expression_data) expected_count = 24552 self.assertEqual(geph_result_count, expected_count)
def test_load_gene_expression_data_for_iso(self): gene_expression_manager = GeneExpressionManager() gene_expression_manager.load_gene_expression_data() iso_result_count = len(gene_expression_manager.iso_gene_expression_data) expected_count = 14703 self.assertEqual(iso_result_count, expected_count)
xerr=chart3_geph9mmsd, yerr=chart3_gephspikesd, linestyle='None', fmt='s', label="Geph") ax1.legend() if len(self.network_geph_gene_expression) > 0: ax3.errorbar(self.network_iso_gene_expression[:, 1], self.network_iso_gene_expression[:, 4], xerr=self.network_iso_gene_expression[:, 3], yerr=self.network_iso_gene_expression[:, 6], linestyle='None', fmt='o', label="Iso") ax3.legend() fig.subplots_adjust(hspace=0) # show all plots plt.show() if __name__ == "__main__": # Instantiate Gene Expression Manager object gene_expression_manager = GeneExpressionManager() # LOAD Gene Expression data gene_expression_manager.load_gene_expression_data() # Create Object of Class objNwGE = SilixNetworkGeneExpression(gene_expression_manager) # Provide Network File path and output folder path objNwGE.silix_nw_file_path = "../data/additiona_analysis/hapto_networks_components.txt" objNwGE.output_silix_nw_exp_data_folder_path = "../output/hapto_networks/gene_expr/" #objNwGE.silix_nw_file_path = "../output/silix/more_than_six_nodes/node_data_geph_ehux.txt" #objNwGE.output_silix_nw_exp_data_folder_path = "../output/silix_more_than_six_nodes/gene_expr/" # LOAD Network Cluster data objNwGE.load_network_data() # MAP Network sequences to gene expression sequences