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)
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
objNwGE.map_network_to_gene_expression()