def test_map_sequence_to_gene_annotation_iso(self): gene_annotation_manager = GeneAnnotationManager() gene_annotation_manager.load_gene_annotation_data() expected_row = gene_annotation_manager.iso_gene_annotation_data[1] expected_row = re.split(r'\t+', expected_row.rstrip('\t')) sequence_no = expected_row[0] expected_annotation_desc = expected_row[1] result_row = gene_annotation_manager.map_sequence_to_gene_annotation(sequence_no) self.assertEqual(expected_annotation_desc, result_row[1])
def test_load_gene_annotation_data_ehux(self): gene_annotation_manager = GeneAnnotationManager() gene_annotation_manager.load_gene_annotation_data() ehux_result_count = len(gene_annotation_manager.ehux_gene_annotation_data) expected_count = 30448 self.assertEqual(ehux_result_count, expected_count)
def test_load_gene_annotation_data_geph(self): gene_annotation_manager = GeneAnnotationManager() gene_annotation_manager.load_gene_annotation_data() geph_result_count = len(gene_annotation_manager.geph_gene_annotation_data) expected_count = 52679 self.assertEqual(geph_result_count, expected_count)
def test_load_gene_annotation_data_iso(self): gene_annotation_manager = GeneAnnotationManager() gene_annotation_manager.load_gene_annotation_data() iso_result_count = len(gene_annotation_manager.iso_gene_annotation_data) expected_count = 18712 self.assertEqual(iso_result_count, expected_count)
f_handle.write( str(v) + ',' + self.get_species_name(str(v)) + str( [value for value in self.blast_graph.node[v].itervalues()]).strip( '[]') + ',') f_handle.write( str(edata['evalue']) + ',' + str(edata['identpct']) + ',' + str(edata['mismatchno']) + ',' + str(edata['aln']) + ',' + str(edata['alnspn']) + ',' + str(edata['gapopenno']) + ',' + str(edata['bitscore']) + '\n') # if self.generate_gml_files: # file_name = "{}/blast_graph.gml".format(self.blast_output_path) # with open(file_name, "a") as f_handle: # nx.write_gml(self.blast_graph, f_handle) if __name__ == "__main__": # Instantiate Gene Expression Manager object gene_expression_manager = GeneExpressionManager() gene_expression_manager.load_gene_expression_data() # Instantiate Gene Annotation Manager object gene_annotation_manager = GeneAnnotationManager() gene_annotation_manager.load_gene_annotation_data() # Filter By Target sequences target_sequences = np.genfromtxt("../data/protein_sequence_files/elong.txt", delimiter='\n', dtype=str) print target_sequences print 'Total Target Sequences:', target_sequences.shape similarity_networks = SimilarityNetworks(gene_expression_manager, gene_annotation_manager, evalue=1e-05, by_sequence=target_sequences) similarity_networks.output_file_identifier = "_elong_for_all_blast_data" similarity_networks.generate_blast_data() similarity_networks.write_blast_graph_file()