def undump_eigen(self): """ undumps self.adj_eigenvals and self.laplacian_matrix """ self.adj_eigenvals, self.adj_eigenvects = undump_object( Dumps.val_eigen) self.cond_eigenvals, self.cond_eigenvects = undump_object( Dumps.cond_eigen)
def undump_matrices(self): """ undumps self.adjacency_Matrix and self.laplacian_matrix """ self.adjacency_Matrix = undump_object( Dumps.interactome_adjacency_matrix) self.laplacian_matrix = undump_object( Dumps.interactome_laplacian_matrix)
def setUpClass(cls): parser_object = UniProtParser(['199310', '405955']) cls.uniprot_dict = parser_object.parse_uniprot(cls.up_to_parse) cls.acces_dict = parser_object.get_access_dicts() # dump_object(cls.ref_parses, (cls.uniprot_dict, cls.acces_dict)) cls.ref_uniprot_dict, cls.ref_acces_dict = undump_object( cls.ref_parses)
def setUpClass(cls): cls.actual_parser = ReactomeParser(cls.reactome_to_parse) cls.actual_parser.parse_all() # print cls.actual_parser.parsed # dump_object(cls.ref_parse, cls.actual_parser) cls.ref_parser = undump_object(cls.ref_parse) # to parse cls.maxDiff = None
def setUpClass(cls): cls.actual_parser = ReactomeParser(cls.reactome_to_parse) cls.actual_parser.parse_all() # print cls.actual_parser.parsed # dump_object(cls.ref_parse, cls.actual_parser) cls.ref_parser = undump_object(cls.ref_parse) # to parse cls.maxDiff = None
def undump_maps(self): """ undumps all the elements required for the mapping between the types and ids of database entries and matrix columns """ log.debug("undumping from %s", Dumps.interactome_maps) self.bulbs_id_2_matrix_index, self.matrix_index_2_bulbs_id, \ self.bulbs_id_2_display_name, self.bulbs_id_2_legacy_id, self.bulbs_id2_node_type, \ self.bulbs_id_2_localization, self.reached_uniprots_bulbs_id_list,\ self.all_uniprots_bulbs_id_list, self.Uniprot_attachments, self.UP2Chrom, \ self.chromosomes_2_uniprot, self.uniprot_matrix_index_list,\ self.entry_point_uniprots_bulbs_ids = \ undump_object(Dumps.interactome_maps) log.debug("post-undump e_p_u_b_i length: %s", len(self.entry_point_uniprots_bulbs_ids))
def auto_analyze(source=None, go_interface_instance=None, processors=3, desired_depth=24, skip_sampling=False, param_set=ref_param_set): """ Automatically analyzes the GO annotation of the RNA_seq results. :param source: :param go_interface_instance: :param processors: :param desired_depth: :param skip_sampling: uses existing mongoDB content without spawning a sampler :param param_set: """ if source is None: dumplist = undump_object(Dumps.RNA_seq_counts_compare) else: dumplist = source if desired_depth % processors != 0: desired_depth = desired_depth / processors + 1 else: desired_depth = desired_depth / processors # noinspection PyTypeChecker for my_list in dumplist: if go_interface_instance is None: go_interface_instance = get_go_interface_instance(param_set) go_interface_instance.set_uniprot_source(my_list) if not skip_sampling: log.info("spawning a sampler for %s proteins @ %s compops/sec", len(go_interface_instance.analytic_uniprots), estimated_comp_ops) # TODO: restructure to spawn a sampler pool that does not share an object in the Threading if len(go_interface_instance.analytic_uniprots) < 200: if not skip_sampling: log.info('length: %s \t sampling depth: %s \t, estimated round time: %s min', len(go_interface_instance.analytic_uniprots), 'full', len(go_interface_instance.analytic_uniprots)**2 / estimated_comp_ops / 60) spawn_sampler_pool(processors, [len(go_interface_instance.analytic_uniprots)], [desired_depth], go_interface_instance=None, param_set=param_set) go_interface_instance.build_extended_conduction_system() nr_nodes, nr_groups = compare_to_blank( len(go_interface_instance.analytic_uniprots), [1100, 1300], p_val=0.9, go_interface_instance=go_interface_instance, param_set=param_set) else: sampling_depth = max(200 ** 2 / len(go_interface_instance.analytic_uniprots), 5) if not skip_sampling: log.info('length: %s \t sampling depth: %s \t, estimated round time: %s min', len(go_interface_instance.analytic_uniprots), sampling_depth, len(go_interface_instance.analytic_uniprots) * sampling_depth / 2 / 60) spawn_sampler_pool(processors, [len(go_interface_instance.analytic_uniprots)], [desired_depth], sparse_rounds=sampling_depth, go_interface_instance=None, param_set=param_set) go_interface_instance.build_extended_conduction_system(sparse_samples=sampling_depth) # go_interface_instance.export_conduction_system() nr_nodes, nr_groups = compare_to_blank( len(go_interface_instance.analytic_uniprots), [1100, 1300], p_val=0.9, sparse_rounds=sampling_depth, go_interface_instance=go_interface_instance, param_set=param_set) go_interface_instance.export_conduction_system() for group in nr_groups: log.info(group) log.info('\t NodeID \t Name \t current \t informativity \t confusion_potential \t p_val \t ' 'UP_list') for node in nr_nodes: log.info('\t %s \t %s \t %s \t %s \t %s \t %s \t %s', *node)
def undump_independent_linear_sets(self): self.Indep_Lapl = undump_object(Dumps.GO_Indep_Linset)
def undump_memoized(): """ :return: undumped memoized analysis """ return undump_object(Dumps.GO_Analysis_memoized)
def setUpClass(cls): parser_object = UniProtParser(['199310', '405955']) cls.uniprot_dict = parser_object.parse_uniprot(cls.up_to_parse) cls.acces_dict = parser_object.get_access_dicts() # dump_object(cls.ref_parses, (cls.uniprot_dict, cls.acces_dict)) cls.ref_uniprot_dict, cls.ref_acces_dict = undump_object(cls.ref_parses)
def undump_independent_linear_sets(self): self.Indep_Lapl = undump_object(Dumps.GO_Indep_Linset)
def undump_inflated_elements(self): self.inflated_Laplacian, self.inflated_idx2lbl, \ self.inflated_lbl2idx, self.binding_intensity = \ undump_object(Dumps.GO_Inflated)
def undump_matrices(self): self.adjacency_matrix, self.dir_adj_matrix, self.laplacian_matrix = undump_object( Dumps.GO_Mats)
def undump_statics(): return undump_object(Dumps.GO_builder_stat)
def undump_memoized(): """ undumps memoized analysis """ return undump_object(Dumps.Interactome_Analysis_memoized)
def undump_statics(): return undump_object(Dumps.GO_builder_stat)
def undump_core(self): self.UP2GO_Dict, self.GO2UP, self.SeedSet, self.Reachable_nodes_dict,\ self.GO_Names, self.GO_Legacy_IDs, self.rev_GO_IDs, self.All_GOs,\ self.GO2Num, self.Num2GO, self.UP_Names, self.UPs_without_GO =\ undump_object(Dumps.GO_dump)
def undump_core(self): self.UP2GO_Dict, self.GO2UP, self.SeedSet, self.Reachable_nodes_dict,\ self.GO_Names, self.GO_Legacy_IDs, self.rev_GO_IDs, self.All_GOs,\ self.GO2Num, self.Num2GO, self.UP_Names, self.UPs_without_GO =\ undump_object(Dumps.GO_dump)
def undump_informativities(self): self.UP2GO_Reachable_nodes, self.GO2UP_Reachable_nodes, self.UP2GO_step_Reachable_nodes, \ self.GO2UP_step_Reachable_nodes, self.GO2_Pure_Inf, self.GO2_Weighted_Ent = \ undump_object(Dumps.GO_Infos)
def undump_matrices(self): self.adjacency_matrix, self.dir_adj_matrix, self.laplacian_matrix = undump_object( Dumps.GO_Mats)
def undump_memoized(): """ :return: undumped memoized analysis """ return undump_object(Dumps.GO_Analysis_memoized)
def undump_informativities(self): self.UP2GO_Reachable_nodes, self.GO2UP_Reachable_nodes, self.UP2GO_step_Reachable_nodes, \ self.GO2UP_step_Reachable_nodes, self.GO2_Pure_Inf, self.GO2_Weighted_Ent = \ undump_object(Dumps.GO_Infos)
def auto_analyze(source=None, go_interface_instance=None, processors=3, desired_depth=24, skip_sampling=False, param_set=ref_param_set): """ Automatically analyzes the GO annotation of the RNA_seq results. :param source: :param go_interface_instance: :param processors: :param desired_depth: :param skip_sampling: uses existing mongoDB content without spawning a sampler :param param_set: """ if source is None: dumplist = undump_object(Dumps.RNA_seq_counts_compare) else: dumplist = source if desired_depth % processors != 0: desired_depth = desired_depth / processors + 1 else: desired_depth = desired_depth / processors # noinspection PyTypeChecker for my_list in dumplist: if go_interface_instance is None: go_interface_instance = get_go_interface_instance(param_set) go_interface_instance.set_uniprot_source(my_list) if not skip_sampling: log.info("spawning a sampler for %s proteins @ %s compops/sec", len(go_interface_instance.analytic_uniprots), estimated_comp_ops) # TODO: restructure to spawn a sampler pool that does not share an object in the Threading if len(go_interface_instance.analytic_uniprots) < 200: if not skip_sampling: log.info( 'length: %s \t sampling depth: %s \t, estimated round time: %s min', len(go_interface_instance.analytic_uniprots), 'full', len(go_interface_instance.analytic_uniprots)**2 / estimated_comp_ops / 60) spawn_sampler_pool( processors, [len(go_interface_instance.analytic_uniprots)], [desired_depth], go_interface_instance=None) go_interface_instance.build_extended_conduction_system() nr_nodes, nr_groups = compare_to_blank( len(go_interface_instance.analytic_uniprots), [1100, 1300], p_val=0.9, go_interface_instance=go_interface_instance, param_set=param_set) else: sampling_depth = max( 200**2 / len(go_interface_instance.analytic_uniprots), 5) if not skip_sampling: log.info( 'length: %s \t sampling depth: %s \t, estimated round time: %s min', len(go_interface_instance.analytic_uniprots), sampling_depth, len(go_interface_instance.analytic_uniprots) * sampling_depth / 2 / 6 / 60) spawn_sampler_pool( processors, [len(go_interface_instance.analytic_uniprots)], [desired_depth], sparse_rounds=sampling_depth, go_interface_instance=None) go_interface_instance.build_extended_conduction_system( sparse_samples=sampling_depth) # go_interface_instance.export_conduction_system() nr_nodes, nr_groups = compare_to_blank( len(go_interface_instance.analytic_uniprots), [1100, 1300], p_val=0.9, sparse_rounds=sampling_depth, go_interface_instance=go_interface_instance, param_set=param_set) go_interface_instance.export_conduction_system() for group in nr_groups: log.info(group) log.info( '\t NodeID \t Name \t current \t informativity \t confusion_potential \t p_val \t ' 'UP_list') for node in nr_nodes: log.info('\t %s \t %s \t %s \t %s \t %s \t %s \t %s', *node)
def undump_inflated_elements(self): self.inflated_Laplacian, self.inflated_idx2lbl, \ self.inflated_lbl2idx, self.binding_intensity = \ undump_object(Dumps.GO_Inflated)