def process_pc_neighborhood(gene_names, neighbor_limit=1): """Returns a BiopaxProcessor for a PathwayCommons neighborhood query. The neighborhood query finds the neighborhood around a set of source genes. http://www.pathwaycommons.org/pc2/#graph http://www.pathwaycommons.org/pc2/#graph_kind Parameters ---------- gene_names : list A list of HGNC gene symbols to search the neighborhood of. Examples: ['BRAF'], ['BRAF', 'MAP2K1'] neighbor_limit : Optional[int] The number of steps to limit the size of the neighborhood around the gene names being queried. Default: 1 Returns ------- bp : BiopaxProcessor A BiopaxProcessor containing the obtained BioPAX model in bp.model. Notes ----- As returned from this function, bp.statements is empty and one has to call methods of bp (e.g. bp.get_complexes()) to populate bp.statements. """ model = pcc.graph_query('neighborhood', gene_names, neighbor_limit=neighbor_limit) if model is not None: return process_model(model)
def process_pc_pathsbetween(gene_names, neighbor_limit=1): """Returns a BiopaxProcessor for a PathwayCommons paths-between query. The paths-between query finds the paths between a set of genes. Here source gene names are given in a single list and all directions of paths between these genes are considered. http://www.pathwaycommons.org/pc2/#graph http://www.pathwaycommons.org/pc2/#graph_kind Parameters ---------- gene_names : list A list of HGNC gene symbols to search for paths between. Examples: ['BRAF', 'MAP2K1'] neighbor_limit : Optional[int] The number of steps to limit the length of the paths between the gene names being queried. Default: 1 Returns ------- bp : BiopaxProcessor A BiopaxProcessor containing the obtained BioPAX model in bp.model. Notes ----- As returned from this function, bp.statements is empty and one has to call methods of bp (e.g. bp.get_complexes()) to populate bp.statements. """ model = pcc.graph_query('pathsbetween', gene_names, neighbor_limit=neighbor_limit) if model is not None: return process_model(model)
def process_pc_pathsfromto(source_genes, target_genes, neighbor_limit=1): """Returns a BiopaxProcessor for a PathwayCommons paths-from-to query. The paths-from-to query finds the paths from a set of source genes to a set of target genes. http://www.pathwaycommons.org/pc2/#graph http://www.pathwaycommons.org/pc2/#graph_kind Parameters ---------- source_genes : list A list of HGNC gene symbols that are the sources of paths being searched for. Examples: ['BRAF', 'RAF1', 'ARAF'] target_genes : list A list of HGNC gene symbols that are the targets of paths being searched for. Examples: ['MAP2K1', 'MAP2K2'] neighbor_limit : Optional[int] The number of steps to limit the length of the paths between the source genes and target genes being queried. Default: 1 Returns ------- bp : BiopaxProcessor A BiopaxProcessor containing the obtained BioPAX model in bp.model. """ model = pcc.graph_query('pathsfromto', source_genes, target_genes, neighbor_limit) if model is not None: return process_model(model)
def process_pc_neighborhood(gene_names, neighbor_limit=1): """Returns a BiopaxProcessor for a PathwayCommons neighborhood query. The neighborhood query finds the neighborhood around a set of source genes. http://www.pathwaycommons.org/pc2/#graph http://www.pathwaycommons.org/pc2/#graph_kind Parameters ---------- gene_names : list A list of HGNC gene symbols to search the neighborhood of. Examples: ['BRAF'], ['BRAF', 'MAP2K1'] neighbor_limit : Optional[int] The number of steps to limit the size of the neighborhood around the gene names being queried. Default: 1 Returns ------- bp : BiopaxProcessor A BiopaxProcessor containing the obtained BioPAX model in bp.model. """ model = pcc.graph_query('neighborhood', gene_names, neighbor_limit=neighbor_limit) if model is not None: return process_model(model)
def process_pc_pathsfromto(source_genes, target_genes, neighbor_limit=1): """Returns a BiopaxProcessor for a PathwayCommons paths-from-to query. The paths-from-to query finds the paths from a set of source genes to a set of target genes. http://www.pathwaycommons.org/pc2/#graph http://www.pathwaycommons.org/pc2/#graph_kind Parameters ---------- source_genes : list A list of HGNC gene symbols that are the sources of paths being searched for. Examples: ['BRAF', 'RAF1', 'ARAF'] target_genes : list A list of HGNC gene symbols that are the targets of paths being searched for. Examples: ['MAP2K1', 'MAP2K2'] neighbor_limit : Optional[int] The number of steps to limit the length of the paths between the source genes and target genes being queried. Default: 1 Returns ------- bp : BiopaxProcessor A BiopaxProcessor containing the obtained BioPAX model in bp.model. Notes ----- As returned from this function, bp.statements is empty and one has to call methods of bp (e.g. bp.get_complexes()) to populate bp.statements. """ model = pcc.graph_query('pathsfromto', source_genes, target_genes, neighbor_limit) if model is not None: return process_model(model)