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_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)
