def process_pc_pathsfromto(source_genes,
target_genes,
neighbor_limit=1,
database_filter=None):
"""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
database_filter : Optional[list]
A list of database identifiers to which the query is restricted.
Examples: ['reactome'], ['biogrid', 'pid', 'psp']
If not given, all databases are used in the query. For a full
list of databases see http://www.pathwaycommons.org/pc2/datasources
Returns
-------
bp : BiopaxProcessor
A BiopaxProcessor containing the obtained BioPAX model in bp.model.
"""
model = model_from_pc_query('pathsfromto',
source=source_genes,
target=target_genes,
limit=neighbor_limit,
datasource=database_filter)
if model is not None:
return process_model(model)
def process_pc_neighborhood(gene_names,
neighbor_limit=1,
database_filter=None):
"""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
database_filter : Optional[list]
A list of database identifiers to which the query is restricted.
Examples: ['reactome'], ['biogrid', 'pid', 'psp']
If not given, all databases are used in the query. For a full
list of databases see http://www.pathwaycommons.org/pc2/datasources
Returns
-------
BiopaxProcessor
A BiopaxProcessor containing the obtained BioPAX model in its model
attribute and a list of extracted INDRA Statements from the model in
its statements attribute.
"""
model = model_from_pc_query('neighborhood',
source=gene_names,
limit=neighbor_limit,
datasource=database_filter)
if model is not None:
return process_model(model)
def process_pc_pathsbetween(gene_names,
neighbor_limit=1,
database_filter=None,
block_size=None):
"""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
database_filter : Optional[list]
A list of database identifiers to which the query is restricted.
Examples: ['reactome'], ['biogrid', 'pid', 'psp']
If not given, all databases are used in the query. For a full
list of databases see http://www.pathwaycommons.org/pc2/datasources
block_size : Optional[int]
Large paths-between queries (above ~60 genes) can error on the server
side. In this case, the query can be replaced by a series of
smaller paths-between and paths-from-to queries each of which contains
block_size genes.
Returns
-------
bp : BiopaxProcessor
A BiopaxProcessor containing the obtained BioPAX model in bp.model.
"""
if not block_size:
model = model_from_pc_query('pathsbetween',
source=gene_names,
limit=neighbor_limit,
datasource=database_filter)
if model is not None:
return process_model(model)
else:
gene_blocks = [
gene_names[i:i + block_size]
for i in range(0, len(gene_names), block_size)
]
stmts = []
# Run pathsfromto between pairs of blocks and pathsbetween
# within each block. This breaks up a single call with N genes into
# (N/block_size)*(N/blocksize) calls with block_size genes
for genes1, genes2 in itertools.product(gene_blocks, repeat=2):
if genes1 == genes2:
bp = process_pc_pathsbetween(genes1,
database_filter=database_filter,
block_size=None)
else:
bp = process_pc_pathsfromto(genes1,
genes2,
database_filter=database_filter)
stmts += bp.statements