repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
sorgerlab/indra | indra/sources/hume/visualize_causal.py | get_sourced_from | def get_sourced_from(entry):
"""Get a list of values from the source_from attribute"""
sourced_from = 'http://worldmodelers.com/DataProvenance#sourced_from'
if sourced_from in entry:
values = entry[sourced_from]
values = [i['@id'] for i in values]
return values | python | def get_sourced_from(entry):
"""Get a list of values from the source_from attribute"""
sourced_from = 'http://worldmodelers.com/DataProvenance#sourced_from'
if sourced_from in entry:
values = entry[sourced_from]
values = [i['@id'] for i in values]
return values | Get a list of values from the source_from attribute | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hume/visualize_causal.py#L127-L134 |
sorgerlab/indra | indra/sources/hume/visualize_causal.py | get_entry_compact_text_repr | def get_entry_compact_text_repr(entry, entries):
"""If the entry has a text value, return that.
If the entry has a source_from value, return the text value of the source.
Otherwise, return None."""
text = get_shortest_text_value(entry)
if text is not None:
return text
else:
sourc... | python | def get_entry_compact_text_repr(entry, entries):
"""If the entry has a text value, return that.
If the entry has a source_from value, return the text value of the source.
Otherwise, return None."""
text = get_shortest_text_value(entry)
if text is not None:
return text
else:
sourc... | If the entry has a text value, return that.
If the entry has a source_from value, return the text value of the source.
Otherwise, return None. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hume/visualize_causal.py#L137-L154 |
sorgerlab/indra | indra/sources/hume/visualize_causal.py | get_entity_type | def get_entity_type(entry):
"""Given a JSON-LD entry, returns the abbreviated @type and the
text attribute that has the shortest length.
Parameters
----------
entry: dict
A JSON-LD entry parsed into a nested python dictionary via the json
module
Returns
-------
short_ty... | python | def get_entity_type(entry):
"""Given a JSON-LD entry, returns the abbreviated @type and the
text attribute that has the shortest length.
Parameters
----------
entry: dict
A JSON-LD entry parsed into a nested python dictionary via the json
module
Returns
-------
short_ty... | Given a JSON-LD entry, returns the abbreviated @type and the
text attribute that has the shortest length.
Parameters
----------
entry: dict
A JSON-LD entry parsed into a nested python dictionary via the json
module
Returns
-------
short_type: str
The shortest type
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/hume/visualize_causal.py#L157-L177 |
sorgerlab/indra | indra/sources/sparser/api.py | process_text | def process_text(text, output_fmt='json', outbuf=None, cleanup=True, key='',
**kwargs):
"""Return processor with Statements extracted by reading text with Sparser.
Parameters
----------
text : str
The text to be processed
output_fmt: Optional[str]
The output format ... | python | def process_text(text, output_fmt='json', outbuf=None, cleanup=True, key='',
**kwargs):
"""Return processor with Statements extracted by reading text with Sparser.
Parameters
----------
text : str
The text to be processed
output_fmt: Optional[str]
The output format ... | Return processor with Statements extracted by reading text with Sparser.
Parameters
----------
text : str
The text to be processed
output_fmt: Optional[str]
The output format to obtain from Sparser, with the two options being
'json' and 'xml'. Default: 'json'
outbuf : Option... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L31-L59 |
sorgerlab/indra | indra/sources/sparser/api.py | process_nxml_str | def process_nxml_str(nxml_str, output_fmt='json', outbuf=None, cleanup=True,
key='', **kwargs):
"""Return processor with Statements extracted by reading an NXML string.
Parameters
----------
nxml_str : str
The string value of the NXML-formatted paper to be read.
output_... | python | def process_nxml_str(nxml_str, output_fmt='json', outbuf=None, cleanup=True,
key='', **kwargs):
"""Return processor with Statements extracted by reading an NXML string.
Parameters
----------
nxml_str : str
The string value of the NXML-formatted paper to be read.
output_... | Return processor with Statements extracted by reading an NXML string.
Parameters
----------
nxml_str : str
The string value of the NXML-formatted paper to be read.
output_fmt: Optional[str]
The output format to obtain from Sparser, with the two options being
'json' and 'xml'. De... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L62-L97 |
sorgerlab/indra | indra/sources/sparser/api.py | process_nxml_file | def process_nxml_file(fname, output_fmt='json', outbuf=None, cleanup=True,
**kwargs):
"""Return processor with Statements extracted by reading an NXML file.
Parameters
----------
fname : str
The path to the NXML file to be read.
output_fmt: Optional[str]
The ou... | python | def process_nxml_file(fname, output_fmt='json', outbuf=None, cleanup=True,
**kwargs):
"""Return processor with Statements extracted by reading an NXML file.
Parameters
----------
fname : str
The path to the NXML file to be read.
output_fmt: Optional[str]
The ou... | Return processor with Statements extracted by reading an NXML file.
Parameters
----------
fname : str
The path to the NXML file to be read.
output_fmt: Optional[str]
The output format to obtain from Sparser, with the two options being
'json' and 'xml'. Default: 'json'
outbuf... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L100-L134 |
sorgerlab/indra | indra/sources/sparser/api.py | process_sparser_output | def process_sparser_output(output_fname, output_fmt='json'):
"""Return a processor with Statements extracted from Sparser XML or JSON
Parameters
----------
output_fname : str
The path to the Sparser output file to be processed. The file can
either be JSON or XML output from Sparser, wit... | python | def process_sparser_output(output_fname, output_fmt='json'):
"""Return a processor with Statements extracted from Sparser XML or JSON
Parameters
----------
output_fname : str
The path to the Sparser output file to be processed. The file can
either be JSON or XML output from Sparser, wit... | Return a processor with Statements extracted from Sparser XML or JSON
Parameters
----------
output_fname : str
The path to the Sparser output file to be processed. The file can
either be JSON or XML output from Sparser, with the output_fmt
parameter defining what format is assumed t... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L137-L167 |
sorgerlab/indra | indra/sources/sparser/api.py | process_xml | def process_xml(xml_str):
"""Return processor with Statements extracted from a Sparser XML.
Parameters
----------
xml_str : str
The XML string obtained by reading content with Sparser, using the
'xml' output mode.
Returns
-------
sp : SparserXMLProcessor
A SparserXM... | python | def process_xml(xml_str):
"""Return processor with Statements extracted from a Sparser XML.
Parameters
----------
xml_str : str
The XML string obtained by reading content with Sparser, using the
'xml' output mode.
Returns
-------
sp : SparserXMLProcessor
A SparserXM... | Return processor with Statements extracted from a Sparser XML.
Parameters
----------
xml_str : str
The XML string obtained by reading content with Sparser, using the
'xml' output mode.
Returns
-------
sp : SparserXMLProcessor
A SparserXMLProcessor which has extracted St... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L190-L212 |
sorgerlab/indra | indra/sources/sparser/api.py | run_sparser | def run_sparser(fname, output_fmt, outbuf=None, timeout=600):
"""Return the path to reading output after running Sparser reading.
Parameters
----------
fname : str
The path to an input file to be processed. Due to the Spaser
executable's assumptions, the file name needs to start with PM... | python | def run_sparser(fname, output_fmt, outbuf=None, timeout=600):
"""Return the path to reading output after running Sparser reading.
Parameters
----------
fname : str
The path to an input file to be processed. Due to the Spaser
executable's assumptions, the file name needs to start with PM... | Return the path to reading output after running Sparser reading.
Parameters
----------
fname : str
The path to an input file to be processed. Due to the Spaser
executable's assumptions, the file name needs to start with PMC
and should be an NXML formatted file.
output_fmt : Opti... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L215-L287 |
sorgerlab/indra | indra/sources/sparser/api.py | get_version | def get_version():
"""Return the version of the Sparser executable on the path.
Returns
-------
version : str
The version of Sparser that is found on the Sparser path.
"""
assert sparser_path is not None, "Sparser path is not defined."
with open(os.path.join(sparser_path, 'version.t... | python | def get_version():
"""Return the version of the Sparser executable on the path.
Returns
-------
version : str
The version of Sparser that is found on the Sparser path.
"""
assert sparser_path is not None, "Sparser path is not defined."
with open(os.path.join(sparser_path, 'version.t... | Return the version of the Sparser executable on the path.
Returns
-------
version : str
The version of Sparser that is found on the Sparser path. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L290-L301 |
sorgerlab/indra | indra/sources/sparser/api.py | make_nxml_from_text | def make_nxml_from_text(text):
"""Return raw text wrapped in NXML structure.
Parameters
----------
text : str
The raw text content to be wrapped in an NXML structure.
Returns
-------
nxml_str : str
The NXML string wrapping the raw text input.
"""
text = _escape_xml(... | python | def make_nxml_from_text(text):
"""Return raw text wrapped in NXML structure.
Parameters
----------
text : str
The raw text content to be wrapped in an NXML structure.
Returns
-------
nxml_str : str
The NXML string wrapping the raw text input.
"""
text = _escape_xml(... | Return raw text wrapped in NXML structure.
Parameters
----------
text : str
The raw text content to be wrapped in an NXML structure.
Returns
-------
nxml_str : str
The NXML string wrapping the raw text input. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sparser/api.py#L304-L322 |
sorgerlab/indra | indra/databases/hgnc_client.py | get_hgnc_name | def get_hgnc_name(hgnc_id):
"""Return the HGNC symbol corresponding to the given HGNC ID.
Parameters
----------
hgnc_id : str
The HGNC ID to be converted.
Returns
-------
hgnc_name : str
The HGNC symbol corresponding to the given HGNC ID.
"""
try:
hgnc_name ... | python | def get_hgnc_name(hgnc_id):
"""Return the HGNC symbol corresponding to the given HGNC ID.
Parameters
----------
hgnc_id : str
The HGNC ID to be converted.
Returns
-------
hgnc_name : str
The HGNC symbol corresponding to the given HGNC ID.
"""
try:
hgnc_name ... | Return the HGNC symbol corresponding to the given HGNC ID.
Parameters
----------
hgnc_id : str
The HGNC ID to be converted.
Returns
-------
hgnc_name : str
The HGNC symbol corresponding to the given HGNC ID. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/databases/hgnc_client.py#L83-L107 |
sorgerlab/indra | indra/databases/hgnc_client.py | get_current_hgnc_id | def get_current_hgnc_id(hgnc_name):
"""Return the HGNC ID(s) corresponding to a current or outdate HGNC symbol.
Parameters
----------
hgnc_name : str
The HGNC symbol to be converted, possibly an outdated symbol.
Returns
-------
str or list of str or None
If there is a singl... | python | def get_current_hgnc_id(hgnc_name):
"""Return the HGNC ID(s) corresponding to a current or outdate HGNC symbol.
Parameters
----------
hgnc_name : str
The HGNC symbol to be converted, possibly an outdated symbol.
Returns
-------
str or list of str or None
If there is a singl... | Return the HGNC ID(s) corresponding to a current or outdate HGNC symbol.
Parameters
----------
hgnc_name : str
The HGNC symbol to be converted, possibly an outdated symbol.
Returns
-------
str or list of str or None
If there is a single HGNC ID corresponding to the given curren... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/databases/hgnc_client.py#L126-L147 |
sorgerlab/indra | indra/databases/hgnc_client.py | get_hgnc_entry | def get_hgnc_entry(hgnc_id):
"""Return the HGNC entry for the given HGNC ID from the web service.
Parameters
----------
hgnc_id : str
The HGNC ID to be converted.
Returns
-------
xml_tree : ElementTree
The XML ElementTree corresponding to the entry for the
given HGN... | python | def get_hgnc_entry(hgnc_id):
"""Return the HGNC entry for the given HGNC ID from the web service.
Parameters
----------
hgnc_id : str
The HGNC ID to be converted.
Returns
-------
xml_tree : ElementTree
The XML ElementTree corresponding to the entry for the
given HGN... | Return the HGNC entry for the given HGNC ID from the web service.
Parameters
----------
hgnc_id : str
The HGNC ID to be converted.
Returns
-------
xml_tree : ElementTree
The XML ElementTree corresponding to the entry for the
given HGNC ID. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/databases/hgnc_client.py#L224-L244 |
sorgerlab/indra | indra/tools/reading/util/log_analysis_tools.py | analyze_reach_log | def analyze_reach_log(log_fname=None, log_str=None):
"""Return unifinished PMIDs given a log file name."""
assert bool(log_fname) ^ bool(log_str), 'Must specify log_fname OR log_str'
started_patt = re.compile('Starting ([\d]+)')
# TODO: it might be interesting to get the time it took to read
# each ... | python | def analyze_reach_log(log_fname=None, log_str=None):
"""Return unifinished PMIDs given a log file name."""
assert bool(log_fname) ^ bool(log_str), 'Must specify log_fname OR log_str'
started_patt = re.compile('Starting ([\d]+)')
# TODO: it might be interesting to get the time it took to read
# each ... | Return unifinished PMIDs given a log file name. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/util/log_analysis_tools.py#L6-L28 |
sorgerlab/indra | indra/tools/reading/util/log_analysis_tools.py | get_logs_from_db_reading | def get_logs_from_db_reading(job_prefix, reading_queue='run_db_reading_queue'):
"""Get the logs stashed on s3 for a particular reading."""
s3 = boto3.client('s3')
gen_prefix = 'reading_results/%s/logs/%s' % (job_prefix, reading_queue)
job_log_data = s3.list_objects_v2(Bucket='bigmech',
... | python | def get_logs_from_db_reading(job_prefix, reading_queue='run_db_reading_queue'):
"""Get the logs stashed on s3 for a particular reading."""
s3 = boto3.client('s3')
gen_prefix = 'reading_results/%s/logs/%s' % (job_prefix, reading_queue)
job_log_data = s3.list_objects_v2(Bucket='bigmech',
... | Get the logs stashed on s3 for a particular reading. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/util/log_analysis_tools.py#L36-L47 |
sorgerlab/indra | indra/tools/reading/util/log_analysis_tools.py | separate_reach_logs | def separate_reach_logs(log_str):
"""Get the list of reach logs from the overall logs."""
log_lines = log_str.splitlines()
reach_logs = []
reach_lines = []
adding_reach_lines = False
for l in log_lines[:]:
if not adding_reach_lines and 'Beginning reach' in l:
adding_reach_lin... | python | def separate_reach_logs(log_str):
"""Get the list of reach logs from the overall logs."""
log_lines = log_str.splitlines()
reach_logs = []
reach_lines = []
adding_reach_lines = False
for l in log_lines[:]:
if not adding_reach_lines and 'Beginning reach' in l:
adding_reach_lin... | Get the list of reach logs from the overall logs. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/util/log_analysis_tools.py#L50-L68 |
sorgerlab/indra | indra/tools/reading/util/log_analysis_tools.py | get_unyielding_tcids | def get_unyielding_tcids(log_str):
"""Extract the set of tcids for which no statements were created."""
tcid_strs = re.findall('INFO: \[.*?\].*? - Got no statements for (\d+).*',
log_str)
return {int(tcid_str) for tcid_str in tcid_strs} | python | def get_unyielding_tcids(log_str):
"""Extract the set of tcids for which no statements were created."""
tcid_strs = re.findall('INFO: \[.*?\].*? - Got no statements for (\d+).*',
log_str)
return {int(tcid_str) for tcid_str in tcid_strs} | Extract the set of tcids for which no statements were created. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/util/log_analysis_tools.py#L115-L119 |
sorgerlab/indra | indra/tools/reading/util/log_analysis_tools.py | analyze_db_reading | def analyze_db_reading(job_prefix, reading_queue='run_db_reading_queue'):
"""Run various analysis on a particular reading job."""
# Analyze reach failures
log_strs = get_logs_from_db_reading(job_prefix, reading_queue)
indra_log_strs = []
all_reach_logs = []
log_stats = []
for log_str in log_... | python | def analyze_db_reading(job_prefix, reading_queue='run_db_reading_queue'):
"""Run various analysis on a particular reading job."""
# Analyze reach failures
log_strs = get_logs_from_db_reading(job_prefix, reading_queue)
indra_log_strs = []
all_reach_logs = []
log_stats = []
for log_str in log_... | Run various analysis on a particular reading job. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/tools/reading/util/log_analysis_tools.py#L156-L195 |
sorgerlab/indra | indra/sources/biopax/api.py | process_pc_neighborhood | 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:... | python | 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:... | 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... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/api.py#L8-L41 |
sorgerlab/indra | indra/sources/biopax/api.py | process_pc_pathsbetween | 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 l... | python | 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 l... | 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... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/api.py#L44-L101 |
sorgerlab/indra | indra/sources/biopax/api.py | process_pc_pathsfromto | 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.path... | python | 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.path... | 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 : lis... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/api.py#L104-L143 |
sorgerlab/indra | indra/sources/biopax/api.py | process_model | def process_model(model):
"""Returns a BiopaxProcessor for a BioPAX model object.
Parameters
----------
model : org.biopax.paxtools.model.Model
A BioPAX model object.
Returns
-------
bp : BiopaxProcessor
A BiopaxProcessor containing the obtained BioPAX model in bp.model.
... | python | def process_model(model):
"""Returns a BiopaxProcessor for a BioPAX model object.
Parameters
----------
model : org.biopax.paxtools.model.Model
A BioPAX model object.
Returns
-------
bp : BiopaxProcessor
A BiopaxProcessor containing the obtained BioPAX model in bp.model.
... | Returns a BiopaxProcessor for a BioPAX model object.
Parameters
----------
model : org.biopax.paxtools.model.Model
A BioPAX model object.
Returns
-------
bp : BiopaxProcessor
A BiopaxProcessor containing the obtained BioPAX model in bp.model. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/biopax/api.py#L163-L186 |
sorgerlab/indra | indra/benchmarks/assembly_eval/batch4/assembly_eval.py | is_protein_or_chemical | def is_protein_or_chemical(agent):
'''Return True if the agent is a protein/protein family or chemical.'''
# Default is True if agent is None
if agent is None:
return True
dbs = set(['UP', 'HGNC', 'CHEBI', 'PFAM-DEF', 'IP', 'INDRA', 'PUBCHEM',
'CHEMBL'])
agent_refs = set(agent... | python | def is_protein_or_chemical(agent):
'''Return True if the agent is a protein/protein family or chemical.'''
# Default is True if agent is None
if agent is None:
return True
dbs = set(['UP', 'HGNC', 'CHEBI', 'PFAM-DEF', 'IP', 'INDRA', 'PUBCHEM',
'CHEMBL'])
agent_refs = set(agent... | Return True if the agent is a protein/protein family or chemical. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/benchmarks/assembly_eval/batch4/assembly_eval.py#L30-L40 |
sorgerlab/indra | indra/benchmarks/assembly_eval/batch4/assembly_eval.py | is_background_knowledge | def is_background_knowledge(stmt):
'''Return True if Statement is only supported by background knowledge.'''
any_background = False
# Iterate over all evidence for the statement
for ev in stmt.evidence:
epi = ev.epistemics
if epi is not None:
sec = epi.get('section_type')
... | python | def is_background_knowledge(stmt):
'''Return True if Statement is only supported by background knowledge.'''
any_background = False
# Iterate over all evidence for the statement
for ev in stmt.evidence:
epi = ev.epistemics
if epi is not None:
sec = epi.get('section_type')
... | Return True if Statement is only supported by background knowledge. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/benchmarks/assembly_eval/batch4/assembly_eval.py#L45-L66 |
sorgerlab/indra | indra/benchmarks/assembly_eval/batch4/assembly_eval.py | multiple_sources | def multiple_sources(stmt):
'''Return True if statement is supported by multiple sources.
Note: this is currently not used and replaced by BeliefEngine score cutoff
'''
sources = list(set([e.source_api for e in stmt.evidence]))
if len(sources) > 1:
return True
return False | python | def multiple_sources(stmt):
'''Return True if statement is supported by multiple sources.
Note: this is currently not used and replaced by BeliefEngine score cutoff
'''
sources = list(set([e.source_api for e in stmt.evidence]))
if len(sources) > 1:
return True
return False | Return True if statement is supported by multiple sources.
Note: this is currently not used and replaced by BeliefEngine score cutoff | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/benchmarks/assembly_eval/batch4/assembly_eval.py#L68-L76 |
sorgerlab/indra | indra/benchmarks/assembly_eval/batch4/assembly_eval.py | run_assembly | def run_assembly(stmts, folder, pmcid, background_assertions=None):
'''Run assembly on a list of statements, for a given PMCID.'''
# Folder for index card output (scored submission)
indexcard_prefix = folder + '/index_cards/' + pmcid
# Folder for other outputs (for analysis, debugging)
otherout_pref... | python | def run_assembly(stmts, folder, pmcid, background_assertions=None):
'''Run assembly on a list of statements, for a given PMCID.'''
# Folder for index card output (scored submission)
indexcard_prefix = folder + '/index_cards/' + pmcid
# Folder for other outputs (for analysis, debugging)
otherout_pref... | Run assembly on a list of statements, for a given PMCID. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/benchmarks/assembly_eval/batch4/assembly_eval.py#L78-L205 |
sorgerlab/indra | indra/sources/geneways/symbols_parser.py | GenewaysSymbols.symbol_to_id | def symbol_to_id(self, symbol):
"""Returns the list of Entrez IDs for a given Geneways symbol
(there may be more than one)"""
if symbol not in self.symbols_to_ids:
m = 'Could not look up Entrez ID for Geneways symbol ' + symbol
raise Exception(m)
return self.symb... | python | def symbol_to_id(self, symbol):
"""Returns the list of Entrez IDs for a given Geneways symbol
(there may be more than one)"""
if symbol not in self.symbols_to_ids:
m = 'Could not look up Entrez ID for Geneways symbol ' + symbol
raise Exception(m)
return self.symb... | Returns the list of Entrez IDs for a given Geneways symbol
(there may be more than one) | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/symbols_parser.py#L50-L57 |
sorgerlab/indra | indra/sources/geneways/symbols_parser.py | GenewaysSymbols.id_to_symbol | def id_to_symbol(self, entrez_id):
"""Gives the symbol for a given entrez id)"""
entrez_id = str(entrez_id)
if entrez_id not in self.ids_to_symbols:
m = 'Could not look up symbol for Entrez ID ' + entrez_id
raise Exception(m)
return self.ids_to_symbols[entrez_id] | python | def id_to_symbol(self, entrez_id):
"""Gives the symbol for a given entrez id)"""
entrez_id = str(entrez_id)
if entrez_id not in self.ids_to_symbols:
m = 'Could not look up symbol for Entrez ID ' + entrez_id
raise Exception(m)
return self.ids_to_symbols[entrez_id] | Gives the symbol for a given entrez id) | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/symbols_parser.py#L59-L66 |
sorgerlab/indra | indra/assemblers/tsv/assembler.py | _format_id | def _format_id(ns, id):
"""Format a namespace/ID pair for display and curation."""
label = '%s:%s' % (ns, id)
label = label.replace(' ', '_')
url = get_identifiers_url(ns, id)
return (label, url) | python | def _format_id(ns, id):
"""Format a namespace/ID pair for display and curation."""
label = '%s:%s' % (ns, id)
label = label.replace(' ', '_')
url = get_identifiers_url(ns, id)
return (label, url) | Format a namespace/ID pair for display and curation. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/tsv/assembler.py#L166-L171 |
sorgerlab/indra | indra/assemblers/tsv/assembler.py | TsvAssembler.make_model | def make_model(self, output_file, add_curation_cols=False, up_only=False):
"""Export the statements into a tab-separated text file.
Parameters
----------
output_file : str
Name of the output file.
add_curation_cols : bool
Whether to add columns to facilit... | python | def make_model(self, output_file, add_curation_cols=False, up_only=False):
"""Export the statements into a tab-separated text file.
Parameters
----------
output_file : str
Name of the output file.
add_curation_cols : bool
Whether to add columns to facilit... | Export the statements into a tab-separated text file.
Parameters
----------
output_file : str
Name of the output file.
add_curation_cols : bool
Whether to add columns to facilitate statement curation. Default
is False (no additional columns).
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/tsv/assembler.py#L109-L163 |
sorgerlab/indra | indra/assemblers/pysb/base_agents.py | BaseAgentSet.get_create_base_agent | def get_create_base_agent(self, agent):
"""Return base agent with given name, creating it if needed."""
try:
base_agent = self.agents[_n(agent.name)]
except KeyError:
base_agent = BaseAgent(_n(agent.name))
self.agents[_n(agent.name)] = base_agent
# If... | python | def get_create_base_agent(self, agent):
"""Return base agent with given name, creating it if needed."""
try:
base_agent = self.agents[_n(agent.name)]
except KeyError:
base_agent = BaseAgent(_n(agent.name))
self.agents[_n(agent.name)] = base_agent
# If... | Return base agent with given name, creating it if needed. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/base_agents.py#L13-L57 |
sorgerlab/indra | indra/assemblers/pysb/base_agents.py | BaseAgent.create_site | def create_site(self, site, states=None):
"""Create a new site on an agent if it doesn't already exist."""
if site not in self.sites:
self.sites.append(site)
if states is not None:
self.site_states.setdefault(site, [])
try:
states = list(states... | python | def create_site(self, site, states=None):
"""Create a new site on an agent if it doesn't already exist."""
if site not in self.sites:
self.sites.append(site)
if states is not None:
self.site_states.setdefault(site, [])
try:
states = list(states... | Create a new site on an agent if it doesn't already exist. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/base_agents.py#L90-L100 |
sorgerlab/indra | indra/assemblers/pysb/base_agents.py | BaseAgent.create_mod_site | def create_mod_site(self, mc):
"""Create modification site for the BaseAgent from a ModCondition."""
site_name = get_mod_site_name(mc)
(unmod_site_state, mod_site_state) = states[mc.mod_type]
self.create_site(site_name, (unmod_site_state, mod_site_state))
site_anns = [Annotation(... | python | def create_mod_site(self, mc):
"""Create modification site for the BaseAgent from a ModCondition."""
site_name = get_mod_site_name(mc)
(unmod_site_state, mod_site_state) = states[mc.mod_type]
self.create_site(site_name, (unmod_site_state, mod_site_state))
site_anns = [Annotation(... | Create modification site for the BaseAgent from a ModCondition. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/base_agents.py#L102-L113 |
sorgerlab/indra | indra/assemblers/pysb/base_agents.py | BaseAgent.add_site_states | def add_site_states(self, site, states):
"""Create new states on an agent site if the state doesn't exist."""
for state in states:
if state not in self.site_states[site]:
self.site_states[site].append(state) | python | def add_site_states(self, site, states):
"""Create new states on an agent site if the state doesn't exist."""
for state in states:
if state not in self.site_states[site]:
self.site_states[site].append(state) | Create new states on an agent site if the state doesn't exist. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/base_agents.py#L115-L119 |
sorgerlab/indra | indra/assemblers/pysb/base_agents.py | BaseAgent.add_activity_form | def add_activity_form(self, activity_pattern, is_active):
"""Adds the pattern as an active or inactive form to an Agent.
Parameters
----------
activity_pattern : dict
A dictionary of site names and their states.
is_active : bool
Is True if the given patte... | python | def add_activity_form(self, activity_pattern, is_active):
"""Adds the pattern as an active or inactive form to an Agent.
Parameters
----------
activity_pattern : dict
A dictionary of site names and their states.
is_active : bool
Is True if the given patte... | Adds the pattern as an active or inactive form to an Agent.
Parameters
----------
activity_pattern : dict
A dictionary of site names and their states.
is_active : bool
Is True if the given pattern corresponds to an active state. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/base_agents.py#L121-L136 |
sorgerlab/indra | indra/assemblers/pysb/base_agents.py | BaseAgent.add_activity_type | def add_activity_type(self, activity_type):
"""Adds an activity type to an Agent.
Parameters
----------
activity_type : str
The type of activity to add such as 'activity', 'kinase',
'gtpbound'
"""
if activity_type not in self.activity_types:
... | python | def add_activity_type(self, activity_type):
"""Adds an activity type to an Agent.
Parameters
----------
activity_type : str
The type of activity to add such as 'activity', 'kinase',
'gtpbound'
"""
if activity_type not in self.activity_types:
... | Adds an activity type to an Agent.
Parameters
----------
activity_type : str
The type of activity to add such as 'activity', 'kinase',
'gtpbound' | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/base_agents.py#L138-L148 |
sorgerlab/indra | indra/sources/geneways/action_parser.py | GenewaysAction.make_annotation | def make_annotation(self):
"""Returns a dictionary with all properties of the action
and each of its action mentions."""
annotation = dict()
# Put all properties of the action object into the annotation
for item in dir(self):
if len(item) > 0 and item[0] != '_' and \... | python | def make_annotation(self):
"""Returns a dictionary with all properties of the action
and each of its action mentions."""
annotation = dict()
# Put all properties of the action object into the annotation
for item in dir(self):
if len(item) > 0 and item[0] != '_' and \... | Returns a dictionary with all properties of the action
and each of its action mentions. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/action_parser.py#L35-L52 |
sorgerlab/indra | indra/sources/geneways/action_parser.py | GenewaysActionParser._search_path | def _search_path(self, directory_name, filename):
"""Searches for a given file in the specified directory."""
full_path = path.join(directory_name, filename)
if path.exists(full_path):
return full_path
# Could not find the requested file in any of the directories
ret... | python | def _search_path(self, directory_name, filename):
"""Searches for a given file in the specified directory."""
full_path = path.join(directory_name, filename)
if path.exists(full_path):
return full_path
# Could not find the requested file in any of the directories
ret... | Searches for a given file in the specified directory. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/action_parser.py#L96-L103 |
sorgerlab/indra | indra/sources/geneways/action_parser.py | GenewaysActionParser._init_action_list | def _init_action_list(self, action_filename):
"""Parses the file and populates the data."""
self.actions = list()
self.hiid_to_action_index = dict()
f = codecs.open(action_filename, 'r', encoding='latin-1')
first_line = True
for line in f:
line = line.rstrip... | python | def _init_action_list(self, action_filename):
"""Parses the file and populates the data."""
self.actions = list()
self.hiid_to_action_index = dict()
f = codecs.open(action_filename, 'r', encoding='latin-1')
first_line = True
for line in f:
line = line.rstrip... | Parses the file and populates the data. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/action_parser.py#L105-L125 |
sorgerlab/indra | indra/sources/geneways/action_parser.py | GenewaysActionParser._link_to_action_mentions | def _link_to_action_mentions(self, actionmention_filename):
"""Add action mentions"""
parser = GenewaysActionMentionParser(actionmention_filename)
self.action_mentions = parser.action_mentions
for action_mention in self.action_mentions:
hiid = action_mention.hiid
... | python | def _link_to_action_mentions(self, actionmention_filename):
"""Add action mentions"""
parser = GenewaysActionMentionParser(actionmention_filename)
self.action_mentions = parser.action_mentions
for action_mention in self.action_mentions:
hiid = action_mention.hiid
... | Add action mentions | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/action_parser.py#L127-L140 |
sorgerlab/indra | indra/sources/geneways/action_parser.py | GenewaysActionParser._lookup_symbols | def _lookup_symbols(self, symbols_filename):
"""Look up symbols for actions and action mentions"""
symbol_lookup = GenewaysSymbols(symbols_filename)
for action in self.actions:
action.up_symbol = symbol_lookup.id_to_symbol(action.up)
action.dn_symbol = symbol_lookup.id_to... | python | def _lookup_symbols(self, symbols_filename):
"""Look up symbols for actions and action mentions"""
symbol_lookup = GenewaysSymbols(symbols_filename)
for action in self.actions:
action.up_symbol = symbol_lookup.id_to_symbol(action.up)
action.dn_symbol = symbol_lookup.id_to... | Look up symbols for actions and action mentions | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/action_parser.py#L142-L147 |
sorgerlab/indra | indra/sources/geneways/action_parser.py | GenewaysActionParser.get_top_n_action_types | def get_top_n_action_types(self, top_n):
"""Returns the top N actions by count."""
# Count action types
action_type_to_counts = dict()
for action in self.actions:
actiontype = action.actiontype
if actiontype not in action_type_to_counts:
action_typ... | python | def get_top_n_action_types(self, top_n):
"""Returns the top N actions by count."""
# Count action types
action_type_to_counts = dict()
for action in self.actions:
actiontype = action.actiontype
if actiontype not in action_type_to_counts:
action_typ... | Returns the top N actions by count. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/geneways/action_parser.py#L149-L188 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler.make_model | def make_model(self):
"""Assemble the graph from the assembler's list of INDRA Statements."""
# Assemble in two stages.
# First, create the nodes of the graph
for stmt in self.statements:
# Skip SelfModification (self loops) -- has one node
if isinstance(stmt, Sel... | python | def make_model(self):
"""Assemble the graph from the assembler's list of INDRA Statements."""
# Assemble in two stages.
# First, create the nodes of the graph
for stmt in self.statements:
# Skip SelfModification (self loops) -- has one node
if isinstance(stmt, Sel... | Assemble the graph from the assembler's list of INDRA Statements. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L105-L144 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler.get_string | def get_string(self):
"""Return the assembled graph as a string.
Returns
-------
graph_string : str
The assembled graph as a string.
"""
graph_string = self.graph.to_string()
graph_string = graph_string.replace('\\N', '\\n')
return graph_strin... | python | def get_string(self):
"""Return the assembled graph as a string.
Returns
-------
graph_string : str
The assembled graph as a string.
"""
graph_string = self.graph.to_string()
graph_string = graph_string.replace('\\N', '\\n')
return graph_strin... | Return the assembled graph as a string.
Returns
-------
graph_string : str
The assembled graph as a string. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L146-L156 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler.save_dot | def save_dot(self, file_name='graph.dot'):
"""Save the graph in a graphviz dot file.
Parameters
----------
file_name : Optional[str]
The name of the file to save the graph dot string to.
"""
s = self.get_string()
with open(file_name, 'wt') as fh:
... | python | def save_dot(self, file_name='graph.dot'):
"""Save the graph in a graphviz dot file.
Parameters
----------
file_name : Optional[str]
The name of the file to save the graph dot string to.
"""
s = self.get_string()
with open(file_name, 'wt') as fh:
... | Save the graph in a graphviz dot file.
Parameters
----------
file_name : Optional[str]
The name of the file to save the graph dot string to. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L158-L168 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler.save_pdf | def save_pdf(self, file_name='graph.pdf', prog='dot'):
"""Draw the graph and save as an image or pdf file.
Parameters
----------
file_name : Optional[str]
The name of the file to save the graph as. Default: graph.pdf
prog : Optional[str]
The graphviz prog... | python | def save_pdf(self, file_name='graph.pdf', prog='dot'):
"""Draw the graph and save as an image or pdf file.
Parameters
----------
file_name : Optional[str]
The name of the file to save the graph as. Default: graph.pdf
prog : Optional[str]
The graphviz prog... | Draw the graph and save as an image or pdf file.
Parameters
----------
file_name : Optional[str]
The name of the file to save the graph as. Default: graph.pdf
prog : Optional[str]
The graphviz program to use for graph layout. Default: dot | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L170-L180 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler._add_edge | def _add_edge(self, source, target, **kwargs):
"""Add an edge to the graph."""
# Start with default edge properties
edge_properties = self.edge_properties
# Overwrite ones that are given in function call explicitly
for k, v in kwargs.items():
edge_properties[k] = v
... | python | def _add_edge(self, source, target, **kwargs):
"""Add an edge to the graph."""
# Start with default edge properties
edge_properties = self.edge_properties
# Overwrite ones that are given in function call explicitly
for k, v in kwargs.items():
edge_properties[k] = v
... | Add an edge to the graph. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L182-L189 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler._add_node | def _add_node(self, agent):
"""Add an Agent as a node to the graph."""
if agent is None:
return
node_label = _get_node_label(agent)
if isinstance(agent, Agent) and agent.bound_conditions:
bound_agents = [bc.agent for bc in agent.bound_conditions if
... | python | def _add_node(self, agent):
"""Add an Agent as a node to the graph."""
if agent is None:
return
node_label = _get_node_label(agent)
if isinstance(agent, Agent) and agent.bound_conditions:
bound_agents = [bc.agent for bc in agent.bound_conditions if
... | Add an Agent as a node to the graph. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L191-L212 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler._add_stmt_edge | def _add_stmt_edge(self, stmt):
"""Assemble a Modification statement."""
# Skip statements with None in the subject position
source = _get_node_key(stmt.agent_list()[0])
target = _get_node_key(stmt.agent_list()[1])
edge_key = (source, target, stmt.__class__.__name__)
if e... | python | def _add_stmt_edge(self, stmt):
"""Assemble a Modification statement."""
# Skip statements with None in the subject position
source = _get_node_key(stmt.agent_list()[0])
target = _get_node_key(stmt.agent_list()[1])
edge_key = (source, target, stmt.__class__.__name__)
if e... | Assemble a Modification statement. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L214-L234 |
sorgerlab/indra | indra/assemblers/graph/assembler.py | GraphAssembler._add_complex | def _add_complex(self, members, is_association=False):
"""Assemble a Complex statement."""
params = {'color': '#0000ff',
'arrowhead': 'dot',
'arrowtail': 'dot',
'dir': 'both'}
for m1, m2 in itertools.combinations(members, 2):
if s... | python | def _add_complex(self, members, is_association=False):
"""Assemble a Complex statement."""
params = {'color': '#0000ff',
'arrowhead': 'dot',
'arrowtail': 'dot',
'dir': 'both'}
for m1, m2 in itertools.combinations(members, 2):
if s... | Assemble a Complex statement. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/graph/assembler.py#L236-L255 |
sorgerlab/indra | indra/sources/signor/api.py | process_from_file | def process_from_file(signor_data_file, signor_complexes_file=None):
"""Process Signor interaction data from CSV files.
Parameters
----------
signor_data_file : str
Path to the Signor interaction data file in CSV format.
signor_complexes_file : str
Path to the Signor complexes data ... | python | def process_from_file(signor_data_file, signor_complexes_file=None):
"""Process Signor interaction data from CSV files.
Parameters
----------
signor_data_file : str
Path to the Signor interaction data file in CSV format.
signor_complexes_file : str
Path to the Signor complexes data ... | Process Signor interaction data from CSV files.
Parameters
----------
signor_data_file : str
Path to the Signor interaction data file in CSV format.
signor_complexes_file : str
Path to the Signor complexes data in CSV format. If unspecified,
Signor complexes will not be expanded... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/signor/api.py#L47-L72 |
sorgerlab/indra | indra/sources/signor/api.py | _handle_response | def _handle_response(res, delimiter):
"""Get an iterator over the CSV data from the response."""
if res.status_code == 200:
# Python 2 -- csv.reader will need bytes
if sys.version_info[0] < 3:
csv_io = BytesIO(res.content)
# Python 3 -- csv.reader needs str
else:
... | python | def _handle_response(res, delimiter):
"""Get an iterator over the CSV data from the response."""
if res.status_code == 200:
# Python 2 -- csv.reader will need bytes
if sys.version_info[0] < 3:
csv_io = BytesIO(res.content)
# Python 3 -- csv.reader needs str
else:
... | Get an iterator over the CSV data from the response. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/signor/api.py#L89-L102 |
sorgerlab/indra | indra/databases/context_client.py | get_protein_expression | def get_protein_expression(gene_names, cell_types):
"""Return the protein expression levels of genes in cell types.
Parameters
----------
gene_names : list
HGNC gene symbols for which expression levels are queried.
cell_types : list
List of cell type names in which expression levels... | python | def get_protein_expression(gene_names, cell_types):
"""Return the protein expression levels of genes in cell types.
Parameters
----------
gene_names : list
HGNC gene symbols for which expression levels are queried.
cell_types : list
List of cell type names in which expression levels... | Return the protein expression levels of genes in cell types.
Parameters
----------
gene_names : list
HGNC gene symbols for which expression levels are queried.
cell_types : list
List of cell type names in which expression levels are queried.
The cell type names follow the CCLE d... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/databases/context_client.py#L13-L44 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | get_aspect | def get_aspect(cx, aspect_name):
"""Return an aspect given the name of the aspect"""
if isinstance(cx, dict):
return cx.get(aspect_name)
for entry in cx:
if list(entry.keys())[0] == aspect_name:
return entry[aspect_name] | python | def get_aspect(cx, aspect_name):
"""Return an aspect given the name of the aspect"""
if isinstance(cx, dict):
return cx.get(aspect_name)
for entry in cx:
if list(entry.keys())[0] == aspect_name:
return entry[aspect_name] | Return an aspect given the name of the aspect | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L13-L19 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | classify_nodes | def classify_nodes(graph, hub):
"""Classify each node based on its type and relationship to the hub."""
node_stats = defaultdict(lambda: defaultdict(list))
for u, v, data in graph.edges(data=True):
# This means the node is downstream of the hub
if hub == u:
h, o = u, v
... | python | def classify_nodes(graph, hub):
"""Classify each node based on its type and relationship to the hub."""
node_stats = defaultdict(lambda: defaultdict(list))
for u, v, data in graph.edges(data=True):
# This means the node is downstream of the hub
if hub == u:
h, o = u, v
... | Classify each node based on its type and relationship to the hub. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L34-L67 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | get_attributes | def get_attributes(aspect, id):
"""Return the attributes pointing to a given ID in a given aspect."""
attributes = {}
for entry in aspect:
if entry['po'] == id:
attributes[entry['n']] = entry['v']
return attributes | python | def get_attributes(aspect, id):
"""Return the attributes pointing to a given ID in a given aspect."""
attributes = {}
for entry in aspect:
if entry['po'] == id:
attributes[entry['n']] = entry['v']
return attributes | Return the attributes pointing to a given ID in a given aspect. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L70-L76 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | cx_to_networkx | def cx_to_networkx(cx):
"""Return a MultiDiGraph representation of a CX network."""
graph = networkx.MultiDiGraph()
for node_entry in get_aspect(cx, 'nodes'):
id = node_entry['@id']
attrs = get_attributes(get_aspect(cx, 'nodeAttributes'), id)
attrs['n'] = node_entry['n']
grap... | python | def cx_to_networkx(cx):
"""Return a MultiDiGraph representation of a CX network."""
graph = networkx.MultiDiGraph()
for node_entry in get_aspect(cx, 'nodes'):
id = node_entry['@id']
attrs = get_attributes(get_aspect(cx, 'nodeAttributes'), id)
attrs['n'] = node_entry['n']
grap... | Return a MultiDiGraph representation of a CX network. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L79-L92 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | get_quadrant_from_class | def get_quadrant_from_class(node_class):
"""Return the ID of the segment of the plane corresponding to a class."""
up, edge_type, _ = node_class
if up == 0:
return 0 if random.random() < 0.5 else 7
mappings = {(-1, 'modification'): 1,
(-1, 'amount'): 2,
(-1, 'acti... | python | def get_quadrant_from_class(node_class):
"""Return the ID of the segment of the plane corresponding to a class."""
up, edge_type, _ = node_class
if up == 0:
return 0 if random.random() < 0.5 else 7
mappings = {(-1, 'modification'): 1,
(-1, 'amount'): 2,
(-1, 'acti... | Return the ID of the segment of the plane corresponding to a class. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L95-L106 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | get_coordinates | def get_coordinates(node_class):
"""Generate coordinates for a node in a given class."""
quadrant_size = (2 * math.pi / 8.0)
quadrant = get_quadrant_from_class(node_class)
begin_angle = quadrant_size * quadrant
r = 200 + 800*random.random()
alpha = begin_angle + random.random() * quadrant_size
... | python | def get_coordinates(node_class):
"""Generate coordinates for a node in a given class."""
quadrant_size = (2 * math.pi / 8.0)
quadrant = get_quadrant_from_class(node_class)
begin_angle = quadrant_size * quadrant
r = 200 + 800*random.random()
alpha = begin_angle + random.random() * quadrant_size
... | Generate coordinates for a node in a given class. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L109-L118 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | get_layout_aspect | def get_layout_aspect(hub, node_classes):
"""Get the full layout aspect with coordinates for each node."""
aspect = [{'node': hub, 'x': 0.0, 'y': 0.0}]
for node, node_class in node_classes.items():
if node == hub:
continue
x, y = get_coordinates(node_class)
aspect.append(... | python | def get_layout_aspect(hub, node_classes):
"""Get the full layout aspect with coordinates for each node."""
aspect = [{'node': hub, 'x': 0.0, 'y': 0.0}]
for node, node_class in node_classes.items():
if node == hub:
continue
x, y = get_coordinates(node_class)
aspect.append(... | Get the full layout aspect with coordinates for each node. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L121-L129 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | get_node_by_name | def get_node_by_name(graph, name):
"""Return a node ID given its name."""
for id, attrs in graph.nodes(data=True):
if attrs['n'] == name:
return id | python | def get_node_by_name(graph, name):
"""Return a node ID given its name."""
for id, attrs in graph.nodes(data=True):
if attrs['n'] == name:
return id | Return a node ID given its name. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L132-L136 |
sorgerlab/indra | indra/assemblers/cx/hub_layout.py | add_semantic_hub_layout | def add_semantic_hub_layout(cx, hub):
"""Attach a layout aspect to a CX network given a hub node."""
graph = cx_to_networkx(cx)
hub_node = get_node_by_name(graph, hub)
node_classes = classify_nodes(graph, hub_node)
layout_aspect = get_layout_aspect(hub_node, node_classes)
cx['cartesianLayout'] =... | python | def add_semantic_hub_layout(cx, hub):
"""Attach a layout aspect to a CX network given a hub node."""
graph = cx_to_networkx(cx)
hub_node = get_node_by_name(graph, hub)
node_classes = classify_nodes(graph, hub_node)
layout_aspect = get_layout_aspect(hub_node, node_classes)
cx['cartesianLayout'] =... | Attach a layout aspect to a CX network given a hub node. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/cx/hub_layout.py#L139-L145 |
sorgerlab/indra | indra/literature/crossref_client.py | get_metadata | def get_metadata(doi):
"""Returns the metadata of an article given its DOI from CrossRef
as a JSON dict"""
url = crossref_url + 'works/' + doi
res = requests.get(url)
if res.status_code != 200:
logger.info('Could not get CrossRef metadata for DOI %s, code %d' %
(doi, res.... | python | def get_metadata(doi):
"""Returns the metadata of an article given its DOI from CrossRef
as a JSON dict"""
url = crossref_url + 'works/' + doi
res = requests.get(url)
if res.status_code != 200:
logger.info('Could not get CrossRef metadata for DOI %s, code %d' %
(doi, res.... | Returns the metadata of an article given its DOI from CrossRef
as a JSON dict | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/crossref_client.py#L30-L41 |
sorgerlab/indra | indra/literature/crossref_client.py | get_fulltext_links | def get_fulltext_links(doi):
"""Return a list of links to the full text of an article given its DOI.
Each list entry is a dictionary with keys:
- URL: the URL to the full text
- content-type: e.g. text/xml or text/plain
- content-version
- intended-application: e.g. text-mining
"""
metad... | python | def get_fulltext_links(doi):
"""Return a list of links to the full text of an article given its DOI.
Each list entry is a dictionary with keys:
- URL: the URL to the full text
- content-type: e.g. text/xml or text/plain
- content-version
- intended-application: e.g. text-mining
"""
metad... | Return a list of links to the full text of an article given its DOI.
Each list entry is a dictionary with keys:
- URL: the URL to the full text
- content-type: e.g. text/xml or text/plain
- content-version
- intended-application: e.g. text-mining | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/crossref_client.py#L43-L55 |
sorgerlab/indra | indra/literature/crossref_client.py | doi_query | def doi_query(pmid, search_limit=10):
"""Get the DOI for a PMID by matching CrossRef and Pubmed metadata.
Searches CrossRef using the article title and then accepts search hits only
if they have a matching journal ISSN and page number with what is obtained
from the Pubmed database.
"""
# Get ar... | python | def doi_query(pmid, search_limit=10):
"""Get the DOI for a PMID by matching CrossRef and Pubmed metadata.
Searches CrossRef using the article title and then accepts search hits only
if they have a matching journal ISSN and page number with what is obtained
from the Pubmed database.
"""
# Get ar... | Get the DOI for a PMID by matching CrossRef and Pubmed metadata.
Searches CrossRef using the article title and then accepts search hits only
if they have a matching journal ISSN and page number with what is obtained
from the Pubmed database. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/crossref_client.py#L81-L177 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | get_agent_rule_str | def get_agent_rule_str(agent):
"""Construct a string from an Agent as part of a PySB rule name."""
rule_str_list = [_n(agent.name)]
# If it's a molecular agent
if isinstance(agent, ist.Agent):
for mod in agent.mods:
mstr = abbrevs[mod.mod_type]
if mod.residue is not None:... | python | def get_agent_rule_str(agent):
"""Construct a string from an Agent as part of a PySB rule name."""
rule_str_list = [_n(agent.name)]
# If it's a molecular agent
if isinstance(agent, ist.Agent):
for mod in agent.mods:
mstr = abbrevs[mod.mod_type]
if mod.residue is not None:... | Construct a string from an Agent as part of a PySB rule name. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L55-L90 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | add_rule_to_model | def add_rule_to_model(model, rule, annotations=None):
"""Add a Rule to a PySB model and handle duplicate component errors."""
try:
model.add_component(rule)
# If the rule was actually added, also add the annotations
if annotations:
model.annotations += annotations
# If th... | python | def add_rule_to_model(model, rule, annotations=None):
"""Add a Rule to a PySB model and handle duplicate component errors."""
try:
model.add_component(rule)
# If the rule was actually added, also add the annotations
if annotations:
model.annotations += annotations
# If th... | Add a Rule to a PySB model and handle duplicate component errors. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L93-L103 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | get_create_parameter | def get_create_parameter(model, param):
"""Return parameter with given name, creating it if needed.
If unique is false and the parameter exists, the value is not changed; if
it does not exist, it will be created. If unique is true then upon conflict
a number is added to the end of the parameter name.
... | python | def get_create_parameter(model, param):
"""Return parameter with given name, creating it if needed.
If unique is false and the parameter exists, the value is not changed; if
it does not exist, it will be created. If unique is true then upon conflict
a number is added to the end of the parameter name.
... | Return parameter with given name, creating it if needed.
If unique is false and the parameter exists, the value is not changed; if
it does not exist, it will be created. If unique is true then upon conflict
a number is added to the end of the parameter name.
Parameters
----------
model : pysb.... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L106-L138 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | get_uncond_agent | def get_uncond_agent(agent):
"""Construct the unconditional state of an Agent.
The unconditional Agent is a copy of the original agent but
without any bound conditions and modification conditions.
Mutation conditions, however, are preserved since they are static.
"""
agent_uncond = ist.Agent(_n... | python | def get_uncond_agent(agent):
"""Construct the unconditional state of an Agent.
The unconditional Agent is a copy of the original agent but
without any bound conditions and modification conditions.
Mutation conditions, however, are preserved since they are static.
"""
agent_uncond = ist.Agent(_n... | Construct the unconditional state of an Agent.
The unconditional Agent is a copy of the original agent but
without any bound conditions and modification conditions.
Mutation conditions, however, are preserved since they are static. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L141-L149 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | grounded_monomer_patterns | def grounded_monomer_patterns(model, agent, ignore_activities=False):
"""Get monomer patterns for the agent accounting for grounding information.
Parameters
----------
model : pysb.core.Model
The model to search for MonomerPatterns matching the given Agent.
agent : indra.statements.Agent
... | python | def grounded_monomer_patterns(model, agent, ignore_activities=False):
"""Get monomer patterns for the agent accounting for grounding information.
Parameters
----------
model : pysb.core.Model
The model to search for MonomerPatterns matching the given Agent.
agent : indra.statements.Agent
... | Get monomer patterns for the agent accounting for grounding information.
Parameters
----------
model : pysb.core.Model
The model to search for MonomerPatterns matching the given Agent.
agent : indra.statements.Agent
The Agent to find matching MonomerPatterns for.
ignore_activites : ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L152-L281 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | get_monomer_pattern | def get_monomer_pattern(model, agent, extra_fields=None):
"""Construct a PySB MonomerPattern from an Agent."""
try:
monomer = model.monomers[_n(agent.name)]
except KeyError as e:
logger.warning('Monomer with name %s not found in model' %
_n(agent.name))
return ... | python | def get_monomer_pattern(model, agent, extra_fields=None):
"""Construct a PySB MonomerPattern from an Agent."""
try:
monomer = model.monomers[_n(agent.name)]
except KeyError as e:
logger.warning('Monomer with name %s not found in model' %
_n(agent.name))
return ... | Construct a PySB MonomerPattern from an Agent. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L293-L319 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | get_site_pattern | def get_site_pattern(agent):
"""Construct a dictionary of Monomer site states from an Agent.
This crates the mapping to the associated PySB monomer from an
INDRA Agent object."""
if not isinstance(agent, ist.Agent):
return {}
pattern = {}
# Handle bound conditions
for bc in agent.bo... | python | def get_site_pattern(agent):
"""Construct a dictionary of Monomer site states from an Agent.
This crates the mapping to the associated PySB monomer from an
INDRA Agent object."""
if not isinstance(agent, ist.Agent):
return {}
pattern = {}
# Handle bound conditions
for bc in agent.bo... | Construct a dictionary of Monomer site states from an Agent.
This crates the mapping to the associated PySB monomer from an
INDRA Agent object. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L322-L375 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | set_base_initial_condition | def set_base_initial_condition(model, monomer, value):
"""Set an initial condition for a monomer in its 'default' state."""
# Build up monomer pattern dict
sites_dict = {}
for site in monomer.sites:
if site in monomer.site_states:
if site == 'loc' and 'cytoplasm' in monomer.site_stat... | python | def set_base_initial_condition(model, monomer, value):
"""Set an initial condition for a monomer in its 'default' state."""
# Build up monomer pattern dict
sites_dict = {}
for site in monomer.sites:
if site in monomer.site_states:
if site == 'loc' and 'cytoplasm' in monomer.site_stat... | Set an initial condition for a monomer in its 'default' state. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L378-L398 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | get_annotation | def get_annotation(component, db_name, db_ref):
"""Construct model Annotations for each component.
Annotation formats follow guidelines at http://identifiers.org/.
"""
url = get_identifiers_url(db_name, db_ref)
if not url:
return None
subj = component
ann = Annotation(subj, url, 'is... | python | def get_annotation(component, db_name, db_ref):
"""Construct model Annotations for each component.
Annotation formats follow guidelines at http://identifiers.org/.
"""
url = get_identifiers_url(db_name, db_ref)
if not url:
return None
subj = component
ann = Annotation(subj, url, 'is... | Construct model Annotations for each component.
Annotation formats follow guidelines at http://identifiers.org/. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L432-L442 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | parse_identifiers_url | def parse_identifiers_url(url):
"""Parse an identifiers.org URL into (namespace, ID) tuple."""
url_pattern = 'http://identifiers.org/([A-Za-z]+)/([A-Za-z0-9:]+)'
match = re.match(url_pattern, url)
if match is not None:
g = match.groups()
if not len(g) == 2:
return (None, None... | python | def parse_identifiers_url(url):
"""Parse an identifiers.org URL into (namespace, ID) tuple."""
url_pattern = 'http://identifiers.org/([A-Za-z]+)/([A-Za-z0-9:]+)'
match = re.match(url_pattern, url)
if match is not None:
g = match.groups()
if not len(g) == 2:
return (None, None... | Parse an identifiers.org URL into (namespace, ID) tuple. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L444-L467 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | complex_monomers_one_step | def complex_monomers_one_step(stmt, agent_set):
"""In this (very simple) implementation, proteins in a complex are
each given site names corresponding to each of the other members
of the complex (lower case). So the resulting complex can be
"fully connected" in that each member can be bound to
all t... | python | def complex_monomers_one_step(stmt, agent_set):
"""In this (very simple) implementation, proteins in a complex are
each given site names corresponding to each of the other members
of the complex (lower case). So the resulting complex can be
"fully connected" in that each member can be bound to
all t... | In this (very simple) implementation, proteins in a complex are
each given site names corresponding to each of the other members
of the complex (lower case). So the resulting complex can be
"fully connected" in that each member can be bound to
all the others. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L917-L932 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler.make_model | def make_model(self, policies=None, initial_conditions=True,
reverse_effects=False, model_name='indra_model'):
"""Assemble the PySB model from the collected INDRA Statements.
This method assembles a PySB model from the set of INDRA Statements.
The assembled model is both retu... | python | def make_model(self, policies=None, initial_conditions=True,
reverse_effects=False, model_name='indra_model'):
"""Assemble the PySB model from the collected INDRA Statements.
This method assembles a PySB model from the set of INDRA Statements.
The assembled model is both retu... | Assemble the PySB model from the collected INDRA Statements.
This method assembles a PySB model from the set of INDRA Statements.
The assembled model is both returned and set as the assembler's
model argument.
Parameters
----------
policies : Optional[Union[str, dict]]
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L546-L626 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler.add_default_initial_conditions | def add_default_initial_conditions(self, value=None):
"""Set default initial conditions in the PySB model.
Parameters
----------
value : Optional[float]
Optionally a value can be supplied which will be the initial
amount applied. Otherwise a built-in default is u... | python | def add_default_initial_conditions(self, value=None):
"""Set default initial conditions in the PySB model.
Parameters
----------
value : Optional[float]
Optionally a value can be supplied which will be the initial
amount applied. Otherwise a built-in default is u... | Set default initial conditions in the PySB model.
Parameters
----------
value : Optional[float]
Optionally a value can be supplied which will be the initial
amount applied. Otherwise a built-in default is used. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L628-L648 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler.set_expression | def set_expression(self, expression_dict):
"""Set protein expression amounts as initial conditions
Parameters
----------
expression_dict : dict
A dictionary in which the keys are gene names and the
values are numbers representing the absolute amount
(... | python | def set_expression(self, expression_dict):
"""Set protein expression amounts as initial conditions
Parameters
----------
expression_dict : dict
A dictionary in which the keys are gene names and the
values are numbers representing the absolute amount
(... | Set protein expression amounts as initial conditions
Parameters
----------
expression_dict : dict
A dictionary in which the keys are gene names and the
values are numbers representing the absolute amount
(count per cell) of proteins expressed. Proteins that
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L650-L694 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler.set_context | def set_context(self, cell_type):
"""Set protein expression amounts from CCLE as initial conditions.
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels for a given cell type and set initial
conditions for Monomers in the model accordingly.
... | python | def set_context(self, cell_type):
"""Set protein expression amounts from CCLE as initial conditions.
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels for a given cell type and set initial
conditions for Monomers in the model accordingly.
... | Set protein expression amounts from CCLE as initial conditions.
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels for a given cell type and set initial
conditions for Monomers in the model accordingly.
Parameters
----------
cell_... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L696-L721 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler.export_model | def export_model(self, format, file_name=None):
"""Save the assembled model in a modeling formalism other than PySB.
For more details on exporting PySB models, see
http://pysb.readthedocs.io/en/latest/modules/export/index.html
Parameters
----------
format : str
... | python | def export_model(self, format, file_name=None):
"""Save the assembled model in a modeling formalism other than PySB.
For more details on exporting PySB models, see
http://pysb.readthedocs.io/en/latest/modules/export/index.html
Parameters
----------
format : str
... | Save the assembled model in a modeling formalism other than PySB.
For more details on exporting PySB models, see
http://pysb.readthedocs.io/en/latest/modules/export/index.html
Parameters
----------
format : str
The format to export into, for instance "kappa", "bngl"... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L746-L789 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler.save_rst | def save_rst(self, file_name='pysb_model.rst', module_name='pysb_module'):
"""Save the assembled model as an RST file for literate modeling.
Parameters
----------
file_name : Optional[str]
The name of the file to save the RST in.
Default: pysb_model.rst
m... | python | def save_rst(self, file_name='pysb_model.rst', module_name='pysb_module'):
"""Save the assembled model as an RST file for literate modeling.
Parameters
----------
file_name : Optional[str]
The name of the file to save the RST in.
Default: pysb_model.rst
m... | Save the assembled model as an RST file for literate modeling.
Parameters
----------
file_name : Optional[str]
The name of the file to save the RST in.
Default: pysb_model.rst
module_name : Optional[str]
The name of the python function defining the mo... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L792-L812 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler._dispatch | def _dispatch(self, stmt, stage, *args):
"""Construct and call an assembly function.
This function constructs the name of the assembly function based on
the type of statement, the corresponding policy and the stage
of assembly. It then calls that function to perform the assembly
... | python | def _dispatch(self, stmt, stage, *args):
"""Construct and call an assembly function.
This function constructs the name of the assembly function based on
the type of statement, the corresponding policy and the stage
of assembly. It then calls that function to perform the assembly
... | Construct and call an assembly function.
This function constructs the name of the assembly function based on
the type of statement, the corresponding policy and the stage
of assembly. It then calls that function to perform the assembly
task. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L814-L842 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler._monomers | def _monomers(self):
"""Calls the appropriate monomers method based on policies."""
for stmt in self.statements:
if _is_whitelisted(stmt):
self._dispatch(stmt, 'monomers', self.agent_set) | python | def _monomers(self):
"""Calls the appropriate monomers method based on policies."""
for stmt in self.statements:
if _is_whitelisted(stmt):
self._dispatch(stmt, 'monomers', self.agent_set) | Calls the appropriate monomers method based on policies. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L844-L848 |
sorgerlab/indra | indra/assemblers/pysb/assembler.py | PysbAssembler._assemble | def _assemble(self):
"""Calls the appropriate assemble method based on policies."""
for stmt in self.statements:
pol = self.processed_policies[stmt.uuid]
if _is_whitelisted(stmt):
self._dispatch(stmt, 'assemble', self.model, self.agent_set,
... | python | def _assemble(self):
"""Calls the appropriate assemble method based on policies."""
for stmt in self.statements:
pol = self.processed_policies[stmt.uuid]
if _is_whitelisted(stmt):
self._dispatch(stmt, 'assemble', self.model, self.agent_set,
... | Calls the appropriate assemble method based on policies. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/assemblers/pysb/assembler.py#L850-L856 |
sorgerlab/indra | indra/sources/trips/client.py | send_query | def send_query(text, service_endpoint='drum', query_args=None):
"""Send a query to the TRIPS web service.
Parameters
----------
text : str
The text to be processed.
service_endpoint : Optional[str]
Selects the TRIPS/DRUM web service endpoint to use. Is a choice between
"drum... | python | def send_query(text, service_endpoint='drum', query_args=None):
"""Send a query to the TRIPS web service.
Parameters
----------
text : str
The text to be processed.
service_endpoint : Optional[str]
Selects the TRIPS/DRUM web service endpoint to use. Is a choice between
"drum... | Send a query to the TRIPS web service.
Parameters
----------
text : str
The text to be processed.
service_endpoint : Optional[str]
Selects the TRIPS/DRUM web service endpoint to use. Is a choice between
"drum" (default), "drum-dev", a nightly build, and "cwms" for use with
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/client.py#L15-L48 |
sorgerlab/indra | indra/sources/trips/client.py | get_xml | def get_xml(html, content_tag='ekb', fail_if_empty=False):
"""Extract the content XML from the HTML output of the TRIPS web service.
Parameters
----------
html : str
The HTML output from the TRIPS web service.
content_tag : str
The xml tag used to label the content. Default is 'ekb'... | python | def get_xml(html, content_tag='ekb', fail_if_empty=False):
"""Extract the content XML from the HTML output of the TRIPS web service.
Parameters
----------
html : str
The HTML output from the TRIPS web service.
content_tag : str
The xml tag used to label the content. Default is 'ekb'... | Extract the content XML from the HTML output of the TRIPS web service.
Parameters
----------
html : str
The HTML output from the TRIPS web service.
content_tag : str
The xml tag used to label the content. Default is 'ekb'.
fail_if_empty : bool
If True, and if the xml content... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/client.py#L51-L88 |
sorgerlab/indra | indra/sources/trips/client.py | save_xml | def save_xml(xml_str, file_name, pretty=True):
"""Save the TRIPS EKB XML in a file.
Parameters
----------
xml_str : str
The TRIPS EKB XML string to be saved.
file_name : str
The name of the file to save the result in.
pretty : Optional[bool]
If True, the XML is pretty pr... | python | def save_xml(xml_str, file_name, pretty=True):
"""Save the TRIPS EKB XML in a file.
Parameters
----------
xml_str : str
The TRIPS EKB XML string to be saved.
file_name : str
The name of the file to save the result in.
pretty : Optional[bool]
If True, the XML is pretty pr... | Save the TRIPS EKB XML in a file.
Parameters
----------
xml_str : str
The TRIPS EKB XML string to be saved.
file_name : str
The name of the file to save the result in.
pretty : Optional[bool]
If True, the XML is pretty printed. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/trips/client.py#L91-L114 |
sorgerlab/indra | indra/sources/sofia/api.py | process_table | def process_table(fname):
"""Return processor by processing a given sheet of a spreadsheet file.
Parameters
----------
fname : str
The name of the Excel file (typically .xlsx extension) to process
Returns
-------
sp : indra.sources.sofia.processor.SofiaProcessor
A SofiaProc... | python | def process_table(fname):
"""Return processor by processing a given sheet of a spreadsheet file.
Parameters
----------
fname : str
The name of the Excel file (typically .xlsx extension) to process
Returns
-------
sp : indra.sources.sofia.processor.SofiaProcessor
A SofiaProc... | Return processor by processing a given sheet of a spreadsheet file.
Parameters
----------
fname : str
The name of the Excel file (typically .xlsx extension) to process
Returns
-------
sp : indra.sources.sofia.processor.SofiaProcessor
A SofiaProcessor object which has a list of ... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sofia/api.py#L9-L32 |
sorgerlab/indra | indra/sources/sofia/api.py | process_text | def process_text(text, out_file='sofia_output.json', auth=None):
"""Return processor by processing text given as a string.
Parameters
----------
text : str
A string containing the text to be processed with Sofia.
out_file : Optional[str]
The path to a file to save the reader's outpu... | python | def process_text(text, out_file='sofia_output.json', auth=None):
"""Return processor by processing text given as a string.
Parameters
----------
text : str
A string containing the text to be processed with Sofia.
out_file : Optional[str]
The path to a file to save the reader's outpu... | Return processor by processing text given as a string.
Parameters
----------
text : str
A string containing the text to be processed with Sofia.
out_file : Optional[str]
The path to a file to save the reader's output into.
Default: sofia_output.json
auth : Optional[list]
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/sofia/api.py#L35-L80 |
sorgerlab/indra | indra/sources/ndex_cx/processor.py | _get_dict_from_list | def _get_dict_from_list(dict_key, list_of_dicts):
"""Retrieve a specific dict from a list of dicts.
Parameters
----------
dict_key : str
The (single) key of the dict to be retrieved from the list.
list_of_dicts : list
The list of dicts to search for the specific dict.
Returns
... | python | def _get_dict_from_list(dict_key, list_of_dicts):
"""Retrieve a specific dict from a list of dicts.
Parameters
----------
dict_key : str
The (single) key of the dict to be retrieved from the list.
list_of_dicts : list
The list of dicts to search for the specific dict.
Returns
... | Retrieve a specific dict from a list of dicts.
Parameters
----------
dict_key : str
The (single) key of the dict to be retrieved from the list.
list_of_dicts : list
The list of dicts to search for the specific dict.
Returns
-------
dict value
The value associated wi... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/ndex_cx/processor.py#L22-L42 |
sorgerlab/indra | indra/sources/ndex_cx/processor.py | NdexCxProcessor._initialize_node_agents | def _initialize_node_agents(self):
"""Initialize internal dicts containing node information."""
nodes = _get_dict_from_list('nodes', self.cx)
invalid_genes = []
for node in nodes:
id = node['@id']
cx_db_refs = self.get_aliases(node)
up_id = cx_db_refs.... | python | def _initialize_node_agents(self):
"""Initialize internal dicts containing node information."""
nodes = _get_dict_from_list('nodes', self.cx)
invalid_genes = []
for node in nodes:
id = node['@id']
cx_db_refs = self.get_aliases(node)
up_id = cx_db_refs.... | Initialize internal dicts containing node information. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/ndex_cx/processor.py#L78-L116 |
sorgerlab/indra | indra/sources/ndex_cx/processor.py | NdexCxProcessor.get_pmids | def get_pmids(self):
"""Get list of all PMIDs associated with edges in the network."""
pmids = []
for ea in self._edge_attributes.values():
edge_pmids = ea.get('pmids')
if edge_pmids:
pmids += edge_pmids
return list(set(pmids)) | python | def get_pmids(self):
"""Get list of all PMIDs associated with edges in the network."""
pmids = []
for ea in self._edge_attributes.values():
edge_pmids = ea.get('pmids')
if edge_pmids:
pmids += edge_pmids
return list(set(pmids)) | Get list of all PMIDs associated with edges in the network. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/ndex_cx/processor.py#L166-L173 |
sorgerlab/indra | indra/sources/ndex_cx/processor.py | NdexCxProcessor.get_statements | def get_statements(self):
"""Convert network edges into Statements.
Returns
-------
list of Statements
Converted INDRA Statements.
"""
edges = _get_dict_from_list('edges', self.cx)
for edge in edges:
edge_type = edge.get('i')
i... | python | def get_statements(self):
"""Convert network edges into Statements.
Returns
-------
list of Statements
Converted INDRA Statements.
"""
edges = _get_dict_from_list('edges', self.cx)
for edge in edges:
edge_type = edge.get('i')
i... | Convert network edges into Statements.
Returns
-------
list of Statements
Converted INDRA Statements. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/ndex_cx/processor.py#L175-L204 |
sorgerlab/indra | indra/sources/ndex_cx/processor.py | NdexCxProcessor._create_evidence | def _create_evidence(self, edge_id):
"""Create Evidence object for a specific edge/Statement in the network.
Parameters
----------
edge_id : int
ID of the edge in the underlying NDEx network.
"""
pmids = None
edge_attr = self._edge_attributes.get(edge... | python | def _create_evidence(self, edge_id):
"""Create Evidence object for a specific edge/Statement in the network.
Parameters
----------
edge_id : int
ID of the edge in the underlying NDEx network.
"""
pmids = None
edge_attr = self._edge_attributes.get(edge... | Create Evidence object for a specific edge/Statement in the network.
Parameters
----------
edge_id : int
ID of the edge in the underlying NDEx network. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/ndex_cx/processor.py#L206-L230 |
sorgerlab/indra | indra/sources/tees/processor.py | TEESProcessor.node_has_edge_with_label | def node_has_edge_with_label(self, node_name, edge_label):
"""Looks for an edge from node_name to some other node with the specified
label. Returns the node to which this edge points if it exists, or None
if it doesn't.
Parameters
----------
G :
The graph obj... | python | def node_has_edge_with_label(self, node_name, edge_label):
"""Looks for an edge from node_name to some other node with the specified
label. Returns the node to which this edge points if it exists, or None
if it doesn't.
Parameters
----------
G :
The graph obj... | Looks for an edge from node_name to some other node with the specified
label. Returns the node to which this edge points if it exists, or None
if it doesn't.
Parameters
----------
G :
The graph object
node_name :
Node that the edge starts at
... | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/tees/processor.py#L83-L104 |
sorgerlab/indra | indra/sources/tees/processor.py | TEESProcessor.general_node_label | def general_node_label(self, node):
"""Used for debugging - gives a short text description of a
graph node."""
G = self.G
if G.node[node]['is_event']:
return 'event type=' + G.node[node]['type']
else:
return 'entity text=' + G.node[node]['text'] | python | def general_node_label(self, node):
"""Used for debugging - gives a short text description of a
graph node."""
G = self.G
if G.node[node]['is_event']:
return 'event type=' + G.node[node]['type']
else:
return 'entity text=' + G.node[node]['text'] | Used for debugging - gives a short text description of a
graph node. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/tees/processor.py#L106-L113 |
sorgerlab/indra | indra/sources/tees/processor.py | TEESProcessor.print_parent_and_children_info | def print_parent_and_children_info(self, node):
"""Used for debugging - prints a short description of a a node, its
children, its parents, and its parents' children."""
G = self.G
parents = G.predecessors(node)
children = G.successors(node)
print(general_node_label(G, no... | python | def print_parent_and_children_info(self, node):
"""Used for debugging - prints a short description of a a node, its
children, its parents, and its parents' children."""
G = self.G
parents = G.predecessors(node)
children = G.successors(node)
print(general_node_label(G, no... | Used for debugging - prints a short description of a a node, its
children, its parents, and its parents' children. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/tees/processor.py#L115-L136 |
sorgerlab/indra | indra/sources/tees/processor.py | TEESProcessor.find_event_parent_with_event_child | def find_event_parent_with_event_child(self, parent_name, child_name):
"""Finds all event nodes (is_event node attribute is True) that are
of the type parent_name, that have a child event node with the type
child_name."""
G = self.G
matches = []
for n in G.node.keys():
... | python | def find_event_parent_with_event_child(self, parent_name, child_name):
"""Finds all event nodes (is_event node attribute is True) that are
of the type parent_name, that have a child event node with the type
child_name."""
G = self.G
matches = []
for n in G.node.keys():
... | Finds all event nodes (is_event node attribute is True) that are
of the type parent_name, that have a child event node with the type
child_name. | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/tees/processor.py#L138-L152 |
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