SIGNOR (indra.sources.signor)¶
SIGNOR API (indra.sources.signor.api)¶
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indra.sources.signor.api.process_from_file(signor_data_file, signor_complexes_file=None)[source]¶ 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 to their constitutents.
Returns: SignorProcessor containing Statements extracted from the Signor data.
Return type: indra.sources.signor.SignorProcessor
SIGNOR Processor (indra.sources.signor.processor)¶
An input processor for the SIGNOR database: a database of causal relationships between biological entities.
See publication:
Perfetto et al., “SIGNOR: a database of causal relationships between biological entities,” Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D548-D554. https://doi.org/10.1093/nar/gkv1048
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class
indra.sources.signor.processor.SignorProcessor(data, complex_map=None)[source]¶ Processor for Signor dataset, available at http://signor.uniroma2.it.
Parameters: - data (iterator) – Iterator over rows of a SIGNOR CSV file.
- complex_map (dict) – A dict containing SIGNOR complexes, keyed by their IDs.
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statements¶ A list of INDRA Statements extracted from the SIGNOR table.
Type: list[indra.statements.Statements]
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no_mech_rows¶ List of rows where no mechanism statements were generated.
Type: list of SignorRow namedtuples
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no_mech_ctr¶ Counter listing the frequency of different MECHANISM types in the list of no-mechanism rows.
Type: collections.Counter