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High-throughput reading CLI's

The reading tools include several Python CLI's to run reading or other related tasks.

Run reading on local files

.. argparse::
    :module: indra.tools.reading.read_files
    :func: make_parser
    :prog: python -m indra.tools.reading.read_files

Run REACH and/or SPARSER locally on a list of PMIDs using S3 caching

.. argparse::
    :module: indra.tools.reading.pmid_reading.read_pmids
    :func: make_parser
    :prog: python -m indra.tools.reading.pmid_reading.read_pmids


Submit AWS Batch reading jobs

.. argparse::
    :module: indra.tools.reading.submit_reading_pipeline
    :func: create_parser
    :prog: python -m indra.tools.reading.submit_reading_pipeline


Monitor running AWS Batch jobs

.. argparse::
    :module: indra.tools.reading.wait_for_complete
    :func: make_parser
    :prog: python -m indra.tools.reading.wait_for_complete


Run the DRUM reading system

.. argparse::
    :module: indra.tools.reading.run_drum_reading
    :func: make_parser
    :prog: python -m indra.tools.reading.run_drum_reading


Generate stats on AWS Batch reading results

.. argparse::
    :module: indra.tools.reading.util.reading_results_stats
    :func: make_parser
    :prog: python -m indra.tools.reading.util.reading_results_stats
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