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Cool-Seq-Tool |version|

PyPI version License

PyPI - supported Python versions

tests status

The Common Operations On Lots-Of Sequences Tool, Cool-Seq-Tool, provides:

  • A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, MANE transcript descriptions, and transcript alignment data from the Universal Transcript Archive
  • Augmented access to the SeqRepo database, including multiple additional methods and tools
  • Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined :ref:`here <transcript_selection_policy>`, that combine the above to support translation between various references sequences and annotation layers, and transcripts

See the :ref:`Installation <installation>` and :ref:`Usage <usage>` pages for information on getting started. Individual classes and methods are documented within the :ref:`API reference <api_reference>`.

Cool-Seq-Tool was created to support the Knowledgebase Integration Project of the Variant Interpretation for Cancer Consortium (VICC). It is developed primarily by the Wagner Lab. Full source code is available on GitHub.

.. toctree::
   :hidden:
   :maxdepth: 2

    Installation<install>
    Usage<usage>
    Transcript Selection<transcript_selection>
    API Reference<reference/index>
    Contributing<contributing>
    Changelog<changelog>
    License<license>