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AnthonyGarza124 merged 1 commit into from
Sep 22, 2026
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Update BLAST documentation #13

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16 changes: 5 additions & 11 deletions docs/api/blast.rst
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Expand Up @@ -12,22 +12,16 @@ sequence-ID index. The existing SCC ``human_mouse_nr`` database was built
without that index and must be rebuilt before it can support an end-to-end
``LocalBlastSearcher`` run.

Both adapters return :class:`lverage.ortholog_searcher.OrthologRecord` objects.
``LocalBlastSearcher`` returns :class:`lverage.ortholog_searcher.OrthologRecord`
objects.
Identity and query coverage are ratios from zero to one. Individual malformed,
excluded, unresolved, or unretrievable hits are skipped and logged; executable,
database, subprocess, HTTP, timeout, and whole-result parsing failures are
raised to the caller.
database, subprocess, timeout, and whole-result parsing failures are raised to
the caller.

``LocalBlastSearcher`` validates a database prefix with ``blastdbcmd -info``
and retrieves complete subject proteins from that database. The remote adapter
runs BLAST+ with ``-remote`` and batch-fetches complete proteins through NCBI
E-utilities. NCBI services are shared: do not parallelize remote searches, and
prefer off-peak hours for larger workloads.
and retrieves complete subject proteins from that database.

.. autoclass:: lverage.blast.LocalBlastSearcher
:members:
:show-inheritance:

.. autoclass:: lverage.blast.RemoteBlastSearcher
:members:
:show-inheritance:
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