From a010174c33bfd1d3e81b41fd2b3318ef98bc9f1e Mon Sep 17 00:00:00 2001 From: Thomas Shin Date: Tue, 22 Sep 2026 10:08:21 -0400 Subject: [PATCH] Update BLAST documentation --- docs/api/blast.rst | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/docs/api/blast.rst b/docs/api/blast.rst index 266654b..398b8c8 100644 --- a/docs/api/blast.rst +++ b/docs/api/blast.rst @@ -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: