feat(blast): expose NCBI web BLAST algorithm parameters (#58)#229
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Elarwei001 wants to merge 3 commits into
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feat(blast): expose NCBI web BLAST algorithm parameters (#58)#229Elarwei001 wants to merge 3 commits into
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Add word_size, gapcosts, matrix, nucl_reward, nucl_penalty, and perc_identity arguments to `gget blast` (Python API and CLI) so the tool more fully matches the "Algorithm parameters" panel of the NCBI web BLAST app. Values are validated and forwarded to the BLAST URL API (WORD_SIZE, GAPCOSTS, MATRIX, NUCL_REWARD, NUCL_PENALTY, PERC_IDENT). All default to None (server default), preserving existing behavior. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #229 +/- ##
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+ Coverage 56.14% 56.67% +0.53%
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Files 29 29
Lines 9244 9275 +31
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+ Hits 5190 5257 +67
+ Misses 4054 4018 -36 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add unit tests for the invalid nucl_reward and nucl_penalty branches of _build_algorithm_params so the helper is fully covered network-free. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #58
Summary
gget blast: Exposed the NCBI web BLAST "Algorithm parameters" sogget blastmore fully matches the web app (resolves issue 58). New argumentsword_size,gapcosts,matrix,nucl_reward,nucl_penalty, andperc_identity(CLI:-ws/--word_size,-gc/--gapcosts,-mx/--matrix,-nr/--nucl_reward,-np/--nucl_penalty,-pi/--perc_identity) are validated and forwarded to the BLAST URL API (WORD_SIZE,GAPCOSTS,MATRIX,NUCL_REWARD,NUCL_PENALTY,PERC_IDENT). All default toNone(server default), so existing behavior is unchanged.Testing
Unit tests added/extended in
tests/test_blast.pywith fixture entries intests/fixtures/test_blast.json; run with pytest.