SAMap v2: samap.io onboarding + samap.analysis interpretation#176

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atarashansky wants to merge 17 commits into

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Commits on Apr 30, 2026

feat(init): warn on low var_names↔BLAST overlap with example IDs
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feat(io): add detect_id_flavor — regex classifier for var_names namespace
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feat(io): add fetch_proteome — derive protein FASTA from var_names
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feat(io): add match_fasta — score header transforms vs var_names
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feat(io): add gnnm_from_pairs + homology_from_eggnog
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feat(io): add run_blast (DIAMOND/BLAST+) and gnnm npz cache
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feat(cli): add `samap` CLI — detect-ids / fetch-proteome / match-fasta / blast
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docs: add docs/io.md onboarding guide; CHANGELOG + README for samap.io
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Commits on May 1, 2026

feat(io): add MMseqs2 engine to run_blast (incl. GPU + 6-frame nucl)
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Commits on May 2, 2026

Commits on May 3, 2026

feat(analysis): gene_modules densification via SNN + within-species coexpression
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Commits on May 4, 2026

Commits on May 5, 2026

docs(analysis): add docs/analysis.md onboarding guide for samap.analysis
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Commits on May 6, 2026

docs(analysis): correct BLAST-graph fragmentation characterization
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