Hmmer again - #41

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AbhirupaGhosh wants to merge 17 commits into

mainfrom

Commits on Jul 30, 2026

Update runHMMER.R
AbhirupaGhosh
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7202f92
Modify HMM download and press
AbhirupaGhosh
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5b2de7b

Commits on Jul 31, 2026

default HMM database, start runHMMER from checking for database existence.
AbhirupaGhosh
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fe9bc57

Commits on Aug 4, 2026

Hmmering
AbhirupaGhosh
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239d716
change the stop with warning
AbhirupaGhosh
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cdc9fa4
protein_cluster_seq
AbhirupaGhosh
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9fe0af0
find the HMMs with old version and remove
AbhirupaGhosh
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a8cc93f
Roxygen skeleton for .defenseHMMER
AbhirupaGhosh
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a9974da
add the file validation check to .defenseHMMER
AbhirupaGhosh
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9ff53b6
Enhance documentation for HMMER functions with detailed parameter descriptions and examples
AbhirupaGhosh
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afd1132

Commits on Aug 5, 2026

hmmscan to hmmsearch
AbhirupaGhosh
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8d4cd66
incorporate description from HMM files in to the final HMMER output. co-authored by @epbrenner
AbhirupaGhosh
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895f53a
add description
AbhirupaGhosh
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f054deb
update .runHmmerJob()
AbhirupaGhosh
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ee55b36
update .proteinAnnotations2Duckdb() based on the new hmmer output parsing
AbhirupaGhosh
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190f84d
Update .defenseHMMER()
AbhirupaGhosh
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d316f2c
Update documentations
AbhirupaGhosh
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ce95c97