databases: accept local FASTA paths for easy nucleotide DB creation#4
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databases: accept local FASTA paths for easy nucleotide DB creation#4antonvnv wants to merge 1 commit into
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Building a nucleotide database from a FASTA file previously required manually chaining createdb, splitsequence, makepaddedseqdb, and createindex with the right flags. Now a single command does it: mmseqs databases ./input.fasta.gz outdb tmp Both relative (./...) and absolute (/...) paths work — any argument containing '/' that isn't a known database name is treated as a local file. Protein inputs are rejected with a clear error since the indexing pipeline is nucleotide-specific. This keeps `databases` as the single entry point to maintain indexing requirements, and makes it suitable for reindexing external or already manually downloaded databases.
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Building a nucleotide database from a FASTA file previously required manually chaining createdb, splitsequence, makepaddedseqdb, and createindex with the right flags. Now a single command does it:
mmseqs databases ./input.fasta.gz outdb tmp
Both relative (./...) and absolute (/...) paths work — any argument containing '/' that isn't a known database name is treated as a local file. Protein inputs are rejected with a clear error since the indexing pipeline is nucleotide-specific.
This keeps
databasesas the single entry point to maintain indexing requirements, and makes it suitable for reindexing external or already manually downloaded databases.