Add RNAcentral databases and download caching to mmseqs databases#5
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antonvnv wants to merge 3 commits into
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Add RNAcentral databases and download caching to mmseqs databases#5antonvnv wants to merge 3 commits 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.
Add a --download-dir parameter (default: "downloads") that provides a persistent cache directory for downloaded files. This avoids re-downloading large files across runs. The directory is resolved to an absolute path and created if it does not exist. The shell script receives it as DOWNLOAD_DIR environment variable.
Add RNAcentral active sequences as downloadable databases: - RNAcentral_current: latest release (non-deterministic) - RNAcentral_26_0: pinned release 26.0 (deterministic) Both use the LOCAL_FASTA pipeline for nucleotide indexing and store downloads under <download-dir>/<dbname>/ subdirectories.
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Add RNAcentral databases and download caching to mmseqs databases
Based on PR #4 which adds local nucleotide database indexing via
mmseqs databases ./file.fasta.gz db tmpChanges
Adds a persistent download cache directory (default: downloads/) so that large files are not re-downloaded across runs. When the file already exists in the cache, the download is skipped. Only active for named
databases — local file paths do not create the directory.
Adds two new named databases:
Both download rnacentral_active.fasta.gz and index it using the nucleotide pipeline (createdb → splitsequence → makepaddedseqdb → createindex). Downloads are stored under // subdirectories.
Usage