rotifer.db#

Access biological sequence and annotation databases.

This package provides a uniform, cursor based interface to remote repositories (NCBI Entrez, the NCBI FTP site, the UniProt REST API) and to local resources (indexed FASTA files, NCBI genome mirrors, SQLite3 stores and the ETE toolkit taxonomy database).

Every data source is wrapped in a cursor class derived from rotifer.db.core.BaseCursor. Cursors share three access styles:

  • dictionary-like access to a single entry, cursor[accession]

  • lazy iteration over many entries, fetchone

  • bulk retrieval of many entries, fetchall

See rotifer.db.ncbi for the most complete set of cursors.

Configuration#

The default path for local sequence databases is read from the user configuration file ~/.rotifer/etc/db.yml (key local_database_path) and falls back to fadb/nr/nr under the directory named by the ROTIFER_DATA environment variable.

Functions

proteins(query[, methods, ...])

Fetch protein sequences from local or remote databases.