rotifer.db.ncbi.ftp

Access genome data from the NCBI FTP site.

Cursors in this module locate genome assemblies under the genomes directory of the NCBI FTP server (ftp.ncbi.nlm.nih.gov by default), download their GenBank flat files and parse them into sequence records, feature tables or gene neighborhoods.

Network and caching

Connections are anonymous; no account or API key is needed. Every downloaded file is verified against the md5checksums.txt published next to it and stored in the rotifer cache directory (rotifer.config['cache']), from which it is removed once parsed. The FTP server address can be changed through the ftpserver entry of the rotifer.db.ncbi configuration.

Classes

GeneNeighborhoodCursor([column, before, ...])	Fetch gene neighborhoods from genomes at the NCBI FTP site.
GenomeCursor([progress, tries, batch_size, ...])	Fetch genome sequences from the NCBI FTP site.
GenomeFeaturesCursor([exclude_type, ...])	Fetch genome annotation from the NCBI FTP site as dataframes.
connection([url, tries, timeout, cache])	A live connection to the NCBI FTP server.