rotifer.db.ncbi.entrez

Access NCBI databases through the Entrez E-utilities.

Cursors in this module download sequences, identical protein group (IPG) reports, taxonomy records, nucleotide feature tables and gene neighborhoods with Biopython’s Bio.Entrez interface to the NCBI E-utilities web service.

Network, authentication and rate limits

Every request sends the user email registered in the rotifer.db.ncbi configuration and the API key from the NCBI_API_KEY environment variable, when set. Without an API key NCBI allows 3 requests per second and the cursors cap themselves at 3 simultaneous threads; with a key the cap is 10 threads. No data is cached locally.

Functions

elink(accessions[, dbfrom, dbto, linkname])	Find related database entries with the ELink E-utility.
nucleotide2assembly(nucids)	Map nucleotide accessions to their genome assemblies.

Classes

FastaCursor([database, progress, tries, ...])	Fetch sequences from NCBI as FASTA, without annotations.
GeneNeighborhoodCursor([column, before, ...])	Fetch gene neighborhoods from nucleotide annotation.
IPGCursor([progress, tries, ...])	Fetch identical protein group (IPG) reports from NCBI.
NucleotideFeaturesCursor([exclude_type, ...])	Fetch nucleotide annotation as feature tables.
SequenceCursor([database, progress, tries, ...])	Fetch annotated sequences from NCBI with the E-utilities.
TaxonomyCursor([progress, tries, ...])	Fetch NCBI Taxonomy records with the E-utilities.