Entrez¶

class Entrez(email, api_key=None, tool='PhyloMAF')[source]¶

Remote class responsible for batch data fetching from NCBI’s Entrez API Schuler et al. [SEOK96]

Create Entrez instance to connect to NCBI database.

Parameters

email (str) – User’s email that will be passed to NCBI server
api_key (Optional[str]) – User’s API key obtained from NCBI account page. Default is None(without key). However, it is recommended to obtain an API key for faster access.
tool (str) – Label of the tool that will be passed to NCBI server. Default is “PhyloMAF”`

Attributes

state

State of the instance.

Methods

`check_init`()	Check instance ready status.
`filter_genes_from_future_table`(seq_raw_io, gene)	Filter/extract genes from NCBI gene feature table.
`get_chromosome_id_by_genome_id`(genome_id)	Get NCBI’s chromosome ID by target genome_id
`get_fasta_sequence_by_param`(accession_id, …)	Get FASTA string from NCBI database by accesion_id
`get_gene_features_by_chromosome_id`(chromosome_id)	Get gene features by chromosome ID.
`get_genome_id_by_taxid`(taxid)	Get NCBI’s genome ID by target taxid
`get_request_logs`()	Get low level request codes for debugging.
`get_taxid_by_query`(query)	Fetch NCBI taxonomy database using query and get a NCBI’s internal taxid.