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entrez-fetch

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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.

When to use

• downloading sequences
• fetching GenBank/GenPept records
• getting document summaries
• parsing nested XML
• navigating GI deprecation
• choosing rettype+retmode combinations
• parsing into Biopython SeqRecord/SwissProt objects
• retrieving nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar records

When not to use

• full GEO downloads via FTP mirror
• using GEOparse

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