Retrieve all annotated features in a GenBank record
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2.1 years ago
al-ash ▴ 190

Is edirect supporting retrieval of all annotated features from a record?

Example: I can retrieve all features annotated as "gene" in GenBank record of a mitochondrial genome sequence :

efetch -db nucleotide -id KP026275  -format gene_fasta


However, the retrieved multifasta is missing the features not annotated as "gene", in this case two ribosomal RNAs. I would like to retrieve all features.

I can think of one solution, where I would first retrieve the feature table, then parse the genomic coordinates of all features and use them to extract the sequences of all the features, but this feels like re-inventing something which might be already implemented in edirect. Thanks for any hints & suggestions!

efetch edirect genbank feature annotations • 548 views
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Don't think there is a way to get those directly without parsing the feature table.