This function allows to search and download data from the the NCBI Nucleotide database. Additionally it uses the NCBI Taxonomy database to get the sequence taxonomic classification.
refdb_import_NCBI(query, full = FALSE, max_seq_length = 10000)
| query | a character string with the query. |
|---|---|
| full | a logical. If FALSE (the default), only a subset of the most important fields is included in the result. |
| max_seq_length | a numeric giving the maximum length of sequences to retrieve. Useful to exclude complete genomes. |
A tibble.
This function uses several functions of the rentrez package to interface with the NCBI's EUtils API.*
Error in curl::curl_fetch_memory(url, handle = handle) :
transfer closed with outstanding read data remaining
This error seems to appear with long sequences.
You can try to decrease max_seq_length to exclude them.