ncbi_byid: Retrieve gene sequences from NCBI by accession number.

In ropensci/traits: Species Trait Data from Around the Web

Retrieve gene sequences from NCBI by accession number.

Description

Retrieve gene sequences from NCBI by accession number.

Usage

ncbi_byid(ids, format = NULL, verbose = TRUE)

Arguments

ids	(character) GenBank ids to search for. One or more. Required.
format	(character) Return type, e.g., "fasta". NOW IGNORED.
verbose	(logical) If TRUE (default), informative messages printed.

Details

If bad ids are included with good ones, the bad ones are silently dropped. If all ids are bad you'll get a stop with error message.

Value

data.frame of the form:

• taxon - taxonomic name (may include some junk, but hard to parse off)

• taxonomy - organism lineage

• gene_desc - gene description

• organelle - if mitochondrial or chloroplast

• gi_no - GI number

• acc_no - accession number

• keyword - if official DNA barcode

• specimen_voucher - museum/lab accession number of vouchered material

• lat_lon - longitude/latitude of specimen collection event

• country - country/location of specimen collection event

• paper_title - title of study

• journal - journal study published in (if published)

• first_author - first author of study

• uploaded_date - date sequence was uploaded to GenBank

• length - sequence length

• sequence - sequence character string

Author(s)

Scott Chamberlain, Rupert Collins

See Also

ncbi_searcher(), ncbi_byname()]

Examples

## Not run: 
# A single gene
ncbi_byid(ids="360040093")

# Many genes (with different accession numbers)
ncbi_byid(ids=c("360040093","347448433"))

## End(Not run)

ropensci/traits documentation built on Sept. 20, 2022, 9:47 a.m.