retrieve_seq {MicrobiotaProcess} | R Documentation |
Retriveing sequences from NCBI with the accession ids.
retrieve_seq( ids, files, databases = "protein", type = "fasta", times = 3, checkids = FALSE )
ids |
vector, the accession number or accession. |
files |
character, the file name specified by a double-quoted string. |
databases |
character, the name of databases to use, default is 'protein',
if nucleotide sequences to retrieve set nuccore,
see also |
type |
character, the format in which to get data,
such as fasta, xml ...,
see also |
times |
integer, the time of sleeping, default is 3, meaning 3 seconds. |
checkids |
logical, whether check the sequence of ids has been retrieved. default is FALSE. |
the files of sequences downloaded by ids
Shuangbin Xu
retrieve_seq(ids=c("ADM52729.1", "AAF82637.1"), files="test.fasta", databases="protein", type="fasta", checkids=TRUE)