mapply_retrieve_seq {MicrobiotaProcess}R Documentation

Retriveing Sequencing from NCBI By mapply

Description

Retriveing sequences from NCBI with the accession ids.

Usage

mapply_retrieve_seq(
  idlist,
  files,
  databases = "protein",
  type = "fasta",
  times = 3,
  checkids = TRUE
)

Arguments

idlist

vector, the accession version.

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 entrez_fetch.

type

character, the format in which to get data,such as fasta, xml ..., see entrez_fetch.

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.

Value

the files of sequences downloaded by ids

Author(s)

Shuangbin Xu

See Also

retrieve_seq

Examples

idslist <- list(c("ADM52729.1", "AAF82637.1"), 
                c("CAA24729.1", "CAA83510.1"))
mapply_retrieve_seq(idlist=idslist,
                  files="test.fasta",
                  databases="protein",
                  type="fasta",
                  times=3,checkids=TRUE)

[Package MicrobiotaProcess version 1.0.5 Index]