retrieve_seq {MicrobiotaProcess}R Documentation

Retriveing Sequencing from NCBI

Description

Retriveing sequences from NCBI with the accession ids.

Usage

retrieve_seq(
  ids,
  files,
  databases = "protein",
  type = "fasta",
  times = 3,
  checkids = FALSE
)

Arguments

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 entrez_fetch.

type

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

Examples

retrieve_seq(ids=c("ADM52729.1", "AAF82637.1"), 
            files="test.fasta",
            databases="protein",
            type="fasta",
            checkids=TRUE)

[Package MicrobiotaProcess version 1.0.5 Index]