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]