R: Select annotation lines in an ACNUC database

prepgetannots {seqinr} | R Documentation

## Select annotation lines in an ACNUC database

### Description

This function is called before using `getAnnot` or `modifylist` with a `scan` type operation to select the annotation lines to be returned or scanned.

### Usage

    prepgetannots(what = "all", setfor = c("scan", "getannots"),
                           socket = autosocket(), verbose = FALSE)
    pga(what = "all", setfor = c("scan", "getannots"),
                           socket = autosocket(), verbose = FALSE)

### Arguments

`what` | the default "all" means that all annotation lines are selected. This can be more specific, see details.
`setfor` | this is used when `what` has its default "all" value. The behaviour is different for `getAnnot` and `modifylist` with a `scan` type operation: annotations but not sequences are scanned, but sequences can be returned by `getAnnot`. The default value is "scan".
`socket` | an object of class `sockconn` connecting to an ACNUC server
`verbose` | logical, if TRUE mode verbose is on

### Details

The names of annotation lines in the opened ACNUC database is returned by `countfreelists`, they are forced to upper case letters by `prepgetannots` when supplied with the `what` argument.

For the EMBL/SWISSPROT format, keys are: ALL, AC, DT, KW, OS, OC, OG, OH, RN, RC, RP, RX, RA, RG, RT, RL, DR, AH, AS, CC, FH, FT, SQ, SEQ.

For GenBank: ALL, ACCESSION, VERSION, KEYWORDS, SOURCE, ORGANISM, REFERENCE, AUTHORS, CONSRTM, TITLE, JOURNAL, PUBMED, REMARK, COMMENT, FEATURES, ORIGIN, SEQUENCE.

For FT (embl, swissprot) and FEATURES (GenBank), one or more specific feature keys can be specified using lines with only uppercase and such as

FEATURES|CDS FT|TRNA

Keys ALL and SEQ/SEQUENCE stand for all annotation and sequence lines, respectively. For the scan operation, key ALL stand for the DE/DEFINITION lines, and SEQ/SEQUENCE cannot be used (annotations but not sequence are scanned).

### Value

The function returns invisibly the annotation lines names.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### See Also

`getAnnot`, `modifylist`, `countfreelists`

### Examples

     ## Not run: # Need internet connection
      choosebank("genbank")
      mylist <- query("mylist","n=AQF16SRRN")
      pga() # We want to scan all annotations, including FEATURES
      mylist <- modifylist("mylist", operation = "strain", type = "scan")
      mylist$nelem # should be 1

    ## End(Not run)

[Package seqinr version 3.4-5 Index]