seqinr (version 3.3-3)

extractseqs: To extract the sequences information of a sequence or a list of sequence in different formats

Description

The function allows to extract large amount of data as whole genome sequences,using different output formats and types of extraction. This function is not yet available for windows in zlib mode.

Usage

extractseqs(listname,socket = autosocket(), format="fasta",
operation="simple",feature="xx", bounds="xx", minbounds="xx", verbose = FALSE, nzlines=1000, zlib = FALSE)
exseq(listname,socket = autosocket(), format="fasta",operation="simple", feature="xx", bounds="xx", minbounds="xx", verbose = FALSE,  nzlines=1000, zlib = FALSE)

Arguments

listname

the name of list on server (may be a virtual list)

socket

an object of class sockconn connecting to a remote ACNUC database (default is a socket to the last opened database).

format

the format of output.Can be acnuc, fasta,flat or coordinates

operation

the type of extraction. Can be simple, translate, fragment, feature or region

feature

-optional- the feature to be extracted (for operations "feature" or "region"): a feature table item (CDS, mRNA,...)

bounds

-optional- the bounds for extraction (for operations "fragment" or "region")

minbounds

-optional- the minimal bounds for extraction (for operations "fragment" or "region")

verbose

if TRUE, verbose mode is on

nzlines

number of line in zlib mode

zlib

logical. If TRUE sequences are download in zlib compress mode.

Value

Sequence data.

Details

To extract a list of sequences (lrank argument) or a single sequence (seqnum argument) using different output formats and types of extraction. All formats except "coordinates" extract sequence data. Format "coordinates" extract coordinate data; start > end indicates the complementary strand.

References

citation("seqinr")

See Also

choosebank, query getlistrank

Examples

 ## Not run: # Need internet connection
#  choosebank("emblTP")
#  mylist <- query("mylist", "k=globin", virtual = TRUE)
#  mylist.fasta <- exseq("mylist", verbose = TRUE)
#  # 103 lines of FASTA 
#  stopifnot(length(mylist.fasta) == 103)
#  closebank()
#  ## End(Not run)