get.seq {bio3d}

Download FASTA Sequence Files

Description

Downloads FASTA sequence files from the NCBI nr, SWISSPROT/UNIPROT, OR RCSB PDB databases.

Usage

get.seq(ids, outfile = "seqs.fasta", db = "nr", verbose = FALSE)

Arguments

ids

A character vector of one or more appropriate database codes/identifiers of the files to be downloaded.

outfile

A single element character vector specifying the name of the local file to which sequences will be written.

db

A single element character vector specifying the database from which sequences are to be obtained.

verbose

logical, if TRUE URL details of the download process are printed.

Details

This is a basic function to automate sequence file download from the databases including NCBI nr, SWISSPROT/UNIPROT, and RCSB PDB.

Value

If all files are successfully downloaded a list object with two components is returned:

ali

an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.

ids

sequence names as identifiers.

This is similar to that returned by read.fasta. However, if some files were not successfully downloaded then a vector detailing which ids were not found is returned.

Note

For a description of FASTA format see: https://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml. When reading alignment files, the dash ‘-’ is interpreted as the gap character.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

blast.pdb, read.fasta, read.fasta.pdb, get.pdb

Examples

## Not run: 
## Sequence identifiers (GI or PDB codes e.g. from blast.pdb etc.)
get.seq( c("P01112", "Q61411", "P20171") )

#aa <-get.seq( c("4q21", "5p21") )
#aa$id
#aa$ali

## End(Not run)