Download FASTA Sequence Files

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, else a progress bar is displayed.

Description

Downloads FASTA sequence files from the NR, or SWISSPROT/UNIPROT databases.

Details

This is a basic function to automate sequence file download from the NR and SWISSPROT/UNIPROT databases.

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.

References

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

Note

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

Examples

## Sequence identifiers (GI or PDB codes e.g. from blast.pdb etc.)
get.seq( c("P01112", "Q61411", "P20171") )




  |======================================================================| 100%



                               1        .         .         .         .         50 
[Truncated_Name:1]gi|131869|   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET
[Truncated_Name:2]gi|3419417   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET
[Truncated_Name:3]gi|3419417   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET
                               ************************************************** 
                               1        .         .         .         .         50 

                              51        .         .         .         .         100 
[Truncated_Name:1]gi|131869|   CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI
[Truncated_Name:2]gi|3419417   CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI
[Truncated_Name:3]gi|3419417   CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI
                               ************************************************** 
                              51        .         .         .         .         100 

                             101        .         .         .         .         150 
[Truncated_Name:1]gi|131869|   KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ
[Truncated_Name:2]gi|3419417   KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ
[Truncated_Name:3]gi|3419417   KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ
                               ************************************************** 
                             101        .         .         .         .         150 

                             151        .         .         .        189 
[Truncated_Name:1]gi|131869|   GVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
[Truncated_Name:2]gi|3419417   GVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
[Truncated_Name:3]gi|3419417   GVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
                               *************************************** 
                             151        .         .         .        189 

Call:
  read.fasta(file = outfile)

Class:
  fasta

Alignment dimensions:
  3 sequence rows; 189 position columns (189 non-gap, 0 gap) 

+ attr: id, ali, call




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

See also

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

Author

Barry Grant