getSeq: Get protein and gene sequences

In YulongNiu/KEGGAPI: A package for providing KEGG databases API in R

Description

KEGG Database API - Get the nucleotide acid and amino acid sequences

Usage

getKEGGGeneSeq(KEGGGeneIDs, seqType = "aaseq", enforceURL = FALSE, n = 1)

doTen(tenWebSeq, seqType)

Arguments

KEGGGeneIDs	A vector of KEGG IDs. Seqences from different species could be combined together.
seqType	Choose nucleotide acid (ntseq) or amino acid (aaseq) seqences, and the default is amino acid sequences.
enforceURL	whether to enfoce get get url until the results returned. The default value is "FALSE".
n	The number of CPUs or processors, and the default value is 1.
tenWebSeq	return results from function getURL()

Details

Get protein and gene sequences in fasta format. This function supports mutiple querys.

Value

A BStringSet.

BStingSet or NULL (for the case one gene has no cording protein sequence)

Author(s)

Yulong Niu [e-mail]

Yulong Niu [e-mail]

References

http://www.kegg.jp/kegg/rest/keggapi.html

See Also

getKEGGTIDGeneSeq

Examples

## two amino acid seqences from different sepecies with 2 threads.
twoAASeqs <- getKEGGGeneSeq(c('mja:MJ_0011', 'hsa:10458'), n = 2)
## Not run: 
## export fasta format files
require('Biostrings')
writeXStringSet(twoAASeqs, 'twoAASeqs.fasta')
## End(Not run)

## Not run: 
## more examples
twoNTSeqs <- getKEGGGeneSeq(c('shy:SHJG_7159', 'shy:SHJG_7160'), 'ntseq')
mutilAASeqs <- getKEGGGeneSeq(c('eco:b0202', 'eco:b0203', 'eco:b0204',
'eco:b0205', 'eco:b0206', 'eco:b0216', 'eco:b0244',
'eco:b4626', 'eco:b3796', 'eco:b3797', 'eco:b3296',
'eco:b3297'))
## End(Not run)

## Not run: 
## get the whole E.coli genome protein seqences
ecoProIDs <- getProID('eco')
ecoGenomePro <- getKEGGGeneSeq(ecoProIDs[, 1])
## End(Not run)

YulongNiu/KEGGAPI documentation built on May 10, 2019, 1:12 a.m.