annotateAWS: Annotate DE transcripts using NCBI BLAST AMI

In croesel/Trans2Kegg: Annotate transcripts and predicted protein sequences

Description

Annotate DE transcripts using NCBI BLAST AMI

Usage

annotateAWS(ids, fasta, out = "annot.csv", instance, dns, threads)

Arguments

ids	A character vector of accessions from FASTA file to be annotated
fasta	FASTA file of transcripts to be annotated
out	csv output file for annotation results
instance	Instance from Amazon EC2 running NCBI BLAST AMI
dns	DNS from Amazon EC2 running NCBI BLAST AMI
threads	Number of threads to use for BLAST

Value

Annotation results are written to the csv file specified by outFile

Examples

instance <- 'i-07da948c2d85b7388'
dns <- 'ec2-54-175-9-203.compute-1.amazonaws.com'
fasta <- system.file("extdata", "aiptasia.fa", package="Trans2Kegg")
annot <- system.file("extdata", "annot.csv", package="Trans2Kegg")
annotateAWS(c("KXJ29331.1"), fasta,annot, instance=instance,
dns=dns, threads=2)

croesel/Trans2Kegg documentation built on May 12, 2019, 3:11 p.m.