Merge pull request #330 from anamariaelek/add_package_rBLAST_support

rBLAST support

packages/rBLAST/install

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set -x
+set -e
+
+apt-get -qq update
+apt-get -qq install ncbi-blast+
+

packages/rBLAST/test.R

@@ -0,0 +1,31 @@
+install.packages(c("devtools","BiocManager"), repos="https://cran.rstudio.com")
+BiocManager::install("Biostrings")
+devtools::install_github("mhahsler/rBLAST")
+library(rBLAST)
+rBLAST::blast_help()
+
+## check if makeblastdb is correctly installed
+Sys.which("makeblastdb")
+
+## see possible arguments
+blast_help("makeblastdb")
+
+## create a database for some example sequences
+seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
+    package="rBLAST"))
+
+## 1. write the FASTA file
+dir <- tempdir()
+writeXStringSet(seq, filepath = file.path(dir, "seqs.fasta"))
+
+## 2. make database
+makeblastdb(file.path(dir, "seqs.fasta"), dbtype = "nucl")
+
+## 3. open database
+db <- blast(file.path(dir, "seqs.fasta"))
+
+## 4. perform search (first sequence in the db should be a perfect match)
+predict(db, seq[1])
+
+## clean up
+unlink(dir, recursive = TRUE)