QuickBLAST

Requires NCBI BLAST C++ includes and libs to compile from source. Binaries available here

??QuickBLAST

It is written in C++ and interfaced with R using Rcpp. Compiling it from source requires ncbi headers and libs so it's better to use the compiled binary. I am just wrapping around ncbi-c++ toolkits CBl2Seq Class with my own class (same with arrow). Not really doing much in the R side except for exposing functions. I use getlogin() to store username as output metadata, this might raise red flags (in arrow_wrapper-functions.hp). Quick BLAST is a bit faster on soft Benchmarking. Ncbi-BLAST is in a bit of a fix because you have to compile the whole BLAST suite repo to use it in R and they have their own "ecosystem" so exposing their classes in R would be a bit of a hassle, that is why I just wrapped parts of the BLAST suite. Essentially, the huge size of the C++ toolkit makes it infeasible (or just annoying) to include the entire toolkit in this repo, hence the hard coding of ncbi-tools++ headers (which are usually installed in /usr/local/). Moreover CRAN would not accept packages which include other libraries (unless compiled from source) hence I had to provide the binary version.

The main difference between this PKG and the rest would be that

• Quick blast is multi-threaded with { file reading (as chunks), BLASTing, wrapping hits into Arrow data structures }, and { writing of Arrow::RecordBatches to the output file in batches } is done in seperate threads. Hits are also converted into Rcpp::List if you want values to be returned to R.
• QuickBLAST does not use Sys.Calls to invoke BLAST. You don't need BLAST programs in you system

Cons :

• Limited score attributes

Let me know if you want more information and please address bugs to me on github.

Installation (under construction)

Install Apache Arrow - (For Windows, install Arrow UCRT). Check Sys.getenv("R_RTOOLS43_PATH") for Windows (you might need to append rtools*/mingw64/include to R_RTOOLS43_PATH)

Compile NCBI-C++ Toolkit

git clone https://github.com/ncbi/ncbi-cxx-toolkit-public
cd ncbi-cxx-toolkit-public

Linux

./configure --with-dll --with-static --with-openmp --with-64 --without-exe --without-vdb --without-debug --without-app --without-gui --with-lfs
make
sudo make install-toolkit

Windows

#Add CMAKE_CMD (Path to cmake.exe) to the system environment variables
cmake-configure --with-generator="Visual Studio 17 2022" --with-dll
#Open ncbi_cpp.sln inside the CMake*/build folder, change the configuration from Debug to Release and build ALL_BUILD project

git clone https://github.com/klauspost/mman-win32
#Open mman.vcproj in Visual Studio, change the configuration from Debug to Release(change arch to x64 if relevant) and build the project
# mman.lib 

#Set _MSC_VER to one of https://dev.to/yumetodo/list-of-mscver-and-mscfullver-8nd
Sys.setenv("_MSC_VER"=)
#Run configure from the R Mingw terminal to satisfy an unmet dependancy to ncbiconf_unix.h
./configure --with-dll --with-static --with-openmp --with-64 --without-exe --without-vdb --without-debug --without-app --without-gui --with-lfs

Copy <PATH TO GCC BUILD DIR>/inc/ncbiconf_unix.h to ncbi-cxx-toolkit-public/include/

Final Install Steps

setwd("ncbi-cxx-toolkit-public")
Sys.setenv("NCBI_BLAST_INC"=file.path(getwd(),"include"))
#Check the line below
Sys.setenv("NCBI_BLAST_LIB"=file.path(getwd(),"<PATH TO BUILD DIRECTORY>","bin","<PATH TO *.dll or *.so files>"))

Usage

remotes::install_local("QuickBLAST_1.0_R_x86_64-pc-linux-gnu.tar.gz", build=F)
tblastx_ptr <- QuickBLAST::CreateNewBLASTInstance(seq_info = list(0,0,F), program = "tblastx", options = list("evalue"=1e-05, "pident"=0.75, "qcovhsp_perc"=0.75))
blastn_ptr <- QuickBLAST::CreateNewBLASTInstance(seq_info = list(0,0,F), program = "blastn", options = "")
 QuickBLAST::BLAST2Files(ptr=tblastx_ptr, query="ungrouped.cds", subject="ungrouped.cds", out_file="out.tmp", seq_limit=1000, show_progress=T,return_values=F, num_threads=5)
QuickBLAST::BLAST2Seqs(ptr=tblastx_ptr, query="AAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGG", subject="TTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC")
QuickBLAST::BLAST2Seqs(ptr=blastn_ptr, query=">i11166\nTGGCACGTCTGGTAGCAGTTTGCAGGGAAGGGGAAGAGGAATACCCGTTTCTCGCCAGACAGATCC", subject=">i11167\nATGGCACGTCTGGTAGCAGTTTGCAGGGAAGGGGAAGAGGAATACCCGTTTCTCGCCAGACAGATCCCCCTCTTCATCGATGACACTCTCACGATGGTGATGGAGTTTTCCGATAGCGTCATGG")
QuickBLAST::BLAST1Folder(ptr = tblastx_ptr, input_folder="test", extension= ".cds", out_folder="test_out", num_threads=7, reciprocal_hits=F)
QuickBLAST::BLAST2Folders(ptr=blastn_ptr, query="query", subject="subject", extension = ".cds", out_folder="test2_out", num_threads=8, reciprocal_hits=F)

QuickBLAST Options

Same as BLAST but DB & OUTPUT Format are not available. List of available options can be checked with QuickBLAST::GetAvailableBLASTOptions() (Empty elements from the list are removed and BLAST defaults are set on the c++ side). Inputs and Outputs are provided as parameters and sequence specification(strand, sequence type) can be provided during QuickBLAST object creation with QuickBLAST::GetQuickBLASTInstance() (or use the QuickBLAST::BLAST*() functions in R). Enums used by QuickBLAST in C++ are not exposed in R and only integers are used, check QuickBLAST::GetQuickBLASTEnums().

BLAST Scores :

Currently supported scores

Future : (Looking for suggestions)

• Implement more scores and filtering options
• Include function for reading the arrow output files
• Convert from arrow to GRanges (maybe with the use of arrow::Visit() functions)

Disclaimers for disclaimers, legal stuff for legal stuff and respect for respect, wherever it should go.

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