run_blast: Run BLAST programs

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run BLAST programs

Description

Runs the BLAST progam and creates BLAST databases

Usage

run_blast(
  input = NULL,
  output = NULL,
  title = NULL,
  database = NULL,
  format = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  blast = NULL,
  version = FALSE
)

Arguments

input	Fasta formatted file for input to makeblastdb or query input fasta for blast
output	Name of output file for blast
title	Title for the blast database
database	Database type e.g. "nucl" 0r "prot", for makeblastdb or database name for blast
format	Output format for blast, numeric e.g 6 is a tabular format
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
blast	Path to the BLAST program
version	Returns the version number

Value

A list with the BLAST commands

Examples

## Not run: 
path_db <- "/software/blast-v2.13.0/bin/makeblastdb"
path_blast <- "/software/blast-v2.13.0/bin/blastn"
or
path_blast <- "/software/blast-v2.13.0/bin/blastp"

version <- run_blast(blast = path_blast,
                     version =TRUE)
version[1]

run_blast(input = "sample1.fasta",
          title = "sample_name",
          database = "nucl",
          blast = path_db)

run_blast(input = "cbp1.fasta",
          output = "sample1.blast",
          database = "blastDB",
          format = 6,
          blast = path_blast)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.