BLASTlord

An R package facilitating filtering of BLAST data.

BLAST and some subsequent data processing takes place in bash before hit filtering is run in R.

Note: Requires the use of a custom BLAST outfmt:

blastn -num_threads 2 -evalue 0.001 -db $DB -query $INPUT -out $OUTPUT -outfmt "6 qseqid stitle sseqid pident length slen sstart send qstart qend qlen mismatch gapopen evalue bitscore"

For more information on BLAST outfmt refer to the following https://www.ncbi.nlm.nih.gov/books/NBK279684/

Installation:

First install devtools:

install.packages("devtools")

Now install BLASTlord:

devtools::install_github("maxlcummins/BLASTlord")

Usage

Running BLASTlord

blastlord(file = "~/Path_to_file/File.txt", output = "Test_run", identity = 95, length = 95, writecsv = TRUE)

Filtering for genes of interest

#install the pacakages below first
#install.packages("magrittr")
#install.packages("dplyr")
library(magrittr)
library(dplyr)



co-occurence_object %>%
  dplyr::filter(grepl("gene_of_interest_1", same_scaff)) %>%
  dplyr::filter(grepl("gene_of_interest_2", same_scaff)) %>%
  dplyr::filter(!grepl("gene_to_avoid_1", same_scaff)) %>%
  View()