A Ruby Gem for Condition Reciprocal Best BLAST
When this gem is install it can be run from the command line with
crb-blast
The options are
--query, -q <s>: query fasta file in nucleotide format
--target, -t <s>: target fasta file as nucleotide or protein
--evalue, -e <f>: e-value cut off for BLAST. Format 1e-5 (default: 1.0e-05)
--threads, -h <i>: number of threads to run BLAST with (default: 1)
--output, -o <s>: output file as tsv
--help, -l: Show this message
To include the gem in your code just require 'crb-blast'
A quick example:
blaster = CRB_Blast.new('test/query.fasta', 'test/target.fasta')
blaster.run(1e-5, 4) # to run with an evalue cutoff of 1e-5 and 4 threads
A longer example with each step at a time:
blaster = CRB_Blast.new('test/query.fasta', 'test/target.fasta')
blaster.makedb
blaster.run_blast(1e-5, 6)
blaster.load_outputs
blaster.find_reciprocals
blaster.find_secondaries