args = []
args << "scan_for_matches"
args << "-c" if comp
- args << "-p" if type == 'protein'
+ args << "-p" if type == :protein
args << "-n #{max_mis}" if max_mis
args << "-m #{max_hit}" if max_hit
args << @pat_file
def results_parse
results = Hash.new { |h, k| h[k] = [] }
- Fasta.open(@out_file, mode='r') do |ios|
+ Fasta.open(@out_file, 'r') do |ios|
ios.each do |entry|
if entry.seq_name =~ /([^:]+):\[(\d+),(\d+)\]/
id = $1.to_i