end
# Method to run Patscan
- def run(comp = nil, type = nil, max_mis = nil, max_hit = nil, verbose = nil)
+ def run(comp = nil, type = nil, max_hit = nil, max_mis = nil, verbose = nil)
args = []
args << "scan_for_matches"
args << "-c" if comp
record[:SEQ_NAME] = seq_name_count
seq_name_count += 1
+ seq = Seq.new_bp(record)
+
if seq_type.nil?
- seq = Seq.new("", record[:SEQ])
seq_type = seq.type_guess
end
+
+ fasta_io.puts seq.to_fasta
end
output.puts record
- fasta_io.puts record
end
end
end
output.puts record
end
+ else
+ output.puts record
end
else
output.puts record