require 'maasha/biopieces'
require 'maasha/seq'
-require 'maasha/digest'
casts = []
casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_record do |record|
if record.has_key? :SEQ_NAME and record.has_key? :SEQ
- seq = Seq.new_bp(record)
- digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
+ seq = Seq.new_bp(record)
- digest.each do |subseq|
- new_record = subseq.to_bp
+ seq.each_digest(options[:pattern].to_s, options[:cut_pos]) do |digest|
+ new_record = digest.to_bp
if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
s_beg = $1
new_record[:S_BEG] = s_beg
new_record[:S_END] = s_end
new_record[:REC_TYPE] = "DIGEST"
+
output.puts new_record
end
else