# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-# Splits sequences in the stream at a given restriction enzyme's cleavage points.
+# Split sequences in the stream at a given restriction enzyme's cleavage points.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'biopieces'
-require 'fasta'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/seq'
casts = []
casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'cut_pos', :short=>'c', :type=>'int', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record[:SEQ_NAME] and record[:SEQ]
+ seq = Seq.new_bp(record)
-options = bp.parse(ARGV, casts)
+ seq.each_digest(options[:pattern].to_s, options[:cut_pos]) do |digest|
+ new_record = digest.to_bp
-bp.each_record do |record|
- if record.has_key? :SEQ_NAME and record.has_key? :SEQ
- seq = Seq.new(record[:SEQ_NAME], record[:SEQ])
- digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
+ if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
+ s_beg = $1
+ s_end = $2
+ end
- digest.each do |subseq|
- new_record = subseq.to_bp
- new_record[:REC_TYPE] = "DIGEST"
- bp.puts new_record
+ new_record[:S_BEG] = s_beg
+ new_record[:S_END] = s_end
+ new_record[:REC_TYPE] = "DIGEST"
+
+ output.puts new_record
+ end
+ else
+ output.puts record
end
- else
- bp.puts record
end
end
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<