--- /dev/null
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Remove adaptors or parts thereof from sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+require 'seq'
+
+def disambiguate(adaptor)
+ adaptor_disamb = adaptor.dup
+ adaptor_disamb.gsub!('U', 'T')
+ adaptor_disamb.gsub!('R', '[AG]')
+ adaptor_disamb.gsub!('Y', '[CT]')
+ adaptor_disamb.gsub!('S', '[GC]')
+ adaptor_disamb.gsub!('W', '[AT]')
+ adaptor_disamb.gsub!('M', '[AC]')
+ adaptor_disamb.gsub!('K', '[GT]')
+ adaptor_disamb.gsub!('V', '[ACG]')
+ adaptor_disamb.gsub!('H', '[ACT]')
+ adaptor_disamb.gsub!('D', '[AGT]')
+ adaptor_disamb.gsub!('B', '[CGT]')
+ adaptor_disamb.gsub!('N', '.')
+ adaptor_disamb
+end
+
+class Seq
+ # Method that finds an adaptor or part thereof in the sequence of a Seq object.
+ # Returns a Match object if the adaptor was found otherwise nil. The ed_percent
+ # indicates the maximum edit distance allowed in all possible overlaps.
+ def adaptor_find(adaptor, adaptor_disamb, pos = 0, ed_percent = 0)
+ raise SeqError, "Edit distance percent out of range #{ed_percent}" unless (0 .. 100).include? ed_percent
+
+ if pos < 0
+ pos = self.length - pos # pos offset from the right end
+ end
+
+ match = adaptor_find_simple(adaptor_disamb, pos) or
+ adaptor_find_complex(adaptor, pos, ed_percent) or
+ adaptor_partial_find_complex(adaptor, ed_percent)
+
+ match
+ end
+
+ private
+
+ # Method to find an adaptor in a sequence taking into account ambiguity
+ # codes, but not considering mismatches, insertions, and deletions.
+ def adaptor_find_simple(adaptor, pos)
+ self.seq.upcase.match(adaptor, pos) do |m|
+ return Match.new($`.length, m, m.to_s.length, 0, 0, 0, m.to_s.length)
+ end
+ end
+
+ # Method to find an adaptor in a sequence taking into account ambiguity
+ # codes, mismatches, insertions, and deletions.
+ def adaptor_find_complex(adaptor, pos, ed_percent)
+ ed_max = (adaptor.length * ed_percent * 0.01).round
+
+ self.scan(adaptor, pos, ed_max).each do |match|
+ return match
+ end
+ end
+
+ # Method to find part of an adaptor at the right end of a sequence taking
+ # into account ambiguity codes, mismatches, insertions, and deletions.
+ def adaptor_partial_find_complex(adaptor, ed_percent)
+ adaptor = adaptor[0 ... -1]
+
+ pos = self.len - adaptor.length
+
+ while adaptor.length > 0
+ ed_max = (adaptor.length * ed_percent * 0.01).round
+
+ if ed_max == 0
+ self.seq.upcase.match(adaptor, pos) do |m|
+ return Match.new($`.length, m, m.to_s.length, 0, 0, 0, m.to_s.length)
+ end
+ else
+ self.scan(adaptor, pos, ed_max).each do |match|
+ return match
+ end
+ end
+
+ adaptor = adaptor[0 ... -1]
+
+ pos = self.len - adaptor.length
+ end
+ end
+end
+
+casts = []
+casts << {:long=>'adaptor', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'edit_distance', :short=>'e', :type=>'uint', :mandatory=>false, :default=>20, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'pos', :short=>'p', :type=>'int', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+adaptor = options[:adaptor].to_s.upcase
+adaptor_disamb = disambiguate(adaptor)
+
+pos = options[:pos]
+pos -= 1 if pos > 0 # pos was 1-based
+
+bp.each_record do |record|
+ if record.has_key? :SEQ
+ entry = Seq.new(record[:SEQ_NAME], record[:SEQ], "dna", record[:SCORES])
+
+ if match = entry.adaptor_find(adaptor, adaptor_disamb, options[:pos], options[:edit_distance])
+ record[:ADAPTOR_POS] = match.pos
+ record[:ADAPTOR_LEN] = match.length
+ record[:ADAPTOR_MATCH] = match.match
+ end
+ end
+
+ bp.puts record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
+++ /dev/null
-#!/usr/bin/env ruby
-
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This program is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Remove adaptors or parts thereof from sequences in the stream.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-require 'biopieces'
-require 'seq'
-require 'profile'
-
-casts = []
-casts << {:long=>'adaptor', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>20, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
-
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
-
-bp.each_record do |record|
- if record.has_key? :SEQ
- entry = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:TYPE], record[:SCORES])
-
- if match = entry.adaptor_find(options[:adaptor], options[:mismatches], options[:insertions], options[:deletions])
- record[:POS] = match.pos
- end
- end
-
- bp.puts record
-end
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__
projects / biopieces.git / commitdiff