+++ /dev/null
-# 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 software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'maasha/filesys'
-require 'open3'
-
-# Module containing code to locate nucleotide patterns in sequences allowing for
-# ambiguity codes and a given maximum mismatches, insertions, and deletions. The
-# pattern match engine is based on scan_for_matches.
-module Patscan
- # ------------------------------------------------------------------------------
- # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]])
- # -> Array
- # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]]) { |match|
- # block
- # }
- # -> Match
- #
- # ------------------------------------------------------------------------------
- # Method to iterate through a sequence to locate pattern matches starting
- # allowing for a maximum number of mismatches, insertions, and deletions.
- # Matches found in block context return the Match object. Otherwise matches are
- # returned in an Array.
- def scan(pattern, max_mismatches = 0, max_insertions = 0, max_deletions = 0)
- @pattern = pattern + "[#{max_mismatches},#{max_insertions},#{max_deletions}]"
- matches = []
-
- pattern_file = Filesys.tmpfile
-
- File.open(pattern_file, mode = 'w') do |ios|
- ios.puts @pattern
- end
-
- cmd = "scan_for_matches #{pattern_file}"
-
- Open3.popen3(cmd) do |stdin, stdout, stderr|
- #raise SeqError, "scan_for_matches failed: #{stderr.gets}" unless stderr.empty?
-
- stdin << ">dummy\n#{self.seq}\n"
-
- stdin.close
-
- while block = stdout.gets($/ + ">")
- if block =~ />dummy:\[(\d+),(\d+)\]\n(.+)/
- start = $1.to_i
- stop = $2.to_i
- match = $3.delete(" ")
- length = stop - start
-
- if block_given?
- yield Match.new(start, length, match)
- else
- matches << Match.new(start, length, match)
- end
- end
- end
- end
-
- matches unless block_given?
- end
-
- class Match
- attr_reader :pos, :length, :match
-
- def initialize(pos, length, match)
- @pos = pos
- @length = length
- @match = match
- end
- end
-end
-
-__END__
-
-
-# Eeeeiiiii - this one is slower than scan_for_matches!
-
-
-# Module containing code to locate nucleotide patterns in sequences allowing for
-# ambiguity codes and a given maximum edit distance. Pattern match engine is based
-# on nrgrep.
-module Patscan
- # ------------------------------------------------------------------------------
- # str.scan(pattern[, max_edit_distance])
- # -> Array
- # str.scan(pattern[, max_edit_distance]) { |match|
- # block
- # }
- # -> Match
- #
- # ------------------------------------------------------------------------------
- # Method to iterate through a sequence to locate pattern matches starting
- # from a given position and allowing for a maximum edit distance.
- # Matches found in block context return the Match object. Otherwise matches are
- # returned in an Array.
- def scan(pattern, edit_distance = 0)
- @pattern = pattern.upcase
- matches = []
-
- pattern_disambiguate
-
- cmd = "nrgrep_coords"
- cmd << " -i"
- cmd << " -k #{edit_distance}s" if edit_distance > 0
- cmd << " #{@pattern}"
-
- Open3.popen3(cmd) do |stdin, stdout, stderr|
- stdin << self.seq
-
- stdin.close
-
- stdout.each_line do |line|
- if line =~ /\[(\d+), (\d+)\]: (.+)/
- start = $1.to_i
- stop = $2.to_i
- match = $3
- length = stop - start
-
- if block_given?
- yield Match.new(start, length, match)
- else
- matches << Match.new(start, length, match)
- end
- end
- end
- end
-
- matches unless block_given?
- end
-
- private
-
- def pattern_disambiguate
- case self.type
- when 'protein'
- @pattern.gsub!('J', '[IFVLWMAGCY]')
- @pattern.gsub!('O', '[TSHEDQNKR]')
- @pattern.gsub!('B', '[DN]')
- @pattern.gsub!('Z', '[EQ]')
- @pattern.gsub!('X', '.')
- when 'dna'
- @pattern.gsub!('R', '[AG]')
- @pattern.gsub!('Y', '[CT]')
- @pattern.gsub!('S', '[GC]')
- @pattern.gsub!('W', '[AT]')
- @pattern.gsub!('M', '[AC]')
- @pattern.gsub!('K', '[GT]')
- @pattern.gsub!('V', '[ACG]')
- @pattern.gsub!('H', '[ACT]')
- @pattern.gsub!('D', '[AGT]')
- @pattern.gsub!('B', '[CGT]')
- @pattern.gsub!('N', '.')
- when 'rna'
- else
- raise SeqError "unknown sequence type: #{self.type}"
- end
- end
-
- class Match
- attr_reader :pos, :length, :match
-
- def initialize(pos, length, match)
- @pos = pos
- @length = length
- @match = match
- end
- end
-end
-
require 'maasha/bits'
require 'maasha/seq/backtrack'
require 'maasha/seq/digest'
+#require 'maasha/seq/patscan'
require 'maasha/seq/patternmatcher'
require 'maasha/seq/trim'
require 'narray'
-#require 'maasha/patscan'
# Residue alphabets
DNA = %w[a t c g]
--- /dev/null
+# 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 software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/filesys'
+require 'open3'
+
+# Module containing code to locate nucleotide patterns in sequences allowing for
+# ambiguity codes and a given maximum mismatches, insertions, and deletions. The
+# pattern match engine is based on scan_for_matches.
+module Patscan
+ # ------------------------------------------------------------------------------
+ # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]])
+ # -> Array
+ # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]]) { |match|
+ # block
+ # }
+ # -> Match
+ #
+ # ------------------------------------------------------------------------------
+ # Method to iterate through a sequence to locate pattern matches starting
+ # allowing for a maximum number of mismatches, insertions, and deletions.
+ # Matches found in block context return the Match object. Otherwise matches are
+ # returned in an Array.
+ def scan(pattern, max_mismatches = 0, max_insertions = 0, max_deletions = 0)
+ @pattern = pattern + "[#{max_mismatches},#{max_insertions},#{max_deletions}]"
+ matches = []
+
+ pattern_file = Filesys.tmpfile
+
+ File.open(pattern_file, mode = 'w') do |ios|
+ ios.puts @pattern
+ end
+
+ cmd = "scan_for_matches #{pattern_file}"
+
+ Open3.popen3(cmd) do |stdin, stdout, stderr|
+ #raise SeqError, "scan_for_matches failed: #{stderr.gets}" unless stderr.empty?
+
+ stdin << ">dummy\n#{self.seq}\n"
+
+ stdin.close
+
+ while block = stdout.gets($/ + ">")
+ if block =~ />dummy:\[(\d+),(\d+)\]\n(.+)/
+ start = $1.to_i
+ stop = $2.to_i
+ match = $3.delete(" ")
+ length = stop - start
+
+ if block_given?
+ yield Match.new(start, length, match)
+ else
+ matches << Match.new(start, length, match)
+ end
+ end
+ end
+ end
+
+ matches unless block_given?
+ end
+
+ class Match
+ attr_reader :pos, :length, :match
+
+ def initialize(pos, length, match)
+ @pos = pos
+ @length = length
+ @match = match
+ end
+ end
+end
+
+__END__
+
+
+# Eeeeiiiii - this one is slower than scan_for_matches!
+
+
+# Module containing code to locate nucleotide patterns in sequences allowing for
+# ambiguity codes and a given maximum edit distance. Pattern match engine is based
+# on nrgrep.
+module Patscan
+ # ------------------------------------------------------------------------------
+ # str.scan(pattern[, max_edit_distance])
+ # -> Array
+ # str.scan(pattern[, max_edit_distance]) { |match|
+ # block
+ # }
+ # -> Match
+ #
+ # ------------------------------------------------------------------------------
+ # Method to iterate through a sequence to locate pattern matches starting
+ # from a given position and allowing for a maximum edit distance.
+ # Matches found in block context return the Match object. Otherwise matches are
+ # returned in an Array.
+ def scan(pattern, edit_distance = 0)
+ @pattern = pattern.upcase
+ matches = []
+
+ pattern_disambiguate
+
+ cmd = "nrgrep_coords"
+ cmd << " -i"
+ cmd << " -k #{edit_distance}s" if edit_distance > 0
+ cmd << " #{@pattern}"
+
+ Open3.popen3(cmd) do |stdin, stdout, stderr|
+ stdin << self.seq
+
+ stdin.close
+
+ stdout.each_line do |line|
+ if line =~ /\[(\d+), (\d+)\]: (.+)/
+ start = $1.to_i
+ stop = $2.to_i
+ match = $3
+ length = stop - start
+
+ if block_given?
+ yield Match.new(start, length, match)
+ else
+ matches << Match.new(start, length, match)
+ end
+ end
+ end
+ end
+
+ matches unless block_given?
+ end
+
+ private
+
+ def pattern_disambiguate
+ case self.type
+ when 'protein'
+ @pattern.gsub!('J', '[IFVLWMAGCY]')
+ @pattern.gsub!('O', '[TSHEDQNKR]')
+ @pattern.gsub!('B', '[DN]')
+ @pattern.gsub!('Z', '[EQ]')
+ @pattern.gsub!('X', '.')
+ when 'dna'
+ @pattern.gsub!('R', '[AG]')
+ @pattern.gsub!('Y', '[CT]')
+ @pattern.gsub!('S', '[GC]')
+ @pattern.gsub!('W', '[AT]')
+ @pattern.gsub!('M', '[AC]')
+ @pattern.gsub!('K', '[GT]')
+ @pattern.gsub!('V', '[ACG]')
+ @pattern.gsub!('H', '[ACT]')
+ @pattern.gsub!('D', '[AGT]')
+ @pattern.gsub!('B', '[CGT]')
+ @pattern.gsub!('N', '.')
+ when 'rna'
+ else
+ raise SeqError "unknown sequence type: #{self.type}"
+ end
+ end
+
+ class Match
+ attr_reader :pos, :length, :match
+
+ def initialize(pos, length, match)
+ @pos = pos
+ @length = length
+ @match = match
+ end
+ end
+end
+
projects / biopieces.git / commitdiff