bio 1.0.0 → 1.1.0

data/lib/bio/appl/gcg/msf.rb

@@ -0,0 +1,212 @@
+#
+# = bio/appl/gcg/msf.rb - GCG multiple sequence alignment (.msf) parser class
+#
+# Copyright::   Copyright (C) 2003, 2006
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: msf.rb,v 1.2 2007/04/05 23:35:39 trevor Exp $
+#
+# = About Bio::GCG::Msf
+#
+# Please refer document of Bio::GCG::Msf.
+#
+
+#---
+# (depends on autoload)
+#require 'bio/appl/gcg/seq'
+#+++
+
+module Bio
+  module GCG
+
+    # The msf is a multiple sequence alignment format developed by Wisconsin.
+    # Bio::GCG::Msf is a msf format parser.
+    class Msf #< DB
+
+      # delimiter used by Bio::FlatFile
+      DELIMITER = RS = nil
+
+      # Creates a new Msf object.
+      def initialize(str)
+        str = str.sub(/\A[\r\n]+/, '')
+        if /^\!\![A-Z]+\_MULTIPLE\_ALIGNMNENT/ =~ str[/.*/] then
+          @heading = str[/.*/] # '!!NA_MULTIPLE_ALIGNMENT 1.0' or like this
+          str.sub!(/.*/, '')
+        end
+        str.sub!(/.*\.\.$/m, '')
+        @description = $&.to_s.sub(/^.*\.\.$/, '').to_s
+        d = $&.to_s
+        if m = /(.+)\s+MSF\:\s+(\d+)\s+Type\:\s+(\w)\s+(.+)\s+(Comp)?Check\:\s+(\d+)/.match(d) then
+          @entry_id = m[1].to_s.strip
+          @length   = (m[2] ? m[2].to_i : nil)
+          @seq_type = m[3]
+          @date     = m[4].to_s.strip
+          @checksum = (m[6] ? m[6].to_i : nil)
+        end
+
+        str.sub!(/.*\/\/$/m, '')
+        a = $&.to_s.split(/^/)
+        @seq_info = []
+        a.each do |x|
+          if /Name\: / =~ x then
+            s = {}
+            x.scan(/(\S+)\: +(\S*)/) { |y| s[$1] = $2 }
+            @seq_info << s
+          end
+        end
+
+        @data = str
+        @description.sub!(/\A(\r\n|\r|\n)/, '')
+        @align = nil
+      end
+
+      # description
+      attr_reader :description
+
+      # ID of the alignment
+      attr_reader :entry_id
+
+      # alignment length
+      attr_reader :length
+
+      # sequence type ("N" for DNA/RNA or "P" for protein)
+      attr_reader :seq_type
+
+      # date
+      attr_reader :date
+
+      # checksum
+      attr_reader :checksum
+
+      # heading
+      # ('!!NA_MULTIPLE_ALIGNMENT 1.0' or whatever like this)
+      attr_reader :heading
+
+      #---
+      ## data (internally used, will be obsoleted)
+      #attr_reader :data
+      #
+      ## seq. info. (internally used, will be obsoleted)
+      #attr_reader :seq_info
+      #+++
+
+      # symbol comparison table
+      def symbol_comparison_table
+        unless defined?(@symbol_comparison_table)
+          /Symbol comparison table\: +(\S+)/ =~ @description
+          @symbol_comparison_table = $1
+        end
+        @symbol_comparison_table
+      end
+
+      # gap weight
+      def gap_weight
+        unless defined?(@gap_weight)
+          /GapWeight\: +(\S+)/ =~ @description
+          @gap_weight = $1
+        end
+        @gap_weight
+      end
+
+      # gap length weight
+      def gap_length_weight
+        unless defined?(@gap_length_weight)
+          /GapLengthWeight\: +(\S+)/ =~ @description
+          @gap_length_weight = $1
+        end
+        @gap_length_weight
+      end
+
+      # CompCheck field
+      def compcheck
+        unless defined?(@compcheck)
+          if /CompCheck\: +(\d+)/ =~ @description then
+            @compcheck = $1.to_i
+          else
+            @compcheck = nil
+          end
+        end
+        @compcheck
+      end
+
+      # parsing
+      def do_parse
+        return if @align
+        a = @data.strip.split(/\n\n/)
+        @seq_data = Array.new(@seq_info.size)
+        @seq_data.collect! { |x| Array.new }
+        a.each do |x|
+          b = x.split(/\n/)
+          nw = 0
+          if b.size > @seq_info.size then
+            if /^ +/ =~ b.shift.to_s
+              nw = $&.to_s.length
+            end
+          end
+          if nw > 0 then
+            b.each_with_index { |y, i| y[0, nw] = ''; @seq_data[i] << y }
+          else
+            b.each_with_index { |y, i|
+              @seq_data[i] << y.strip.split(/  +/, 2)[1].to_s
+            }
+          end
+        end
+
+        case seq_type
+        when 'P', 'p'
+          k = Bio::Sequence::AA
+        when 'N', 'n'
+          k = Bio::Sequence::NA
+        else
+          k = Bio::Sequence::Generic
+        end
+        @seq_data.collect! do |x|
+          y = x.join('')
+          y.gsub!(/[\s\d]+/, '')
+          k.new(y)
+        end
+
+        aln = Bio::Alignment.new
+        @seq_data.each_with_index do |x, i|
+          aln.store(@seq_info[i]['Name'], x)
+        end
+        @align = aln
+      end
+      private :do_parse
+
+      # returns Bio::Alignment object.
+      def alignment
+        do_parse
+        @align
+      end
+
+      # gets seq data (used internally) (will be obsoleted)
+      def seq_data
+        do_parse
+        @seq_data
+      end
+
+      # validates checksum
+      def validate_checksum
+        do_parse
+        valid = true
+        total = 0
+        @seq_data.each_with_index do |x, i|
+          sum = Bio::GCG::Seq.calc_checksum(x)
+          if sum != @seq_info[i]['Check'].to_i
+            valid = false
+            break
+          end
+          total += sum
+        end
+        return false unless valid
+        if @checksum != 0 # "Check:" field of BioPerl is always 0
+          valid = ((total % 10000) == @checksum)
+        end
+        valid
+      end
+
+    end #class Msf
+  end #module GCG
+end # module Bio

data/lib/bio/appl/gcg/seq.rb

@@ -0,0 +1,195 @@
+#
+# = bio/appl/gcg/seq.rb - GCG sequence file format class (.seq/.pep file)
+#
+# Copyright::   Copyright (C) 2003, 2006
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: seq.rb,v 1.3 2007/04/05 23:35:39 trevor Exp $
+#
+# = About Bio::GCG::Seq
+#
+# Please refer document of Bio::GCG::Seq.
+#
+
+module Bio
+  module GCG
+
+    # 
+    # = Bio::GCG::Seq
+    # 
+    # This is GCG sequence file format (.seq or .pep) parser class.
+    #
+    # = References
+    #
+    # * Information about GCG Wisconsin Package(R)
+    # http://www.accelrys.com/products/gcg_wisconsin_package .
+    # * EMBOSS sequence formats
+    # http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/SequenceFormats.html
+    # * BioPerl document
+    # http://docs.bioperl.org/releases/bioperl-1.2.3/Bio/SeqIO/gcg.html
+    class Seq #< DB
+
+      # delimiter used by Bio::FlatFile
+      DELIMITER = RS = nil
+
+      # Creates new instance of this class.
+      # str must be a GCG seq formatted string.
+      def initialize(str)
+        @heading = str[/.*/] # '!!NA_SEQUENCE 1.0' or like this
+        str = str.sub(/.*/, '')
+        str.sub!(/.*\.\.$/m, '')
+        @definition = $&.to_s.sub(/^.*\.\.$/, '').to_s
+        desc = $&.to_s
+        if m = /(.+)\s+Length\:\s+(\d+)\s+(.+)\s+Type\:\s+(\w)\s+Check\:\s+(\d+)/.match(desc) then
+          @entry_id = m[1].to_s.strip
+          @length   = (m[2] ? m[2].to_i : nil)
+          @date     = m[3].to_s.strip
+          @seq_type = m[4]
+          @checksum = (m[5] ? m[5].to_i : nil)
+        end
+        @data = str
+        @seq = nil
+        @definition.strip!
+      end
+
+      # ID field.
+      attr_reader :entry_id
+
+      # Description field.
+      attr_reader :definition
+
+      # "Length:" field.
+      # Note that sometimes this might differ from real sequence length.
+      attr_reader :length
+
+      # Date field of this entry.
+      attr_reader :date
+
+      # "Type:" field, which indicates sequence type.
+      # "N" means nucleic acid sequence, "P" means protein sequence.
+      attr_reader :seq_type
+
+      # "Check:" field, which indicates checksum of current sequence.
+      attr_reader :checksum
+
+      # heading
+      # ('!!NA_SEQUENCE 1.0' or whatever like this)
+      attr_reader :heading
+
+      #---
+      ## data (internally used, will be obsoleted)
+      #attr_reader :data
+      #+++
+
+      # Sequence data.
+      # The class of the sequence is Bio::Sequence::NA, Bio::Sequence::AA
+      # or Bio::Sequence::Generic, according to the sequence type.
+      def seq
+        unless @seq then
+          case @seq_type
+          when 'N', 'n'
+            k = Bio::Sequence::NA
+          when 'P', 'p'
+            k = Bio::Sequence::AA
+          else
+            k = Bio::Sequence
+          end
+          @seq = k.new(@data.tr('^-a-zA-Z.~', ''))
+        end
+        @seq
+      end
+
+      # If you know the sequence is AA, use this method.
+      # Returns a Bio::Sequence::AA object.
+      #
+      # If you call naseq for protein sequence,
+      # or aaseq for nucleic sequence, RuntimeError will be raised.
+      def aaseq
+        if seq.is_a?(Bio::Sequence::AA) then
+          @seq
+        else
+          raise 'seq_type != \'P\''
+        end
+      end
+
+      # If you know the sequence is NA, use this method.
+      # Returens a Bio::Sequence::NA object.
+      #
+      # If you call naseq for protein sequence,
+      # or aaseq for nucleic sequence, RuntimeError will be raised.
+      def naseq
+        if seq.is_a?(Bio::Sequence::NA) then
+          @seq
+        else
+          raise 'seq_type != \'N\''
+        end
+      end
+
+      # Validates checksum.
+      # If validation succeeds, returns true.
+      # Otherwise, returns false.
+      def validate_checksum
+        checksum == self.class.calc_checksum(seq)
+      end
+
+      #---
+      # class methods
+      #+++
+
+      # Calculates checksum from given string.
+      def self.calc_checksum(str)
+        # Reference: Bio::SeqIO::gcg of BioPerl-1.2.3
+        idx = 0
+        sum = 0
+        str.upcase.tr('^A-Z.~', '').each_byte do |c|
+          idx += 1
+          sum += idx * c
+          idx = 0 if idx >= 57
+        end
+        (sum % 10000)
+      end
+
+      # Creates a new GCG sequence format text.
+      # Parameters can be omitted.
+      #
+      # Examples:
+      #  Bio::GCG::Seq.to_gcg(:definition=>'H.sapiens DNA',
+      #                       :seq_type=>'N', :entry_id=>'gi-1234567',
+      #                       :seq=>seq, :date=>date)
+      #
+      def self.to_gcg(hash)
+        seq = hash[:seq]
+        if seq.is_a?(Bio::Sequence::NA) then
+          seq_type = 'N'
+        elsif seq.is_a?(Bio::Sequence::AA) then
+          seq_type = 'P'
+        else
+          seq_type = (hash[:seq_type] or 'P')
+        end
+        if seq_type == 'N' then
+          head = '!!NA_SEQUENCE 1.0'
+        else
+          head = '!!AA_SEQUENCE 1.0'
+        end
+        date = (hash[:date] or Time.now.strftime('%B %d, %Y %H:%M'))
+        entry_id = hash[:entry_id].to_s.strip
+        len = seq.length
+        checksum = self.calc_checksum(seq)
+        definition = hash[:definition].to_s.strip
+        seq = seq.upcase.gsub(/.{1,50}/, "\\0\n")
+        seq.gsub!(/.{10}/, "\\0 ")
+        w = len.to_s.size + 1
+        i = 1
+        seq.gsub!(/^/) { |x| s = sprintf("\n%*d ", w, i); i += 50; s }
+
+        [ head, "\n", definition, "\n\n",
+          "#{entry_id}  Length: #{len}  #{date}  " \
+          "Type: #{seq_type}  Check: #{checksum}  ..\n",
+          seq, "\n" ].join('')
+      end
+
+    end #class Seq
+  end #module GCG
+end #module Bio
+

data/lib/bio/appl/genscan/report.rb

@@ -1,36 +1,18 @@
 #
 # = bio/appl/genscan/report.rb - Genscan report classes
 #
-# Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
-# License::    LGPL
+# Copyright::  Copyright (C) 2003 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: report.rb,v 1.8 2005/12/18 15:58:40 k Exp $
+#  $Id: report.rb,v 1.10 2007/04/05 23:35:39 trevor Exp $
 #
 # == Description
 #
 #
 # == Example
-# == References
-#
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library 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
-#  Lesser General Public License for more details.
 #
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: report.rb,v 1.8 2005/12/18 15:58:40 k Exp $
-#
-#++
+# == References
 #
 
 require 'bio/db/fasta'

data/lib/bio/appl/hmmer.rb

@@ -2,47 +2,10 @@
 # = bio/appl/hmmer.rb - HMMER wrapper
 # 
 # Copyright::   Copyright (C) 2002 
-#               KATAYAMA Toshiaki <k@bioruby.org>
-# Lisence::     LGPL
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
 #
-# $Id: hmmer.rb,v 1.5 2006/02/02 17:08:36 nakao Exp $
-#
-# == Description
-#
-# A wrapper for the HMMER programs (hmmsearch or hmmpfam).
-#
-# == Examples
-#
-#   require 'bio'
-#   program = 'hmmsearch' # or 'hmmpfam'
-#   hmmfile = 'test.hmm'
-#   seqfile = 'test.faa'
-#   
-#   factory = Bio::HMMER.new(program, hmmfile, seqfile)
-#   p factory.query
-#
-# == References
-#
-# * HMMER
-#   http://hmmer.wustl.edu/
-#
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library 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
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
+# $Id: hmmer.rb,v 1.9 2007/04/05 23:35:39 trevor Exp $
 #
 
 require 'bio/command'
@@ -50,6 +13,8 @@ require 'shellwords'
 
 module Bio
 
+# == Description
+# 
 # A wapper for HMMER programs (hmmsearch or hmmpfam).
 #
 # === Examples
@@ -61,7 +26,7 @@ module Bio
 #   
 #   factory = Bio::HMMER.new(program, hmmfile, seqfile)
 #   report = factory.query
-#   report.class #=> Bio::HMMER::Report
+#   report.class # => Bio::HMMER::Report
 #
 # === References
 #
@@ -72,8 +37,6 @@ class HMMER
 
   autoload :Report, 'bio/appl/hmmer/report'
 
-  include Bio::Command::Tools
-
   # Prgrams name. (hmmsearch or hmmpfam).
   attr_accessor :program
   
@@ -112,7 +75,7 @@ class HMMER
   # Gets options by String.
   # backward compatibility.
   def option
-    make_command_line(@options)
+    Bio::Command.make_command_line(@options)
   end
 
 
@@ -131,7 +94,7 @@ class HMMER
       
     report = nil
     
-    @output = call_command_local(cmd, nil)
+    @output = Bio::Command.query_command(cmd, nil)
     report = parse_result(@output)
       
     return report