bio 1.3.1 → 1.4.0

data/lib/bio/appl/hmmer.rb

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: hmmer.rb,v 1.9 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
 require 'bio/command'
@@ -110,17 +110,3 @@ end # class HMMER
 
 end # module Bio
 
-
-
-if __FILE__ == $0
-
-  require 'pp'
-
-  program = ARGV.shift # hmmsearch, hmmpfam
-  hmmfile = ARGV.shift
-  seqfile = ARGV.shift
-
-  factory = Bio::HMMER.new(program, hmmfile, seqfile)
-  pp factory.query
-
-end

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

@@ -566,7 +566,6 @@ end # class HMMER
 end # module Bio
 
 
-if __FILE__ == $0
 
 =begin
 
@@ -582,102 +581,3 @@ if __FILE__ == $0
 
 =end
 
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  rep = Bio::HMMER::Report.new(ARGF.read)
-  p rep
-
-  indent = 18
-
-  puts "### hmmer result"
-  print "name : ".rjust(indent)
-  p  rep.program['name']
-  print "version : ".rjust(indent)
-  p rep.program['version']
-  print "copyright : ".rjust(indent)
-  p rep.program['copyright']
-  print "license : ".rjust(indent)
-  p rep.program['license']
-
-  print "HMM file : ".rjust(indent)
-  p rep.parameter['HMM file']
-  print "Sequence file : ".rjust(indent)
-  p rep.parameter['Sequence file']
-
-  print "Query sequence : ".rjust(indent)
-  p rep.query_info['Query sequence']
-  print "Accession : ".rjust(indent)
-  p rep.query_info['Accession']
-  print "Description : ".rjust(indent)
-  p rep.query_info['Description']
-
-  rep.each do |hit|
-    puts "## each hit"
-    print "accession : ".rjust(indent)
-    p [ hit.accession, hit.target_id, hit.hit_id, hit.entry_id ]
-    print "description : ".rjust(indent)
-    p [ hit.description, hit.definition ]
-    print "target_def : ".rjust(indent)
-    p hit.target_def
-    print "score : ".rjust(indent)
-    p [ hit.score, hit.bit_score ]
-    print "evalue : ".rjust(indent)
-    p hit.evalue
-    print "num : ".rjust(indent)
-    p hit.num
-
-    hit.each do |hsp|
-      puts "## each hsp"
-      print "accession : ".rjust(indent)
-      p [ hsp.accession, hsp.target_id ]
-      print "domain : ".rjust(indent)
-      p hsp.domain
-      print "seq_f : ".rjust(indent)
-      p hsp.seq_f
-      print "seq_t : ".rjust(indent)
-      p hsp.seq_t
-      print "seq_ft : ".rjust(indent)
-      p hsp.seq_ft
-      print "hmm_f : ".rjust(indent)
-      p hsp.hmm_f
-      print "hmm_t : ".rjust(indent)
-      p hsp.hmm_t
-      print "hmm_ft : ".rjust(indent)
-      p hsp.hmm_ft
-      print "score : ".rjust(indent)
-      p [ hsp.score, hsp.bit_score ]
-      print "evalue : ".rjust(indent)
-      p hsp.evalue
-      print "midline : ".rjust(indent)
-      p hsp.midline
-      print "hmmseq : ".rjust(indent)
-      p hsp.hmmseq
-      print "flatseq : ".rjust(indent)
-      p hsp.flatseq
-      print "query_frame : ".rjust(indent)
-      p hsp.query_frame
-      print "target_frame : ".rjust(indent)
-      p hsp.target_frame
-
-      print "query_seq : ".rjust(indent)
-      p hsp.query_seq		# hmmseq, flatseq
-      print "target_seq : ".rjust(indent)
-      p hsp.target_seq		# flatseq, hmmseq
-      print "target_from : ".rjust(indent)
-      p hsp.target_from		# seq_f, hmm_f
-      print "target_to : ".rjust(indent)
-      p hsp.target_to		# seq_t, hmm_t
-      print "query_from : ".rjust(indent)
-      p hsp.query_from		# hmm_f, seq_f
-      print "query_to : ".rjust(indent)
-      p hsp.query_to		# hmm_t, seq_t
-    end 
-  end
-
-end 
-
-

data/lib/bio/appl/meme/mast.rb

@@ -0,0 +1,156 @@
+#
+# = bio/appl/meme/mast.rb - Wrapper for running MAST program
+#
+# Copyright::  Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>,
+#
+# License::    The Ruby License
+#
+# == Description
+#
+# This file contains a wrapper for running the MAST tool for searching sequence databases using motifs
+#
+# == References
+#
+# * http://meme.sdsc.edu/meme/intro.html
+#
+require "bio/command"
+
+module Bio
+module Meme
+
+  # == Description
+  #
+  # Bio::Meme::Mast is a wrapper for searching a database using sequence motifs.  The code
+  # will read options from a Hash and run the program.  Parsing of the output is provided by
+  # Bio::Meme::Mast::Report.  Before running, options[:mfile] and options[:d] must be set 
+  # in the constructor or Mast.config(options = {})
+  #
+  # == Usage
+  #
+  #   mast = Mast.new('/path/to/mast')
+  #   or with options
+  #   mast = Mast.new('/path/to/mast', {:mfile => 'meme.out', :d => '/shared/db/nr'})
+  #
+  #   report = Mast::Report.new(mast.run)
+  #   report.each do |motif|
+  #     puts motif.length
+  #   end
+  #
+  #
+  class Mast
+    
+    include Bio::Command
+    
+    autoload :Report, 'bio/appl/meme/mast/report'
+    
+    # A Hash of options for Mast
+    attr_accessor :options
+
+    DEFAULT_OPTIONS = {
+      # required
+      :mfile => nil, 
+      :d => nil,
+      # optional 
+      :stdin => nil, # may not work as expected
+      :count => nil, 
+      :alphabet => nil, 
+      :stdout => true, 
+      :text => false, 
+      :sep => false, 
+      :norc => false, 
+      :dna => false, 
+      :comp => false, 
+      :rank => nil, 
+      :smax => nil, 
+      :ev => nil, 
+      :mt => nil,
+      :w => false, 
+      :bfile => nil, 
+      :seqp => false, 
+      :mf => nil, 
+      :df => nil, 
+      :minseqs => nil, 
+      :mev => nil, 
+      :m => nil, 
+      :diag => nil, 
+      :best => false, 
+      :remcorr => false, 
+      :brief => false, 
+      :b => false, 
+      :nostatus => true, 
+      :hit_list => true, 
+    }
+
+    # The command line String to be executed
+    attr_reader :cmd
+    
+    # Create a mast instance
+    #
+    #   m = Mast.new('/usr/local/bin/mast')
+    # ---
+    # *Arguments*:
+    # * (required) _mast_location_: String
+    # *Raises*:: ArgumentError if mast program is not found
+    # *Returns*:: a Bio::Meme::Mast object
+    
+    def initialize(mast_location, options = {})
+      unless File.exists?(mast_location)
+        raise ArgumentError.new("mast: command not found : #{mast_location}")
+      end
+      @binary = mast_location
+      options.empty? ? config(DEFAULT_OPTIONS) : config(options)
+    end
+
+    # Builds the command line string
+    # any options passed in will be merged with DEFAULT_OPTIONS
+    # Mast usage: mast <mfile> <opts> <flags>
+    #
+    #   mast.config({:mfile => "meme.out", :d => "/path/to/fasta/db"})
+    # ---
+    # *Arguments*:
+    # * (required) _options_: Hash (see DEFAULT_OPTIONS)
+    # *Returns*:: the command line string
+
+    def config(options)
+      @options = DEFAULT_OPTIONS.merge(options)
+      mfile, opts, flags = "", "", ""
+      @options.each_pair do |opt, val|
+        if val.nil? or val == false
+          next
+        elsif opt == :mfile
+          mfile = val
+        elsif val == true
+          flags << " -#{opt}"
+        else
+          opts << " -#{opt} #{val}"
+        end
+      end
+      @cmd = "#{@binary} #{mfile + opts + flags}"
+    end
+
+    # Checks if input/database files exist and options are valid
+    # *Raises*:: ArgumentError if the motifs file does not exist
+    # *Raises*:: ArgumentError if the database file does not exist
+    # *Raises*:: ArgumentError if there is an invalid option
+    
+    def check_options
+      @options.each_key do |k|
+        raise ArgumentError.new("Invalid option: #{k}") unless DEFAULT_OPTIONS.has_key?(k)
+      end
+      raise ArgumentError.new("Motif file not found: #{@options[:mfile]}") if @options[:mfile].nil? or !File.exists?(@options[:mfile])
+      raise ArgumentError.new("Database not found: #{@options[:d]}") if @options[:d].nil? or !File.exists?(@options[:d])
+    end
+
+    # Run the mast program
+    # ---
+    # *Returns*:: Bio::Meme::Mast::Report object
+    
+    def run
+      check_options
+      call_command(@cmd) {|io| @output = io.read }
+      Report.new(@output)
+    end
+    
+  end # End class Mast
+end # End module Meme
+end # End module Bio

data/lib/bio/appl/meme/mast/report.rb

@@ -0,0 +1,91 @@
+#
+# = bio/appl/meme/mast/report.rb - Mast output parser class
+#
+# Copyright::  Copyright (C) 2008, Adam Kraut <adamnkraut@gmail.com>,
+
+#
+# License::    The Ruby License
+#
+# == Description
+#
+# This file contains a class to parse Mast output
+#
+# == Examples
+#
+# == References
+#
+# * http://meme.sdsc.edu/meme/intro.html
+
+require "bio/appl/meme/mast"
+require "bio/appl/meme/motif"
+
+module Bio
+  module Meme
+    class Mast
+
+      # == Description
+      #
+      # A class to parse the output from Mast
+      #
+      # WARNING: Currently support is only for -hit_list (machine readable) format
+      #          HTML (default) output is not supported
+      #
+      # == Examples
+      #
+
+      class Report
+        
+        attr_reader :motifs
+
+        def initialize(mast_hitlist)
+          @motifs = parse_hit_list(mast_hitlist)
+        end
+        
+        # Iterates each motif (Bio::Meme::Motif)
+        def each
+          @motifs.each do |motif|
+            yield motif
+          end
+        end
+        alias :each_motif :each
+        
+        
+        private
+        
+        # Each line corresponds to one motif occurrence in one sequence.
+        #         The format of the hit lines is
+        #                [<sequence_name> <strand><motif> <start> <end> <p-value>]+
+        #         where 
+        #                 <sequence_name> is the name of the sequence containing the hit
+        #                 <strand>        is the strand (+ or - for DNA, blank for protein),
+        #                 <motif>         is the motif number,
+        #                 <start>         is the starting position of the hit,
+        #                 <end>           is the ending position of the hit, and
+        #                 <p-value>       is the position p-value of the hit.
+        def parse_hit_list(data)
+          motifs = []
+          data.each_line do |line|
+            
+            line.chomp!
+            
+            # skip comments
+            next if line =~ /^#/
+            
+            fields = line.split(/\s/)
+            
+            if fields.size == 5
+              motifs << Motif.new(fields[0], strand = nil, fields[1], fields[2], fields[3], fields[4])
+            elsif fields.size == 6
+              motifs << Motif.new(fields[0], fields[1], fields[2], fields[3], fields[4], fields[5])
+            else
+              raise RuntimeError.new("Could not parse mast output")
+            end
+            
+          end
+          motifs
+        end
+
+      end # Result
+    end # Mast
+  end # Meme
+end # Bio

data/lib/bio/appl/meme/motif.rb

@@ -0,0 +1,48 @@
+#
+# = bio/appl/meme/motif.rb - Class to represent a sequence motif
+#
+# Copyright::  Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>,
+#
+# License::    The Ruby License
+#
+# == Description
+#
+# This file contains a minimal class to represent meme motifs
+#
+# == References
+#
+# * http://meme.sdsc.edu/meme/intro.html
+#
+module Bio
+module Meme
+
+  # == Description
+  #
+  # This class minimally represents a sequence motif according to the MEME program
+  #
+  # TODO: integrate with Bio::Sequence class
+  # TODO: parse PSSM data
+  #
+  class Motif
+    attr_accessor :sequence_name, :strand, :motif, :start_pos, :end_pos, :pvalue
+
+    # Creates a new Bio::Meme::Motif object
+    # arguments are 
+    def initialize(sequence_name, strand, motif, start_pos, end_pos, pvalue)
+      @sequence_name = sequence_name.to_s
+      @strand = strand.to_s
+      @motif = motif.to_i
+      @start_pos = start_pos.to_i
+      @end_pos = end_pos.to_i
+      @pvalue = pvalue.to_f
+    end
+
+    # Computes the motif length
+    def length
+      @end_pos - @start_pos
+    end
+
+  end
+  
+end  
+end

data/lib/bio/appl/psort.rb

@@ -435,114 +435,3 @@ require 'uri'
 
 end # module Bio
 
-
-
-
-
-if __FILE__ == $0
-
-  begin
-    require 'psort/report.rb'
-  rescue LoadError
-  end
-
-
-  seq = ">hoge mit
-MALEPIDYTT RDEDDLDENE LLMKISNAAG SSRVNDNNDD LTFVENDKII 
-ARYSIQTSSK QQGKASTPPV EEAEEAAPQL PSRSSAAPPP PPRRATPEKK 
-DVKDLKSKFE GLAASEKEEE EMENKFAPPP KKSEPTIISP KPFSKPQEPV
-FKGYHVQVTA HSREIDAEYL KIVRGSDPDT TWLIISPNAK KEYEPESTGS 
-KKSFTPSKSP APVSKKEPVK TPSPAPAAKI PKENPWATAE YDYDAAEDNE
-NIEFVDDDWW LGELEKDGSK GLFPSNYVSL LPSRNVASGA PVQKEEPEQE 
-SFHDFLQLFD ETKVQYGLAR RKAKQNSGNA ETKAEAPKPE VPEDEPEGEP
-DDWNEPELKE RDFDQAPLKP NQSSYKPIGK IDLQKVIAEE KAKEDPRLVQ
-DYKKIGNPLP GMHIEADNEE EPEENDDDWD DDEDEAAQPP ANFAAVANNL 
-KPTAAGSKID DDKVIKGFRN EKSPAQLWAE VSPPGSDVEK IIIIGWCPDS 
-APLKTRASFA PSSDIANLKN ESKLKRDSEF NSFLGTTKPP SMTESSLKND
-KAEEAEQPKT EIAPSLPSRN SIPAPKQEEA PEQAPEEEIE GN
-"
-  Seq1 = ">hgoe
-LTFVENDKII NI
-"
-
-  puts "\n Bio::PSORT::PSORT"
-  
-  puts "\n ==> p serv = Bio::PSORT::PSORT.imsut"
-  p serv = Bio::PSORT::PSORT1.imsut
-
-  puts "\n ==> p serv.class "  
-  p serv.class
-
-  puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
-  p serv.title = 'Query_title_splited_by_white space'
-
-  puts "\n ==> p serv.exec(seq, false) "  
-  p serv.exec(seq, false)
-
-  puts "\n ==> p serv.exec(seq) "  
-  p serv.exec(seq)
-
-  puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) "  
-  p report = serv.exec(Bio::FastaFormat.new(seq))
-
-  puts "\n ==> p report.class"
-  p report.class
-
-
-  puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) "  
-  p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
-
-  puts "\n ==> p report_raw.class"
-  p report_raw.class
-
-
-  puts "\n ==> p report.methods" 
-  p report.methods
-
-  methods = ['entry_id', 'origin', 'title', 'sequence','result_info',
-             'reasoning', 'final_result', 'raw']
-  methods.each do |method|
-    puts "\n ==> p report.#{method}"
-    p eval("report.#{method}")
-  end
-
-
-
-  puts "\n Bio::PSORT::PSORT2"
-
-  puts "\n ==> p serv = Bio::PSORT::PSORT2.imsut"
-  p serv = Bio::PSORT::PSORT2.imsut
-
-  puts "\n ==> p serv.class "
-  p serv.class
-
-  puts "\n ==> p seq "
-  p seq
-
-  puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
-  p serv.title = 'Query_title_splited_by_white space'
-
-  puts "\n ==> p serv.exec(seq) # parsed report" 
-  p serv.exec(seq)
-
-  puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) # parsed report" 
-  p report = serv.exec(Bio::FastaFormat.new(seq))
-
-
-
-  puts "\n ==> p serv.exec(seq, false) # report in plain text"
-  p serv.exec(seq, false)
-
-  puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) # report in plain text"
-  p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
-
-
-  puts "\n ==> p report.methods"
-  p report.methods
-
-  methods = ['entry_id', 'scl', 'definition', 'seq', 'features', 'prob', 'pred', 'k', 'raw']
-  methods.each do |method|
-    puts "\n ==> p report.#{method}"
-    p eval("report.#{method}")
-  end
-end