scbi_blast 0.0.30

data/History.txt

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+=== 0.0.1 2010-10-19
+
+* 1 major enhancement:
+  * Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+PostInstall.txt
+README.rdoc
+Rakefile
+lib/scbi_blast.rb
+script/console
+script/destroy
+script/generate
+test/test_helper.rb
+test/test_scbi_blast.rb
+test/blast.xml
+test/empty_blast.xml
+test/blast.txt
+lib/scbi_blast/blast_hit.rb
+lib/scbi_blast/blast_query.rb
+lib/scbi_blast/blast_table_result.rb
+lib/scbi_blast/blast_xml_result.rb
+lib/scbi_blast/blast_simplexml_result.rb
+lib/scbi_blast/batch_blast.rb
+lib/scbi_blast/dust_masker.rb

data/PostInstall.txt

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+
+For more information on scbi_blast, see http://scbi_blast.rubyforge.org
+
+NOTE: Change this information in PostInstall.txt 
+You can also delete it if you don't want it.
+
+

data/README.rdoc

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+= scbi_blast
+
+* http://github.com/#{github_username}/#{project_name}
+
+== DESCRIPTION:
+
+FIX (describe your package)
+
+== FEATURES/PROBLEMS:
+
+* FIX (list of features or problems)
+
+== SYNOPSIS:
+
+  FIX (code sample of usage)
+
+== REQUIREMENTS:
+
+* FIX (list of requirements)
+
+== INSTALL:
+
+* FIX (sudo gem install, anything else)
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2010 Dario Guerrero
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+'Software'), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Rakefile

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+require 'rubygems'
+gem 'hoe', '>= 2.1.0'
+require 'hoe'
+require 'fileutils'
+require './lib/scbi_blast'
+
+Hoe.plugin :newgem
+# Hoe.plugin :website
+# Hoe.plugin :cucumberfeatures
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+$hoe = Hoe.spec 'scbi_blast' do
+  self.developer 'Dario Guerrero & Almudena Bocinos', 'dariogf@gmail.com, alkoke@gmail.com'
+  self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
+  self.rubyforge_name       = self.name # TODO this is default value
+  # self.extra_deps         = [['activesupport','>= 2.0.2']]
+
+end
+
+require 'newgem/tasks'
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# remove_task :default
+# task :default => [:spec, :features]

data/lib/scbi_blast.rb

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+$: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FILE__)))		
+
+require 'batch_blast'
+require 'dust_masker'
+require 'blast_query'
+# require 'blast_xml_result'
+require 'blast_simplexml_result'
+require 'blast_hit'
+require 'blast_table_result'
+
+module ScbiBlast
+  VERSION = '0.0.30'
+end
+
+

data/lib/scbi_blast/batch_blast.rb

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+#!/usr/bin/env ruby
+
+
+class BatchBlast
+
+  def initialize(database, blast_type = 'blastn', extra_params = '')
+
+  		@blast_type = blast_type
+      @database = database
+      @extra_params = extra_params
+    
+   
+  end
+
+  def get_blast_cmd(fmt = :table)
+
+      if fmt==:table 
+      	format = ' -outfmt "7 qseqid sacc pident length mismatch gapopen qstart qend sstart send evalue bitscore score qframe sframe qseq sseq" '    	
+      elsif fmt ==:xml
+      	format = ' -outfmt 5 '    
+      end
+
+      dust=''
+
+      #disable dust flag if blastn
+      # if @blast_type.index('blastn')
+      #   dust=' -dust no '
+      # end
+      
+      cmd = @blast_type+' '+dust+@extra_params + format + @database
+      
+      return cmd
+
+  end
+
+  def do_blast(seqs, fmt = :table,parse_output=true)
+    
+      if seqs.is_a?(Array)
+        seq_fasta=seqs.join("\n")
+      else
+        seq_fasta=seqs
+      end
+
+      cmd = get_blast_cmd(fmt)
+    
+  		res=''
+
+      # Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se  encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando sólo los 20 primeros nt.
+      IO.popen(cmd,'w+') {|blast|
+         blast.sync = true
+         blast.write(seq_fasta)
+         blast.close_write
+         res = blast.readlines
+         blast.close_read
+      }
+    
+      if !$?.exitstatus.nil? && $?.exitstatus>0
+        raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
+      end
+    
+      # check if all sequences where processed
+    
+      if parse_output
+        if fmt == :table 
+      		res = BlastTableResult.new(res)
+        elsif fmt == :xml
+      		res = BlastSimplexmlResult.new(res)
+        # elsif fmt ==:xml2
+        # res = BlastXmlResult.new(res)
+        end
+        
+        # puts "#{seq_fasta.count('>')}, #{res.querys.count}"
+        
+        if seq_fasta.count('>')!=res.querys.count
+          not_processed = seqs.select{|e| e.index('>')}
+          
+          res.querys.each do |query|
+            if not_processed.include?('>'+query.query_id)
+              not_processed.delete('>'+query.query_id)
+            end
+          end
+          
+          raise "These sequences #{seq_fasta.count('>')},#{res.querys.count} where not processed by #{cmd}:\n #{not_processed} \n Full_data:\n seqs=#{seqs};\n"
+        end
+        
+      end
+      
+      return res
+      
+  end
+  
+  def do_blast_seqs(seqs, fmt = :table,parse_output=true)
+
+  
+      cmd = get_blast_cmd(fmt)
+   
+      fastas=[]
+      
+      seqs.each do |seq|
+        fastas.push '>'+seq.seq_name
+        fastas.push seq.seq_fasta
+      end
+    
+      return do_blast(fastas,fmt,parse_output)
+
+  end
+  
+
+  def close
+	
+  end
+
+end
+
+

data/lib/scbi_blast/blast_hit.rb

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+class BlastHit
+   
+  def initialize(q_beg,q_end,s_beg,s_end)
+  
+     @q_beg = q_beg.to_i-1  #to storage in array [0 .. ]
+     @q_end = q_end.to_i-1  #to storage in array [0 .. ]     
+     @s_beg = s_beg.to_i-1
+     @s_end = s_end.to_i-1
+     
+     @reversed = false
+     
+     # TODO -Reversed should be taken from q_frame and s_frame instead of s_end. In proteins comes from q_frame. In nt from s_frames.
+     
+     if @s_beg > @s_end
+       @s_beg = s_end.to_i-1
+       @s_end = s_beg.to_i-1
+       @reversed = true       
+     end
+
+          
+     
+      #              2. S_ID - Subject ID.
+      #              3. IDENT - Identity (%).
+      #              4. ALIGN_LEN - Alignment length.
+      #              5. MISMATCHES - Number of mismatches.
+      #              6. GAPS - Number of gaps.
+      #              7. Q_BEG - Query begin.
+      #              8. Q_END - Query end.
+      #              9. S_BEG - Subject begin.
+      #             10. S_END - Subject end.
+      #             11. E_VAL - Expect value.
+      #             12. BIT_SCORE - Bit score.
+      
+  end
+   
+  def subject_id=(v)   
+   @subject_id = v
+  end
+
+  def ident=(v)
+   @ident = v.to_f
+  end
+
+  def align_len=(v)
+   @align_len = v.to_i
+  end
+
+  def mismatches=(v)
+   @mismatches = v.to_i
+  end
+
+  def gaps=(v)
+   @gaps = v.to_i
+  end
+
+  def e_val=(v)     
+   @e_val = v.to_f
+  end
+
+  def bit_score=(v)
+   @bit_score = v.to_f
+  end
+
+  def score=(v)
+ 
+   @score = v.to_f
+  end
+
+  def acc=(v)
+   @acc = v
+  end
+
+  def definition=(v)
+   @definition = v
+  end
+
+  def q_frame=(v)
+   @q_frame = v.to_i
+  end
+
+  def s_frame=(v)
+   @s_frame = v.to_i
+  end
+
+  def s_seq=(v)
+   @s_seq = v
+  end
+
+  def q_seq=(v)
+   @q_seq = v
+  end
+
+  def full_subject_length=(v)
+   @full_subject_length = v
+  end
+
+  def inspect
+   res =  "Hit: #{@subject_id.ljust(10)} #{@ident.to_s.rjust(4)} #{@align_len.to_s.rjust(2)} #{@mismatches.to_s.rjust(2)} #{@gaps.to_s.rjust(2)} #{@q_beg.to_s.rjust(5)} #{@q_end.to_s.rjust(5)} #{@s_beg.to_s.rjust(5)} #{@s_end.to_s.rjust(5)} #{@e_val.to_s.rjust(5)}  #{@bit_score.to_s.rjust(5)} #{@reversed.to_s.rjust(5)}"
+   res += " #{@score.to_s.rjust(5)} #{@acc.ljust(10)} #{@definition.ljust(10)} #{@q_frame.to_s.rjust(2)} #{@s_frame.to_s.rjust(2)} #{@full_subject_length.to_s.rjust(5)} #{@q_seq}.#{@s_seq}."
+ 
+   return res
+  end
+
+  def get_subject
+    return @subject_id
+  end
+
+  attr_accessor :q_beg, :q_end, :s_beg, :s_end
+
+  attr_reader :subject_id, :align_len, :gaps, :mismatches
+  attr_accessor :reversed
+  attr_reader :score, :acc, :definition, :q_frame, :s_frame, :full_subject_length, :ident, :e_val, :bit_score
+  attr_reader :q_seq, :s_seq
+     
+end

data/lib/scbi_blast/blast_query.rb

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+ class BlastQuery
+   
+   attr_accessor :hits
+   attr_accessor :query_id, :query_def, :full_query_length
+   
+   
+  def initialize(query_id)
+    @query_id = query_id
+    @query_def = query_id
+    @full_query_length = 0
+    @hits = []
+   # inspect
+  end
+  
+  def add_hit(h)
+    @hits.push h
+  end
+  
+  def inspect
+    res = "\n * Query  #{@query_id} :" 
+    res += "subject_id ident align_len mismatches gaps q_beg q_end s_beg s_end e_val bit_score reversed\n\n"
+    @hits.each{ |h| res+= h.inspect+"\n" }
+    
+    return res
+  end     
+  
+  def size
+    return @hits.size
+  end  
+  
+  def sort(comand)
+    return @hits.sort(comand)
+  end
+  
+ end
+
+ 

data/lib/scbi_blast/blast_simplexml_result.rb

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+require "blast_query.rb"
+require "blast_hit.rb"
+
+require 'zlib'
+require 'xmlsimple'
+#xml=File.open('orf.1.xml').read
+#data = XmlSimple.xml_in(xml)
+#
+#
+#data['best_orf'][0]['start'][0]
+#data['best_orf'][0]['content']
+
+######################################
+# Author:: Almudena Bocinos Rioboo
+# Extracts results from blast table's file and uses it to create instances of "BlastQuery" and "BlastHit"
+
+######################################
+
+class BlastSimplexmlResult
+
+  def initialize(input)
+
+    @querys = []
+    lines=[]
+    if input.is_a?(Array)
+      lines=input
+    elsif !input.strip.empty?
+      if File.exists?(input)
+        fich = File.open(input,'r')
+        lines = fich.readlines
+        fich.close
+      else
+        raise "File #{input} doesn't exists"
+      end
+
+    end
+
+    # puts "lines length #{lines.length}"
+    if !lines.empty?
+      data = XmlSimple.xml_in(lines.join)
+      iterations = data['BlastOutput_iterations']
+      #require 'json'
+      #puts iterations.to_json
+
+      iterations[0]['Iteration'].each do |iteration|
+
+        # puts JSON::pretty_generate(iteration)
+
+        query_id = iteration['Iteration_query-ID'][0]
+        full_query_length = iteration['Iteration_query-len'][0]
+        query_def = iteration['Iteration_query-def'][0]
+
+        if query_def =~ /^([^\s]+)/
+          query_def=$1
+        end
+
+        #@query_def = iteration['Iteration_query-def'][0]
+
+        query = BlastQuery.new(query_id)
+        query.query_def = query_def
+        query.full_query_length = full_query_length
+        @querys.push query
+
+
+
+        hits = iteration['Iteration_hits'][0]['Hit']
+        if !hits.nil?
+          hits.each do |h|
+            #puts JSON::pretty_generate(h)
+
+
+
+            subject_id=h['Hit_id'][0]
+            acc =h['Hit_accession'][0]
+            full_subject_length = h['Hit_len'][0].to_i
+            hit_def=h['Hit_def'][0]
+            if hit_def=='No definition line'
+              hit_def =subject_id
+            end
+
+            hsps = h['Hit_hsps'][0]['Hsp']
+
+            hsps.each do |hsp|
+
+              q_beg=hsp['Hsp_query-from'][0].to_i
+              q_end=hsp['Hsp_query-to'][0].to_i
+              s_beg=hsp['Hsp_hit-from'][0].to_i
+              s_end=hsp['Hsp_hit-to'][0].to_i
+
+              # creates the hit
+              hit = BlastHit.new(q_beg,q_end,s_beg,s_end)
+
+              hit.align_len=hsp['Hsp_align-len'][0].to_i
+              hit.ident=(hsp['Hsp_identity'][0].to_f/hit.align_len)*100
+              hit.gaps=hsp['Hsp_gaps'][0].to_i
+              hit.mismatches=hsp['Hsp_midline'][0].count(' ').to_i - hit.gaps
+              hit.e_val=hsp['Hsp_evalue'][0].to_f
+              hit.e_val = (hit.e_val*1000).round/1000.0
+              hit.bit_score=hsp['Hsp_bit-score'][0].to_f
+              hit.bit_score = (hit.bit_score*100).round/100.0
+
+              hit.score = hsp['Hsp_score'][0].to_f
+              hit.q_frame = hsp['Hsp_query-frame'][0].to_i
+              hit.s_frame =hsp['Hsp_hit-frame'][0].to_i
+
+              hit.q_seq = hsp['Hsp_qseq'][0]
+              hit.s_seq = hsp['Hsp_hseq'][0]
+						  
+
+              hit.subject_id= subject_id
+              hit.full_subject_length=full_subject_length
+              # hit.full_query_length = full_query_length
+              hit.definition=hit_def
+              hit.acc=acc
+
+              query.add_hit(hit)
+
+            end
+          end
+        end
+      end
+    end
+    #inspect
+  end
+
+
+
+  def inspect
+
+    res = "Blast results:\n"
+    res+= '-'*20
+    res+= "\nQuerys: #{@querys.count}\n"
+    @querys.each{|q| res+=q.inspect+"\n"}
+    return res
+  end
+
+  def find_query(querys,name_q)
+    #  newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
+    new_q=nil
+
+    if !querys.empty?
+      new_q=querys.find{|q| (q.query_id==name_q)}
+    end
+
+    return new_q
+  end
+
+  def empty?
+
+    return @querys.empty?
+  end
+
+  def size
+    @querys.size
+  end
+
+  attr_accessor :querys
+end