scbi_blast 0.0.30 → 0.0.31

data/lib/scbi_blast/blast_table_result.rb

@@ -1,173 +1,186 @@
-require "blast_query.rb"
-require "blast_hit.rb"
+# Copyright (c) 2010 Dario Guerrero & Almudena Bocinos
+#
+# 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.
 
 
+require "blast_query.rb"
+require "blast_hit.rb"
 
-######################################
-# Author:: Almudena Bocinos Rioboo
-# Extracts results from blast table's file and uses it to create instances of "BlastQuery" and "BlastHit" 
 
-######################################
 
+# Extracts results from blast table's file and uses it to create instances of "BlastQuery" and "BlastHit"
 class BlastTableResult
-                      
+
+  # Parser initialization
   def initialize(input)
-    
+
     @querys = []
-    
-    
+
+
     if input.is_a?(Array)
       lines=input
-      
+
     else
-      
+
       fich = File.open(input,'r')
       lines = fich.readlines
       fich.close
-      
+
     end
-    
-    # puts "lines length #{lines.length}" 
+
     query_name=''
-    
+
     lines.each do |line|
-      
+
       line.chomp! #delete end of line
-   
-        if line =~ /^\s*#/
-          if line =~ /^#\sQuery:\s+(.+)$/
-            query_name = $1
-          elsif line =~ /^#\s0\shits\sfound$/
-            @querys.push BlastQuery.new(query_name)
-          end
-          # 0 hits found
-          
-          
-        else
-           params = line.split(/\t+/)
-           
-           # creates the hit
-           #hit = BlastHit.new( params[1], params[2], params[3], params[4], params[5], params[6], params[7], params[8], params[9], params[10], params[11])
-           
-           # puts "Extracted #{params[0]} #{params[1]} #{params[2]} #{params[3]} #{params[4]} #{params[5]} #{params[6]} #{params[7]} #{params[8]} #{params[9]} #{params[10]} #{params[11]}"
- #         Options 6, 7, and 10 can be additionally configured to produce
-#   a custom format specified by space delimited format specifiers.
-#   The supported format specifiers are:
-#            qseqid means Query Seq-id
-#               qgi means Query GI
-#              qacc means Query accesion
-#            sseqid means Subject Seq-id
-#         sallseqid means All subject Seq-id(s), separated by a ';'
-#               sgi means Subject GI
-#            sallgi means All subject GIs
-#              sacc means Subject accession
-#           sallacc means All subject accessions
-#            qstart means Start of alignment in query
-#              qend means End of alignment in query
-#            sstart means Start of alignment in subject
-#              send means End of alignment in subject
-#              qseq means Aligned part of query sequence
-#              sseq means Aligned part of subject sequence
-#            evalue means Expect value
-#          bitscore means Bit score
-#             score means Raw score
-#            length means Alignment length
-#                        pident means Percentage of identical matches
-#            nident means Number of identical matches
-#          mismatch means Number of mismatches
-#          positive means Number of positive-scoring matches
-#           gapopen means Number of gap openings
-#              gaps means Total number of gaps
-#              ppos means Percentage of positive-scoring matches
-#            frames means Query and subject frames separated by a '/'
-#            qframe means Query frame
-#            sframe means Subject frame
-#   When not provided, the default value is:
-#   'qseqid sseqid pident length mismatch gapopen qstart qend sstart send
-#   evalue bitscore', which is equivalent to the keyword 'std'
-
-           # if  the query doesn't exist, then create a new one,
-           # else the hit will be added to the last query  
-
-           qseqid,sacc,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,score,qframe,sframe,qseq,sseq = params
-            
-   							   # creates the hit
-								   hit = BlastHit.new(qstart,qend,sstart,send)
-
-								   hit.align_len=length								   
-								   hit.ident=pident
-								   
-								   hit.gaps=gapopen
-		 				       hit.mismatches=mismatch
-							     hit.e_val=evalue
-								   hit.bit_score=bitscore
-								   
-								   hit.score = score
-								   hit.q_frame = qframe
-								   hit.s_frame = sframe
-								   
-								   hit.subject_id = sacc
-								   hit.full_subject_length=0
-								   hit.definition=sacc
-								   hit.acc=sacc
-								   hit.q_seq=qseq
-								   hit.s_seq=sseq
-
-            query=find_query(@querys,qseqid)
-            
-            if (query)   #if it is a new query, it is created and added
-              query.add_hit(hit)
-                            
-            else      # else the hit is added in last query added        
-              query = BlastQuery.new(qseqid)
-              query.add_hit(hit)
-              @querys.push query     
-            end
-           
-           
-           #Description
-
-           # read_blast_tab read tabular BLAST format created with blast_seq and written to file with write_blast - or with blastall and the -m 8 or -m 9 switch. 
-           #           Each column in the table corresponds to the following keys:
-           # 
-           #              1. Q_ID - Query ID.
-           #              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. 
-           # 
-           #           Furthermore, two extra keys are added to the record:
-           # 
-           #               * STRAND - Strand.
-           #               * REC_TYPE - Record type.
+
+      if line =~ /^\s*#/
+        if line =~ /^#\sQuery:\s+(.+)$/
+          query_name = $1
+        elsif line =~ /^#\s0\shits\sfound$/
+          @querys.push BlastQuery.new(query_name)
+        end
+        # 0 hits found
+
+
+      else
+        params = line.split(/\t+/)
+
+        # puts "Extracted #{params[0]} #{params[1]} #{params[2]} #{params[3]} #{params[4]} #{params[5]} #{params[6]} #{params[7]} #{params[8]} #{params[9]} #{params[10]} #{params[11]}"
+        #         Options 6, 7, and 10 can be additionally configured to produce
+        #   a custom format specified by space delimited format specifiers.
+        #   The supported format specifiers are:
+        #            qseqid means Query Seq-id
+        #               qgi means Query GI
+        #              qacc means Query accesion
+        #            sseqid means Subject Seq-id
+        #         sallseqid means All subject Seq-id(s), separated by a ';'
+        #               sgi means Subject GI
+        #            sallgi means All subject GIs
+        #              sacc means Subject accession
+        #           sallacc means All subject accessions
+        #            qstart means Start of alignment in query
+        #              qend means End of alignment in query
+        #            sstart means Start of alignment in subject
+        #              send means End of alignment in subject
+        #              qseq means Aligned part of query sequence
+        #              sseq means Aligned part of subject sequence
+        #            evalue means Expect value
+        #          bitscore means Bit score
+        #             score means Raw score
+        #            length means Alignment length
+        #                        pident means Percentage of identical matches
+        #            nident means Number of identical matches
+        #          mismatch means Number of mismatches
+        #          positive means Number of positive-scoring matches
+        #           gapopen means Number of gap openings
+        #              gaps means Total number of gaps
+        #              ppos means Percentage of positive-scoring matches
+        #            frames means Query and subject frames separated by a '/'
+        #            qframe means Query frame
+        #            sframe means Subject frame
+        #   When not provided, the default value is:
+        #   'qseqid sseqid pident length mismatch gapopen qstart qend sstart send
+        #   evalue bitscore', which is equivalent to the keyword 'std'
+
+        # if  the query doesn't exist, then create a new one,
+        # else the hit will be added to the last query
+
+        qseqid,sacc,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,score,qframe,sframe,qseq,sseq = params
+
+        # creates the hit
+        hit = BlastHit.new(qstart,qend,sstart,send)
+
+        hit.align_len=length
+        hit.ident=pident
+
+        hit.gaps=gapopen
+        hit.mismatches=mismatch
+        hit.e_val=evalue
+        hit.bit_score=bitscore
+
+        hit.score = score
+        hit.q_frame = qframe
+        hit.s_frame = sframe
+
+        hit.subject_id = sacc
+        hit.full_subject_length=0
+        hit.definition=sacc
+        hit.acc=sacc
+        hit.q_seq=qseq
+        hit.s_seq=sseq
+
+        query=find_query(@querys,qseqid)
+
+        if (query)   #if it is a new query, it is created and added
+          query.add_hit(hit)
+
+        else      # else the hit is added in last query added
+          query = BlastQuery.new(qseqid)
+          query.add_hit(hit)
+          @querys.push query
         end
+
+
+        #Description
+
+        # read_blast_tab read tabular BLAST format created with blast_seq and written to file with write_blast - or with blastall and the -m 8 or -m 9 switch.
+        #           Each column in the table corresponds to the following keys:
+        #
+        #              1. Q_ID - Query ID.
+        #              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.
+        #
+        #           Furthermore, two extra keys are added to the record:
+        #
+        #               * STRAND - Strand.
+        #               * REC_TYPE - Record type.
       end
-      
-      #inspect
-    
+    end
+
+    #inspect
+
   end
-  
-  
-  
-  def inspect    
-#    puts "Table Results:"
-#    puts(@querys.each{|q| q.inspect}).join("\n")
- res = "Blast results:\n"
+
+
+  # inspect results
+  def inspect
+    res = "Blast results:\n"
     res+= '-'*20
     res+= "\nQuerys: #{@querys.count}\n"
     @querys.each{|q| res+=q.inspect+"\n"}
-    return res    
+    return res
   end
-  
-  def find_query(querys,name_q)  
-  #  newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
+
+  # find query by name
+  def find_query(querys,name_q)
+    #  newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
     new_q=nil
 
     if !querys.empty?
@@ -176,12 +189,14 @@ class BlastTableResult
 
     return new_q
   end
-  
+
+  # check if there are querys
   def empty?
-    
+
     return @querys.empty?
-  end  
-  
+  end
+
+  # get query count
   def size
     @querys.size
   end

data/lib/scbi_blast/blast_xml_result.rb

@@ -1,27 +1,38 @@
-require "blast_query.rb"
-require "blast_hit.rb"
-
-require 'nokogiri'
-#xml=File.open('orf.1.xml').read
-#data = XmlSimple.xml_in(xml)
+# Copyright (c) 2010 Dario Guerrero & Almudena Bocinos
+#
+# 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.
 #
-#data['best_orf'][0]['start'][0]
-#data['best_orf'][0]['content']
+# 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.
 
-######################################
-# Author:: Almudena Bocinos Rioboo
-# Extracts results from blast table's file and uses it to create instances of "BlastQuery" and "BlastHit" 
 
-######################################
+require "blast_query.rb"
+require "blast_hit.rb"
+
+require 'nokogiri'
 
+# Another XML parser using nokogiri library
 class BlastXmlResult
-                      
+
   def initialize(input)
-    
+
     @querys = []
     lines=[]
-    
+
     if input.is_a?(Array)
       lines=input
     else
@@ -30,106 +41,106 @@ class BlastXmlResult
         lines = fich.readlines
         fich.close
       end
-      
+
     end
-    
-    # puts "lines length #{lines.length}" 
+
+    # puts "lines length #{lines.length}"
     if !lines.empty?
-     data = Nokogiri::XML(lines.join)
-     data.root.xpath('//Iteration').each do |iteration|
-      
-       # puts JSON::pretty_generate(iteration)
+      data = Nokogiri::XML(lines.join)
+      data.root.xpath('//Iteration').each do |iteration|
+
+        # puts JSON::pretty_generate(iteration)
         query_id = iteration.xpath('Iteration_query-ID').text
 
         full_query_length = iteration.xpath('Iteration_query-len').text
         query_def = iteration.xpath('Iteration_query-def').text
-      
+
         if query_def =~ /^([^\s]+)/
-        	query_def=$1
+          query_def=$1
         end
-      
-                        #@query_def = iteration['Iteration_query-def'][0]            
+
+        #@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.xpath('Iteration_hits/Hit')
         if !hits.nil?
-  				  hits.each do |h|
-  			 				#puts JSON::pretty_generate(h)
-
-
-				               
-  				       subject_id=h.xpath('Hit_id').text
-  				       acc =h.xpath('Hit_accession').text
-  				       full_subject_length = h.xpath('Hit_len').text.to_i
-  				       hit_def=h.xpath('Hit_def').text
-  				       if hit_def=='No definition line'
-  				       	hit_def =subject_id
-  				       end
-				       
-  				       hsps = h.xpath('Hit_hsps/Hsp')
-				       
-  				       hsps.each do |hsp|
-
-  								   q_beg=hsp.xpath('Hsp_query-from').text.to_i
-  								   q_end=hsp.xpath('Hsp_query-to').text.to_i
-  								   s_beg=hsp.xpath('Hsp_hit-from').text.to_i
-  								   s_end=hsp.xpath('Hsp_hit-to').text.to_i
-	
-  								   # creates the hit
-  								   hit = BlastHit.new(q_beg,q_end,s_beg,s_end)
-
-  								   hit.align_len=hsp.xpath('Hsp_align-len').text.to_i
-  								   hit.ident=(hsp.xpath('Hsp_identity').text.to_f/hit.align_len)*100
-  								   hit.gaps=hsp.xpath('Hsp_gaps').text.to_i
-  		 				       hit.mismatches=hsp.xpath('Hsp_midline').text.count(' ').to_i - hit.gaps
-  							     hit.e_val=hsp.xpath('Hsp_evalue').text.to_f
-  							     hit.e_val = (hit.e_val*1000).round/1000.0
-  								   hit.bit_score=hsp.xpath('Hsp_bit-score').text.to_f
-   							     hit.bit_score = (hit.bit_score*100).round/100.0
-								   
-  								   hit.score = hsp.xpath('Hsp_score').text.to_f
-  								   hit.q_frame = hsp.xpath('Hsp_query-frame').text.to_i
-  								   hit.s_frame =hsp.xpath('Hsp_hit-frame').text.to_i
-								   
-  								   hit.q_seq = hsp.xpath('Hsp_qseq').text
-  								   hit.s_seq = hsp.xpath('Hsp_hseq').text
-  								   
-								   
-  								   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          
+          hits.each do |h|
+            #puts JSON::pretty_generate(h)
+
+
+
+            subject_id=h.xpath('Hit_id').text
+            acc =h.xpath('Hit_accession').text
+            full_subject_length = h.xpath('Hit_len').text.to_i
+            hit_def=h.xpath('Hit_def').text
+            if hit_def=='No definition line'
+              hit_def =subject_id
+            end
+
+            hsps = h.xpath('Hit_hsps/Hsp')
+
+            hsps.each do |hsp|
+
+              q_beg=hsp.xpath('Hsp_query-from').text.to_i
+              q_end=hsp.xpath('Hsp_query-to').text.to_i
+              s_beg=hsp.xpath('Hsp_hit-from').text.to_i
+              s_end=hsp.xpath('Hsp_hit-to').text.to_i
+
+              # creates the hit
+              hit = BlastHit.new(q_beg,q_end,s_beg,s_end)
+
+              hit.align_len=hsp.xpath('Hsp_align-len').text.to_i
+              hit.ident=(hsp.xpath('Hsp_identity').text.to_f/hit.align_len)*100
+              hit.gaps=hsp.xpath('Hsp_gaps').text.to_i
+              hit.mismatches=hsp.xpath('Hsp_midline').text.count(' ').to_i - hit.gaps
+              hit.e_val=hsp.xpath('Hsp_evalue').text.to_f
+              hit.e_val = (hit.e_val*1000).round/1000.0
+              hit.bit_score=hsp.xpath('Hsp_bit-score').text.to_f
+              hit.bit_score = (hit.bit_score*100).round/100.0
+
+              hit.score = hsp.xpath('Hsp_score').text.to_f
+              hit.q_frame = hsp.xpath('Hsp_query-frame').text.to_i
+              hit.s_frame =hsp.xpath('Hsp_hit-frame').text.to_i
+
+              hit.q_seq = hsp.xpath('Hsp_qseq').text
+              hit.s_seq = hsp.xpath('Hsp_hseq').text
+
+
+              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
-      #inspect
-    
+    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)})}
+
+  def find_query(querys,name_q)
+    #  newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
     new_q=nil
 
     if !querys.empty?
@@ -138,15 +149,15 @@ class BlastXmlResult
 
     return new_q
   end
-  
+
   def empty?
-    
+
     return @querys.empty?
-  end  
-  
+  end
+
   def size
     @querys.size
   end
-  
+
   attr_accessor :querys
 end