scbi_blast 0.0.37 → 0.0.40

checksums.yaml

@@ -0,0 +1,7 @@
+--- 
+SHA1: 
+  metadata.gz: abd62dc048e15cc41de0e5540c28cdb76b255823
+  data.tar.gz: c7d96d24d714d3641fe144241a6e9c8d4c2d9add
+SHA512: 
+  metadata.gz: 2c9216022a183a69a5f6417ddc69a6bb70c95c646acf84e2a9c97150c5fca40cb3d02f3ad91551bf506f1deb338e44d5af603bcf64f8ca28a9476108bc0d70f2
+  data.tar.gz: c54e86e65fbbb372e1c2e9c4031a2e05a2ac7b89daa47698c8e74398f4a3c7d74c94496ce1a7da2b332c7d8bc2e095fc79e8af2ecc96f46727840f40643ed95a

data/History.txt

@@ -1,3 +1,15 @@
+=== 0.0.40 2013-05-24
+
+qlen en query
+
+=== 0.0.39 2013-05-14
+
+Add intermediate file support
+
+=== 0.0.38 2013-04-24
+
+adding slen qlen
+
 === 0.0.37 2012-11-28
 
 Fixed empty seqs

data/lib/scbi_blast.rb

@@ -22,6 +22,21 @@
 
 $: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FILE__)))		
 
+v='0.0.0'
+begin
+  s=`blastn -version`
+  v=s.split("\n").first.split(' ').last.gsub('+','')
+
+rescue Exception => e
+  raise "Blast not installed"
+end
+
+if Gem::Version.new(v) < Gem::Version.new('2.2.28')
+    puts "Blast #{v} is older than 2.2.28+, please use scbi_blast version 0.0.37 or upgrade your blast to 2.2.28 or greater"
+    exit
+end
+
+
 require 'batch_blast'
 require 'dust_masker'
 require 'blast_query'
@@ -33,7 +48,7 @@ require 'blast_hit'
 require 'blast_table_result'
 
 module ScbiBlast
-   VERSION = '0.0.37'
+   VERSION = '0.0.40'
 end
 
 

data/lib/scbi_blast/batch_blast.rb

@@ -35,24 +35,30 @@ class BatchBlast
   end
 
   # returns the blast cmd that will be used to launch blast
-  def get_blast_cmd(fmt = :table)
+  def get_blast_cmd(fmt = :table, file=nil)
 
     if fmt==:table
-      format = ' -outfmt "7 qseqid sacc pident length mismatch gapopen qstart qend sstart send evalue bitscore score qframe sframe qseq sseq" '
+      format = ' -outfmt "7 qseqid sacc pident length mismatch gapopen qstart qend sstart send evalue bitscore score qframe sframe qseq sseq qlen slen stitle" '
     elsif fmt ==:xml
       format = ' -outfmt 5 '
     end
+    
+    out=''
+    
+    if !file.nil? and !file.empty?
+      out=" -out #{file}"
+    end
 
     dust=''
 
-    cmd = @blast_type+' '+dust+@extra_params + format + @database
+    cmd = @blast_type+' '+dust+@extra_params + format + @database + out
 
     return cmd
 
   end
 
   # do a blast to seqs
-  def do_blast(seqs, fmt = :table,parse_output=true)
+  def do_blast(seqs, fmt = :table,parse_output=true,file=nil)
 
     if seqs.is_a?(Array)
       seq_fasta=seqs.join("\n")
@@ -60,10 +66,13 @@ class BatchBlast
       seq_fasta=seqs
     end
 
-    cmd = get_blast_cmd(fmt)
+    cmd = get_blast_cmd(fmt,file)
 
     if !seqs.empty?
-      res = BatchBlast.do_blast_cmd(seq_fasta,cmd)
+        res = BatchBlast.do_blast_cmd(seq_fasta,cmd)
+        if !file.nil? and !file.empty?
+          res=file
+        end
     else
       res=''
     end
@@ -120,7 +129,7 @@ class BatchBlast
   end
 
   # do blast to an array of Sequence objects
-  def do_blast_seqs(seqs, fmt = :table,parse_output=true)
+  def do_blast_seqs(seqs, fmt = :table,parse_output=true, file=nil)
 
 
     cmd = get_blast_cmd(fmt)
@@ -132,7 +141,7 @@ class BatchBlast
       fastas.push seq.seq_fasta
     end
 
-    return do_blast(fastas,fmt,parse_output)
+    return do_blast(fastas,fmt,parse_output,file)
 
   end
 

data/lib/scbi_blast/blast_hit.rb

@@ -35,6 +35,9 @@ class BlastHit
     @s_beg = s_beg.to_i-1
     @s_end = s_end.to_i-1
     # puts "Set limits2 #{[@q_beg,@q_end,@s_beg,@s_end].join(',')}"
+    
+    @s_len=0
+    @q_len=0
 
     @reversed = false
 
@@ -109,14 +112,22 @@ class BlastHit
     @q_seq = v
   end
 
+  def s_len=(v)
+    @s_len = v.to_i
+  end
+
+  def q_len=(v)
+    @q_len = v.to_i
+  end
+
   def full_subject_length=(v)
-    @full_subject_length = v
+    @full_subject_length = v.to_i
   end
 
   # puts all hit info on a string
   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}."
+    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}.#{@q_len}.#{@s_len}"
 
     return res
   end
@@ -179,6 +190,6 @@ class BlastHit
   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
+  attr_reader :q_seq, :s_seq, :s_len, :q_len
 
 end

data/lib/scbi_blast/blast_table_result.rb

@@ -108,7 +108,7 @@ class BlastTableResult < BlastResult
         # 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
+        qseqid,sacc,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,score,qframe,sframe,qseq,sseq,qlen,slen,stitle = params
 
         # creates the hit
         hit = BlastHit.new(qstart,qend,sstart,send)
@@ -126,11 +126,14 @@ class BlastTableResult < BlastResult
         hit.s_frame = sframe
 
         hit.subject_id = sacc
-        hit.full_subject_length=0
-        hit.definition=sacc
+        hit.full_subject_length=slen # era 0
+        hit.definition=stitle # era sacc
         hit.acc=sacc
         hit.q_seq=qseq
         hit.s_seq=sseq
+        hit.q_len=qlen
+        hit.s_len=slen
+        
 
         query=find_query(@querys,qseqid)
 
@@ -143,6 +146,7 @@ class BlastTableResult < BlastResult
           @querys.push query
         end
 
+        query.full_query_length=qlen
 
         #Description
 

data/test/test_scbi_blast.rb

@@ -8,15 +8,26 @@ class TestScbiBlast < Test::Unit::TestCase
   end
 
   def test_blast
-    blast=BatchBlast.new('-db ~/progs/ruby/DB/formatted/mids.fasta')
+    blast=BatchBlast.new('-db ~/progs/ruby/DB/formatted/mids.fasta -task blastn-short')
 
-    seqs=[">GFIJCBT03F4XVR","GACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
+    seqs=[">GFIJCBT03F4XVR","ACGCGTCTAGTGACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
     
     res=blast.do_blast(seqs)
     
     puts res.inspect
   end
   
+  def test_blast_outfile
+    blast=BatchBlast.new('-db ~/progs/ruby/DB/formatted/mids.fasta -task blastn-short')
+
+    seqs=[">GFIJCBT03F4XVR","ACGCGTCTAGTGACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
+    
+    res=blast.do_blast(seqs,:table,true,'/tmp/blast.txt')
+    puts "="*30
+    puts res.inspect
+  end
+  
+  
   def test_querys
     res = BlastSimplexmlResult.new(File.join(File.dirname(__FILE__),'blast.xml'))   
     # puts "BLAST.XML"

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: scbi_blast
 version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 0.0.37
+  version: 0.0.40
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,13 +9,12 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-11-28 00:00:00 Z
+date: 2013-06-05 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: xml-simple
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -27,7 +25,6 @@ dependencies:
   name: hoe
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -74,6 +71,8 @@ files:
 homepage: http://www.scbi.uma.es/downloads
 licenses: []
 
+metadata: {}
+
 post_install_message: 
 rdoc_options: 
 - --main
@@ -81,23 +80,20 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
-  - - ">="
+  - &id003 
+    - ">="
     - !ruby/object:Gem::Version 
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  - *id003
 requirements: []
 
 rubyforge_project: scbi_blast
-rubygems_version: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: scbi_blast is a ruby gem to handle blast+ executions without the need of temporary files,  it has been developed at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero.
 test_files: 
 - test/test_helper.rb