scbi_blast 0.0.40 → 0.0.42

data/History.txt

@@ -1,3 +1,11 @@
+=== 0.0.42 2013-09-19
+
+Using PTY to avoid blocking of popen in newer systems
+
+=== 0.0.41 2013-06-19
+
+Add query count check
+
 === 0.0.40 2013-05-24
 
 qlen en query

data/README.rdoc

@@ -4,14 +4,14 @@
 
 == DESCRIPTION:
 
-scbi_blast is a ruby gem to handle blast+ executions without the need of temporary files, 
+scbi_blast is a ruby gem to handle blast+ executions using pipes when possible to read data without the need of temporary files, 
 it has been developed at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero.
 
 == FEATURES:
 
-* Execute blast within ruby without creating temporary files (using pipes)
+* Execute blast (using pipe to read output). Pipes cannot be used for input since it will block if writing more 64kb.
 * Parse XML and table results into Query and Hit objects
-* Execute DustMasker without temporary files (using pipes)
+* Execute DustMasker without temporary files (using pipes for both input and output)
 
 == SYNOPSIS:
 
@@ -86,6 +86,10 @@ An example that shows how to use it to find dust into some sequences:
 
 * NCBI blast+ already installed
 
+== ENVIRONMENT
+
+You can set the SCBI_BLAST_TMPDIR environment variable to choose where input temfiles should be written.
+
 == INSTALL:
 
 gem install scbi_blast

data/lib/scbi_blast.rb

@@ -48,7 +48,7 @@ require 'blast_hit'
 require 'blast_table_result'
 
 module ScbiBlast
-   VERSION = '0.0.40'
+   VERSION = '0.0.42'
 end
 
 

data/lib/scbi_blast/batch_blast.rb

@@ -31,7 +31,6 @@ class BatchBlast
     @database = database
     @extra_params = extra_params
 
-
   end
 
   # returns the blast cmd that will be used to launch blast
@@ -47,6 +46,13 @@ class BatchBlast
     
     if !file.nil? and !file.empty?
       out=" -out #{file}"
+    else
+      # if  RUBY_PLATFORM.index('darwin')
+      #   out =" | sed -l"
+      # else
+      #   out =" | sed -l 0"
+      # end
+      # out =" | grep --line-buffered ''"
     end
 
     dust=''
@@ -111,17 +117,69 @@ class BatchBlast
     res=''
     if !seq_fasta.empty?
       # 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 solo 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? && $?.exitstatus>0
-        raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
+
+      # Change the buffering type in factor command,
+      # assuming that factor uses stdio for stdout buffering.
+      # If IO.pipe is used instead of PTY.open,
+      # this code deadlocks because factor's stdout is fully buffered.
+      
+      
+      # require 'pty'
+      # require 'io/console' # for IO#raw!
+      # res = []
+      # m, s = PTY.open
+      # s.raw! # disable newline conversion.
+      # r, w = IO.pipe
+      # pid = spawn(cmd, :in=>r, :out=>s)
+      # r.close
+      # s.close
+      # w.puts seq_fasta
+      # w.close
+      # while !m.eof do
+      #   res << m.gets
+      # end
+      
+      
+      
+      # puts "="*60
+      # puts res
+      # puts "="*60
+      require 'tempfile'
+        if !ENV['SCBI_BLAST_TMPDIR'].nil?
+          file = Tempfile.new('scbi_blast_',ENV['SCBI_BLAST_TMPDIR'])
+        else
+          file = Tempfile.new('scbi_blast_')
+        end
+      begin
+        file.puts seq_fasta
+        file.close
+        
+        res=`#{cmd} -query #{file.path}`
+        res=res.split("\n")
+        
+        if !$?.exitstatus.nil? && $?.exitstatus>0
+          raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
+        end
+        
+         # puts "FILEPATH"+file.path
+      ensure
+         file.close!   # Closes the file handle. If the file wasn't unlinked
+                       # because #unlink failed, then this method will attempt
+                       # to do so again.
+         file.unlink   # On Windows this silently fails.
       end
+      
+          # IO.popen(cmd,'w+') {|blast|
+          #         blast.sync = true
+          #         blast.write(seq_fasta)
+          #         blast.close_write
+          #         res = blast.readlines
+          #         blast.close_read
+          #       }
+          #         
+      # if !$?.exitstatus.nil? && $?.exitstatus>0
+      #   raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
+      # end
     end
     
     return res
@@ -131,8 +189,7 @@ class BatchBlast
   # do blast to an array of Sequence objects
   def do_blast_seqs(seqs, fmt = :table,parse_output=true, file=nil)
 
-
-    cmd = get_blast_cmd(fmt)
+    # cmd = get_blast_cmd(fmt)
 
     fastas=[]
 

data/lib/scbi_blast/blast_table_result.rb

@@ -49,6 +49,9 @@ class BlastTableResult < BlastResult
   
   def parse(lines)
     
+    if !(lines.last =~ /# BLAST processed (\d+) queries/)
+      raise "Blast didn't processed your queries"
+    end
     
     query_name=''
 

data/test/test_scbi_blast.rb

@@ -8,6 +8,8 @@ class TestScbiBlast < Test::Unit::TestCase
   end
 
   def test_blast
+    puts "TEST BLAST"
+    
     blast=BatchBlast.new('-db ~/progs/ruby/DB/formatted/mids.fasta -task blastn-short')
 
     seqs=[">GFIJCBT03F4XVR","ACGCGTCTAGTGACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
@@ -18,6 +20,7 @@ class TestScbiBlast < Test::Unit::TestCase
   end
   
   def test_blast_outfile
+    puts "TEST BLAST OUTFILE"
     blast=BatchBlast.new('-db ~/progs/ruby/DB/formatted/mids.fasta -task blastn-short')
 
     seqs=[">GFIJCBT03F4XVR","ACGCGTCTAGTGACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
@@ -25,6 +28,8 @@ class TestScbiBlast < Test::Unit::TestCase
     res=blast.do_blast(seqs,:table,true,'/tmp/blast.txt')
     puts "="*30
     puts res.inspect
+    
+    
   end
   
   
@@ -108,6 +113,22 @@ class TestScbiBlast < Test::Unit::TestCase
   	
   end
 
+  def test_good_table
+  	  res = BlastTableResult.new(File.join(File.dirname(__FILE__),'table.txt'))
+
+      assert_equal(999,res.querys.count)
+      
+  	
+  end
+
+
+  def test_bad_table
+      assert_raise RuntimeError do
+  	    BlastTableResult.new(File.join(File.dirname(__FILE__),'bad_table.txt'))
+      end
+  	
+  end
+
 
   def test_dust
     dust_masker=DustMasker.new()
@@ -147,7 +168,7 @@ class TestScbiBlast < Test::Unit::TestCase
     
     seqs=">GFIJCBT03G3M1I"
     
-    res = dust_masker.do_dust(seqs)
+    dust_masker.do_dust(seqs)
     # puts res.to_json
     # assert_equal(res.count,2)
     # assert_equal(res[0].dust.count,4)
@@ -214,7 +235,7 @@ class TestScbiBlast < Test::Unit::TestCase
     # seqs.push 'actggtacgacgtacaccagtactacgatcgtacgtacggatcgatcgatcgttagtgtacgtacgttgtacgtactgac'
     
     assert_raise(RuntimeError) {
-      res = dust_masker.do_dust("name")      
+      dust_masker.do_dust("name")
     }
     
   end

metadata

@@ -1,50 +1,93 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: scbi_blast
-version: !ruby/object:Gem::Version 
-  version: 0.0.40
+version: !ruby/object:Gem::Version
+  version: 0.0.42
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Dario Guerrero & Almudena Bocinos
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2013-06-05 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2013-09-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: xml-simple
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.0.12
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: hoe
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 2.8.0
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.12
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: newgem
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
   type: :development
-  version_requirements: *id002
-description: |-
-  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.
-email: 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+- !ruby/object:Gem::Dependency
+  name: hoe
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.6'
+description: ! "scbi_blast is a ruby gem to handle blast+ executions using pipes when
+  possible to read data without the need of temporary files, \nit has been developed
+  at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero."
+email:
 - dariogf@gmail.com, alkoke@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - History.txt
 - Manifest.txt
 - PostInstall.txt
-files: 
+- README.rdoc
+files:
 - History.txt
 - Manifest.txt
 - PostInstall.txt
@@ -68,33 +111,35 @@ files:
 - lib/scbi_blast/blast_streamxml_result.rb
 - lib/scbi_blast/batch_blast.rb
 - lib/scbi_blast/dust_masker.rb
+- .gemtest
 homepage: http://www.scbi.uma.es/downloads
 licenses: []
-
-metadata: {}
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --main
 - README.rdoc
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - &id003 
-    - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - *id003
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: scbi_blast
-rubygems_version: 2.0.3
+rubygems_version: 1.8.24
 signing_key: 
-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: 
+specification_version: 3
+summary: scbi_blast is a ruby gem to handle blast+ executions using pipes when possible
+  to read data 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
 - test/test_scbi_blast.rb

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@@ -1,7 +0,0 @@
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