scbi_blast 0.0.30

data/test/empty_blast.xml

@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastn</BlastOutput_program>
+  <BlastOutput_version>BLASTN 2.2.22+</BlastOutput_version>
+  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>../DB/formatted/mids.fasta</BlastOutput_db>
+  <BlastOutput_query-ID>1</BlastOutput_query-ID>
+  <BlastOutput_query-def>No definition line</BlastOutput_query-def>
+  <BlastOutput_query-len>29</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_expect>10</Parameters_expect>
+      <Parameters_sc-match>1</Parameters_sc-match>
+      <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
+      <Parameters_gap-open>5</Parameters_gap-open>
+      <Parameters_gap-extend>2</Parameters_gap-extend>
+      <Parameters_filter>L;m;</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>1</Iteration_iter-num>
+      <Iteration_query-ID>1</Iteration_query-ID>
+      <Iteration_query-def>No definition line</Iteration_query-def>
+      <Iteration_query-len>29</Iteration_query-len>
+      <Iteration_hits></Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>24</Statistics_db-num>
+          <Statistics_db-len>252</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>3168</Statistics_eff-space>
+          <Statistics_kappa>0.710602795216363</Statistics_kappa>
+          <Statistics_lambda>1.37406312246009</Statistics_lambda>
+          <Statistics_entropy>1.30724660390929</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+      <Iteration_message>No hits found</Iteration_message>
+    </Iteration>
+  </BlastOutput_iterations>
+</BlastOutput>

data/test/test_helper.rb

@@ -0,0 +1,4 @@
+require 'stringio'
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/scbi_blast.rb'
+

data/test/test_scbi_blast.rb

@@ -0,0 +1,178 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+require 'json'
+
+class TestScbiBlast < Test::Unit::TestCase
+
+  def setup
+
+  end
+
+  def test_blast
+    blast=BatchBlast.new('-db ~/progs/ruby/DB/formatted/mids.fasta')
+
+    seqs=[">GFIJCBT03F4XVR","GACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
+    
+    res=blast.do_blast(seqs)
+    
+    puts res.inspect
+  end
+  
+	def test_querys
+	  res = BlastSimplexmlResult.new(File.join(File.dirname(__FILE__),'blast.xml'))  	
+    # puts "BLAST.XML"
+    # puts res.inspect
+  	assert_equal(2,res.querys.count)
+  	assert_equal(2,res.querys[0].hits.count)
+  	assert_equal(2,res.querys[1].hits.count)
+  	
+	end
+  
+  def test_hits
+    assert true
+  end
+  
+  def test_empty_blast
+  	  res = BlastSimplexmlResult.new(File.join(File.dirname(__FILE__),'empty_blast.xml'))  	
+      # puts "EMPTY_BLAST.XML"
+      # puts res.inspect
+  		assert_equal(1,res.querys.count)
+  		assert_equal(0,res.querys[0].hits.count)
+  	
+  end
+
+  def test_empty_results
+  	  res = BlastSimplexmlResult.new('')  	
+      # puts "EMPTY_RESULTS.XML"
+      # puts res.inspect
+  		assert_equal(0,res.querys.count)
+  	
+  end
+
+  def test_table_result_with_empty_querys
+  	  res = BlastTableResult.new(File.join(File.dirname(__FILE__),'sp_blast_result.txt'))
+      # puts "TABLE RESULTS.XML"
+      # puts res.inspect
+      assert_equal(4,res.querys.count)
+      assert_equal(0,res.querys[2].hits.count)
+      assert_equal('RL1',res.querys[0].hits[0].subject_id)
+      assert_equal('dos',res.querys[1].query_id)
+      assert_equal('tres',res.querys[2].query_id)
+      # res.querys.each do |q|
+      #   puts q.query_id
+      # end
+      
+  	
+  end
+
+
+  def test_dust
+    dust_masker=DustMasker.new()
+    
+    seqs=[]
+    
+    # seqs.push ">name"
+    # seqs.push 'ATATACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTAACTAACTAACTAACTAACTAACTAACTAACTAACGTAACGTAACTAACTAACGTAACTAACTAACTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGGTACGTACGTACGTACGTACGACGACGACGAGAGAGAGAGNGNNNactacgactacgatcgATATACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTAACTAACTAACTAACTAACTAACTAACTAACTAACGTAACGTAACTAACTAACGTAACTAACTAACTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGGTACGTACGTACGTACGTACGACGACGACGAGAGAGAGAGNGNNN'
+    
+    seqs=[">GFIJCBT03F4XVR","GACTACACGACGACCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTNTTTTATTTTATTTTATTTATTATATATATATATATATATATATATATANNNNCNCACACANACACNNGAGNGNGNGNGAGNGAGNGAGTAGTAGTAGTAGTGTATATATACTACTACTACTACTACACACGACGACGTACGTACGTACGTACGTACGTACGTACGTACGTAACGTAAGTAAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTATATATATATATAGTAGTAGTAGTAGTAGTAGTAGTACGTACGTACGTACGTACGTACGTACGTACGACGACGACGACGACGACGACGACGAGATATATACTACTAACTAACTAACAACGTACGACGACGACGACGACGACGTACGTACGTACGTACGTACGTACTACTACTACTACGTACGTACGTACGTACGTACGTACGTACGTAGTAGTAGTAGTACGTACGTACGTCGTCGTCGTCGTCGTCGTCGTCGTACGTACGACGACGACGAGAGNGNGNNNNNNNNNNNN",">GFIJCBT03G3M1I","GACTACACGACGACTTTATTTATTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTATTTTTTTTTATTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTTAGTTTTTTTTTTTTTACGTTTTTTTTTTTTACGTTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTACGTTTTTTTTTTTTAGTTTTTTTTTTTTAGTTTTTTTTTTTTTTTTTTTNNNNNNNN"]
+    
+    res = dust_masker.do_dust(seqs.join("\n"))
+    # puts res.to_json
+    assert_equal(res.count,2)
+    assert_equal(res[0].dust.count,4)
+    assert_equal(res[0].query_id,'GFIJCBT03F4XVR')
+    
+    assert_equal(res[0].dust[0][0],15)
+    assert_equal(res[0].dust[0][1],99)
+    assert_equal(res[0].dust[1][0],118)
+    assert_equal(res[0].dust[1][1],139)
+    
+    
+    assert_equal(res[1].dust[0][0],14)
+    assert_equal(res[1].dust[0][1],961)
+    
+    
+  end
+
+  def test_dust_partial_ok
+    dust_masker=DustMasker.new()
+    
+    seqs=[]
+    
+    # seqs.push ">name"
+    # seqs.push 'ATATACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTAACTAACTAACTAACTAACTAACTAACTAACTAACGTAACGTAACTAACTAACGTAACTAACTAACTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGGTACGTACGTACGTACGTACGACGACGACGAGAGAGAGAGNGNNNactacgactacgatcgATATACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTAACTAACTAACTAACTAACTAACTAACTAACTAACGTAACGTAACTAACTAACGTAACTAACTAACTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGGTACGTACGTACGTACGTACGACGACGACGAGAGAGAGAGNGNNN'
+    
+    seqs=">GFIJCBT03G3M1I"
+    
+    res = dust_masker.do_dust(seqs)
+    # puts res.to_json
+    # assert_equal(res.count,2)
+    # assert_equal(res[0].dust.count,4)
+    # assert_equal(res[0].query_id,'GFIJCBT03F4XVR')
+    # 
+    # assert_equal(res[0].dust[0][0],15)
+    # assert_equal(res[0].dust[0][1],99)
+    # assert_equal(res[0].dust[1][0],118)
+    # assert_equal(res[0].dust[1][1],139)
+    # 
+    # 
+    # assert_equal(res[1].dust[0][0],14)
+    # assert_equal(res[1].dust[0][1],961)
+    
+    
+  end
+
+
+  def test_no_dust
+    dust_masker=DustMasker.new()
+    seqs=[]
+    
+    seqs.push ">name"
+    seqs.push 'actggtacgacgtacaccagtactacgatcgtacgtacggatcgatcgatcgttagtgtacgtacgttgtacgtactgac'
+    
+    res = dust_masker.do_dust(seqs.join("\n"))
+    assert_equal(res.count,1)
+    assert_equal(res[0].query_id,'name')    
+    assert_equal(res[0].dust.count,0)
+    
+  end
+  
+  def test_empty_dust
+    dust_masker=DustMasker.new()
+    seqs=[]
+    
+    # seqs.push ">name"
+    # seqs.push 'actggtacgacgtacaccagtactacgatcgtacgtacggatcgatcgatcgttagtgtacgtacgttgtacgtactgac'
+    
+    res = dust_masker.do_dust(seqs.join("\n"))
+    assert_equal(res.count,0)
+
+    res = dust_masker.do_dust(nil)
+    assert_equal(res.count,0)
+
+    
+  end
+
+  def test_dust_fail
+    dust_masker=DustMasker.new()
+    # seqs=[]    
+    # seqs.push ">name"
+    # seqs.push 'actggtacgacgtacaccagtactacgatcgtacgtacggatcgatcgatcgttagtgtacgtacgttgtacgtactgac'
+    
+    res = dust_masker.do_dust(">name")
+    assert_equal(res.count,0)
+    
+  end
+
+  def test_dust_bad_fasta
+    dust_masker=DustMasker.new()
+    # seqs=[]    
+    # seqs.push ">name"
+    # seqs.push 'actggtacgacgtacaccagtactacgatcgtacgtacggatcgatcgatcgttagtgtacgtacgttgtacgtactgac'
+    
+    assert_raise(RuntimeError) {
+      res = dust_masker.do_dust("name")      
+    }
+    
+  end
+  
+end

metadata

@@ -0,0 +1,89 @@
+--- !ruby/object:Gem::Specification 
+name: scbi_blast
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.30
+platform: ruby
+authors: 
+- Dario Guerrero & Almudena Bocinos
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-04-26 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.8.0
+  type: :development
+  version_requirements: *id001
+description: FIX (describe your package)
+email: 
+- dariogf@gmail.com, alkoke@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+files: 
+- 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
+homepage: http://github.com/#{github_username}/#{project_name}
+licenses: []
+
+post_install_message: PostInstall.txt
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+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: 1.7.2
+signing_key: 
+specification_version: 3
+summary: FIX (describe your package)
+test_files: 
+- test/test_helper.rb
+- test/test_scbi_blast.rb