bio-polyploid-tools 0.1.0 → 0.2.3

data/lib/bio/BIOExtensions.rb

@@ -1,128 +1,4 @@
 
-module Bio::NucleicAcid::Data
-  IUPAC_CODES = {
-
-    'y'	=> 'ct',
-    'r'	=> 'ag',
-    'w'	=> 'at',
-    's'	=> 'cg',
-    'k'	=> 'gt',
-    'm'	=> 'ac',
-
-    'b'	=> 'cgt',
-    'd'	=> 'agt',
-    'h'	=> 'act',
-    'v'	=> 'acg',
-
-    'n'	=> 'acgt',
-
-    'a'	=> 'a',
-    't'	=> 't',
-    'g'	=> 'g',
-    'c'	=> 'c',
-    'u'	=> 'u',
-
-    'ct' => 'y',
-    'ag' => 'r',
-    'at' => 'w',
-    'cg' => 's',
-    'gt' => 'k',
-    'ac' => 'm',
-
-    'cgt' => 'b',
-    'agt' => 'd',
-    'act' => 'h',
-    'acg' => 'v',
-
-    'acgt' => 'n'
-  }
-
-
-end
-
-class Bio::NucleicAcid
-
-  IUPAC_CODES = {
-
-    'y'	=> 'ct',
-    'r'	=> 'ag',
-    'w'	=> 'at',
-    's'	=> 'cg',
-    'k'	=> 'gt',
-    'm'	=> 'ac',
-
-    'b'	=> 'cgt',
-    'd'	=> 'agt',
-    'h'	=> 'act',
-    'v'	=> 'acg',
-
-    'n'	=> 'acgt',
-
-    'a'	=> 'a',
-    't'	=> 't',
-    'g'	=> 'g',
-    'c'	=> 'c',
-    'u'	=> 'u',
-
-    'ct' => 'y',
-    'ag' => 'r',
-    'at' => 'w',
-    'cg' => 's',
-    'gt' => 'k',
-    'ac' => 'm',
-
-    'cgt' => 'b',
-    'agt' => 'd',
-    'act' => 'h',
-    'acg' => 'v',
-
-    'acgt' => 'n'
-  }
-
-  def self.is_unambiguous(base)
-    "acgtACGT".match(base)
-  end
-
-  def self.to_IUAPC(bases)    
-    base = IUPAC_CODES[bases.to_s.downcase.chars.sort.uniq.join]
-    if base == nil
-      p "Invalid base! #{base}"
-      base = 'n' #This is a patch... as one of the scripts failed here. 
-    end
-    base.upcase
-  end
-
-  def self.is_valid(code, base)
-    IUPAC_CODES[code.downcase].chars.include? base.downcase
-  end
-
-end
-
-class Bio::Sequence
-  def self.snps_between(seq1, seq2)
-    snps=0
-    for i in (0..seq1.size-1)
-      snps += 1 if seq1[i] != seq2[i] 
-    end
-    snps
-  end
-end
-
-class  String
-  def count_ambiguities
-    snps=0
-
-    for i in (0..self.size-1)
-
-      snps += 1 if !Bio::NucleicAcid.is_unambiguous(self[i])
-    end
-    snps
-  end
-  
-  def upper_case_count
-    match(/[^A-Z]*/).to_s.size
-  end
-end
 
 class Bio::Blat
   def self.align(database , query , output)

data/lib/bio/PolyploidTools/ChromosomeArm.rb

@@ -8,7 +8,7 @@ module Bio::PolyploidTools
 
     def initialize(name, path_to_fasta)
       @name = name
-      @fasta_db = Bio::DB::Fasta::FastaFile.new(path_to_fasta)
+      @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path_to_fasta})
       #$stderr.puts "Loading entries for #{name}"
       
       @genes = Hash.new

data/lib/bio/PolyploidTools/ExonContainer.rb

@@ -17,11 +17,11 @@ module Bio::PolyploidTools
     end
 
     def gene_models(path)
-      @gene_models_db = Bio::DB::Fasta::FastaFile.new(path)
+      @gene_models_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
       @gene_models_path = path
     end
 
-    #Retunrs the sequence for a region in the gene models (exon)
+    #Returns the sequence for a region in the gene models (exon)
     def gene_model_sequence(region)
       seq=@gene_models_db.fetch_sequence(region)
 
@@ -30,7 +30,7 @@ module Bio::PolyploidTools
 
     #Sets the reference file for the gene models
     def chromosomes(path)
-      @chromosomes_db = Bio::DB::Fasta::FastaFile.new(path)
+      @chromosomes_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
       @chromosomes_path = path
     end
 
@@ -54,7 +54,7 @@ module Bio::PolyploidTools
       name = opts[:name]
       path = opts[:reference_path]
       path = opts[:alig_path]
-      chromosomes[name] = Bio::DB::Fasta::FastaFile.new(path)
+      chromosomes[name] = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
     end
     
     def add_snp(snp)
@@ -119,11 +119,12 @@ module Bio::PolyploidTools
       @snp_map.each do | gene, snp_array|
         snp_array.each do |snp|
           #file.puts snp.primer_fasta_string 
+       
           begin 
             file.puts snp.aligned_sequences_fasta
           rescue Exception=>e
             @missing_exons << snp.to_s
-#            $stderr.puts e.to_s
+            $stderr.puts e.to_s
           end
         end
       end

data/lib/bio/PolyploidTools/Marker.rb

@@ -126,12 +126,12 @@ module Bio::PolyploidTools
     end
 
     def global_reference(reference)
-      @global_reference = Bio::DB::Fasta::FastaFile.new(reference)
+      @global_reference = Bio::DB::Fasta::FastaFile.new({:fasta=>reference})
       @global_reference.load_fai_entries
     end
 
     def reference(reference)
-      @reference = Bio::DB::Fasta::FastaFile.new(reference)
+      @reference = Bio::DB::Fasta::FastaFile.new({:fasta=>reference})
       @reference.load_fai_entries
     end
 

data/lib/bio/PolyploidTools/SNP.rb

@@ -435,9 +435,10 @@ module Bio::PolyploidTools
     end
 
     def sequences_to_align
+       p @sequences_to_align.inspect
       @sequences_to_align = surrounding_parental_sequences.merge(surrounding_exon_sequences) unless @sequences_to_align
     #  p "sequences_to_align"
-     # p @sequences_to_align.inspect
+     
       @sequences_to_align
     end
 
@@ -446,10 +447,10 @@ module Bio::PolyploidTools
       return @aligned_sequences if @aligned_sequences
       options = ['--maxiterate', '1000', '--localpair', '--quiet']
       mafft = Bio::MAFFT.new( "mafft" , options)
-      #puts "Before MAFT:#{sequences_to_align.inspect}"
+    #  puts "Before MAFT:#{sequences_to_align.inspect}"
       report = mafft.query_align(sequences_to_align)
       @aligned_sequences = report.alignment
-      #puts "MAFFT: #{report.alignment.inspect}" 
+   #   puts "MAFFT: #{report.alignment.inspect}" 
       @aligned_sequences
     end
 
@@ -640,7 +641,7 @@ module Bio::PolyploidTools
       @surrounding_exon_sequences =  Bio::Alignment::SequenceHash.new
       self.exon_list.each do |chromosome, exon| 
         #puts "surrounding_exon_sequences #{flanking_size}"
-       #puts chromosome
+        #puts chromosome
         #puts exon
         flanquing_region  = exon.target_flanking_region_from_position(position,flanking_size)
         #TODO: Padd when the exon goes over the regions... 

data/lib/bio/db/exonerate.rb

@@ -16,7 +16,7 @@ module Bio::DB::Exonerate
 
     target=opts[:target]
     query=opts[:query]
- 
+ #
 
     cmdline = "exonerate --verbose 0 --showalignment no --bestn #{opts[:bestn]} --showvulgar no  --model #{opts[:model]}   --ryo '#{opts[:ryo]}' #{query} #{target}"
     status, stdout, stderr = systemu cmdline

data/test/test_bfr.rb

@@ -4,6 +4,7 @@ path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools
 
 #puts path
 require path
+require 'bio-samtools'
 require "test/unit"
 
 class TestPolyploidTools < Test::Unit::TestCase
@@ -18,13 +19,15 @@ class TestPolyploidTools < Test::Unit::TestCase
     @b=data_path + "/LIB1722.bam"
     @f2_a=data_path + "/LIB1716.bam"
     @f2_b=data_path + "/LIB1719.bam"
-    @fasta_db = Bio::DB::Fasta::FastaFile.new(@ref)
+    
+    @bfr_path=data_path + "/bfr_out_test.csv"
+    @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>@ref})
     @fasta_db.load_fai_entries
     @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
     @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
     @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
     @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
-    puts "SETUP"
+   # puts "SETUP"
   end
   
   def teardown
@@ -35,16 +38,105 @@ class TestPolyploidTools < Test::Unit::TestCase
     setupre
     
     reg="gnl|UG|Ta#S22380157"
-    region = @fasta_db.index.region_for_entry(reg).to_region.to_s
-    min_cov=2
-    
+    region = @fasta_db.index.region_for_entry(reg).to_region
+    min_cov=20
     puts region.to_s
     
-    cons_1 = @bam_a.consensus_with_ambiguities({:region=>region, :case=>true, :min_cov=>min_cov})
-    cons_2 = @bam_b.consensus_with_ambiguities({:region=>region, :case=>true, :min_cov=>min_cov})
+    #puts @bam_a.methods
+    ref_seq=@fasta_db.fetch_sequence(region)
+    reg_a = @bam_a.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
+    reg_b = @bam_b.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
+    cons_1 = reg_a.consensus
+    cons_2 = reg_b.consensus
+    
+    snps_1 = cons_1.count_ambiguities
+    snps_2 = cons_2.count_ambiguities
+    
+    called_1 = reg_a.called
+    called_2 = reg_b.called
+    
+    snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
+    block_size = 1000
+    snps_per_1k_1   = (block_size * snps_1.to_f   ) / region.size
+    snps_per_1k_2   = (block_size * snps_2.to_f   ) / region.size
+    snps_per_1k_tot = (block_size * snps_tot.to_f ) / region.size
+
+    
+
+    #puts "#{region.entry}\t#{region.size}\t"
+    #puts "#{snps_1}\t#{called_1}\t#{snps_per_1k_1}\t"
+    #puts "#{snps_2}\t#{called_2}\t#{snps_per_1k_2}\t"
+    #puts "#{snps_tot}\t#{snps_per_1k_tot}\n"
+    
+    
+    snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
+    snps_to_ref = Bio::Sequence.snps_between(cons_1, ref_seq)
+    #puts ">ref\n#{ref_seq}"
+    #puts ">a\n#{cons_1}"
+    #puts ">b\n#{cons_2}"
+    #puts "SNPS between: #{snps_tot}"
+    #puts "SNPS ref: #{snps_to_ref}"
+    #puts "SNPS call: #{snps_to_ref}"
+    assert_equal(ref_seq.to_s, "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatctttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggtggcggttccgtcgccggaggagtctaaggccctcgttgtcgccgagaatgacgctgagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtcgcgaccgagaagaggatttcgctgatcaaggcatgggaggagaacgagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcggaangagaagcgtgccgcggcggaagcgcggcacggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaagcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
+    assert_equal(cons_1.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggagtctaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcrcggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaggatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")  
+    assert_equal(cons_2.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggasgaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggartcyaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcgcggcgaggagatcgtcgcggcggaggagrccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
+    assert_equal(snps_tot , 6)
+    assert_equal(snps_to_ref , 12)
+    assert_equal(snps_1,10)
+    assert_equal(snps_2,13)
+    assert_equal(called_1,617)
+    assert_equal(called_2,612)
+  end
+  
+  def test_bfr
+    setupre
+    container = Bio::BFRTools::BFRContainer.new
+    
+    container.reference @ref
+    container.parental_1  ( {:path => @a } )
+    container.parental_2  ( {:path => @b } )
+    container.bulk_1 ( {:path => @f2_a  })
+    container.bulk_2 ( {:path => @f2_b  })
+
+    i = -1
+
+    container.init_counters
+    output_file =  File.open(@bfr_path, "w")
+  #  puts "Range: #{min}:#{max}"
+    assert_equal(@fasta_db.index.entries.size,1)
+    reg = nil
+    @fasta_db.index.entries.each do | r |
+      i = i  + 1
+       
+      reg = container.process_region({:region => r.get_full_region.to_s,:output_file => output_file , :min_cov => 5} )
+      #puts reg.inspect
+    end
+    
+    with_bfr = [210, 297, 300, 645, 674]
+    
+    bases_1 = Array.new
+    bases_2 = Array.new
+    bases_1  << {:A=>0, :C=>24, :G=>120, :T=>0}
+    bases_2  << {:A=>0, :C=>24, :G=>112, :T=>0}
+    bases_1  << {:A=>34, :C=>0, :G=>138, :T=>0}
+    bases_2  << {:A=>26, :C=>0, :G=>138, :T=>0}
+    bases_1  << {:A=>0, :C=>32, :G=>0, :T=>141}
+    bases_2  << {:A=>0, :C=>26, :G=>0, :T=>142}
+    bases_1  << {:A=>22, :C=>0, :G=>56, :T=>0}
+    bases_2  << {:A=>62, :C=>0, :G=>25, :T=>0}
+    bases_1  << {:A=>27, :C=>0, :G=>22, :T=>0}
+    bases_2  << {:A=>46, :C=>0, :G=>9, :T=>0}
+    i = 0
+    with_bfr.each do | pos |
+      puts pos
+      assert_equal(reg.bases_bulk_1[pos - 1 ] , bases_1[i] )
+      assert_equal(reg.bases_bulk_2[pos - 1 ] , bases_2[i] )
+      i += 1
+    end
+   
+   
     
-    puts cons_2
-    puts cons_1
+    output_file.close
     
   end
   

metadata

@@ -1,43 +1,43 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.3
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-31 00:00:00.000000000 Z
+date: 2014-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: bio-samtools
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.2
+        version: 2.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.2
+        version: 2.0.3
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -66,6 +66,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: systemu
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.5.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.5.2
 description: Repository of tools developed in TGAC and Crop Genetics in JIC to work
   with polyploid wheat
 email: ricardo.ramirez-gonzalez@tgac.ac.uk
@@ -74,6 +88,7 @@ executables:
 - count_variations.rb
 - filter_blat_by_target_coverage.rb
 - find_best_blat_hit.rb
+- find_best_exonerate.rb
 - hexaploid_primers.rb
 - homokaryot_primers.rb
 - map_markers_to_contigs.rb
@@ -83,16 +98,19 @@ executables:
 extensions: []
 extra_rdoc_files:
 - README
+- README.md
 files:
 - Gemfile
 - Gemfile.lock
 - README
+- README.md
 - Rakefile
 - VERSION
 - bin/bfr.rb
 - bin/count_variations.rb
 - bin/filter_blat_by_target_coverage.rb
 - bin/find_best_blat_hit.rb
+- bin/find_best_exonerate.rb
 - bin/hexaploid_primers.rb
 - bin/homokaryot_primers.rb
 - bin/map_markers_to_contigs.rb
@@ -143,9 +161,7 @@ files:
 - lib/bio/PolyploidTools/PrimerRegion.rb
 - lib/bio/PolyploidTools/SNP.rb
 - lib/bio/PolyploidTools/SNPSequence.rb
-- lib/bio/SAMToolsExtensions.rb
 - lib/bio/db/exonerate.rb
-- lib/bio/db/fastadb.rb
 - lib/bio/db/primer3.rb
 - lib/bioruby-polyploid-tools.rb
 - test/data/BS00068396_51.fa