bio-samtools 0.4.1 → 0.4.2

data/test/coverage.rb

@@ -1,26 +0,0 @@
-$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
-$: << File.expand_path('.')
-
-require "bio/db/sam"
-require "bio/db/sam/sam"
-
-bam_file = ARGV[0]
-fasta_file = ARGV[1]
-chromosmes = ARGV[2]
-i = 0
-sam       = Bio::DB::Sam.new({:bam=>bam_file, :fasta=>fasta_file})
-sam.open
-File.open(chromosmes, "r") do |file|
-  file.each_line{|line|
-    $stderr.puts i.to_s + " done" if i%10 == 0
-    ObjectSpace.each_object(Bio::DB::Sam) {|x|  $stderr.puts x } if i%10 == 0
-    count =  ObjectSpace.each_object() {|x|  } if i%10 == 0
-    $stderr.puts count if i%10 == 0
-    i = i + 1
-    fetching = line.split(' ')[0]
-	  
-	  cov = sam.average_coverage(fetching, 0, 16000)
-	  puts fetching + " " + cov.to_s
-  }
-end
-sam.close

data/test/coverage_plot.rb

@@ -1,28 +0,0 @@
-$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
-$: << File.expand_path('.')
-
-require "bio/db/sam"
-require "bio/db/sam/sam"
-
-bam_file = ARGV[0]
-fasta_file = ARGV[1]
-chromosmes = ARGV[2]
-
-
-sam       = Bio::DB::Sam.new({:bam=>bam_file, :fasta=>fasta_file})
-sam.open
-File.open(chromosmes, "r") do |file|
-    file.each_line{|line|
-      
-      
-      
-     
-      fetching = line.split()[0]
-	    last = line.split()[1].to_i
-	    covs = sam.chromosome_coverage(fetching, 0, last)
-	    puts "POS\tCOV"
-	   # puts "#{fetching}\t#{last}"
-	    covs.each_with_index{ |cov, i| puts "#{i}\t#{cov}" }
-    }
-end
-sam.close

data/test/test_pileup.rb

@@ -1,68 +0,0 @@
-$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
-$: << File.expand_path('.')
-
-require "bio/db/sam/pileup"
-require "test/unit"
-
-class TestPileup < Test::Unit::TestCase
-  
-  def setup
-    @six_col = Pileup.new("seq1\t272\tT\t24\t,.$.....,,.,.,...,,,.,..^+.\t<<<+;<<<<<<<<<<<=<;<;7<&")
-    @ten_col = Pileup.new("seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<")
-    @snp = Pileup.new("seq1\t272\tT\t24\t,.$.....,,.gGgGgGgGgGgGg^+.\t<<<+;<<<<<<<<<<<=<;<;7<&") 
-    @snp_2 = Pileup.new("seq1\t272\tT\t24\t......aaaaaaggggggcccccc$^+\t<<<+;<<<<<<<<<<<=<;<;7<&")
-    @snp_3 = Pileup.new("seq1\t272\tT\t24\t......aaaaaaaagggggccccc$^+\t<<<+;<<<<<<<<<<<=<;<;7<&")
-  end
-  
-  def test_new_from_6_column
-    assert_equal("seq1", @six_col.ref_name)
-    assert_equal(272, @six_col.pos)
-    assert_equal("T", @six_col.ref_base)
-    assert_equal(24, @six_col.coverage)
-    assert_equal(",.$.....,,.,.,...,,,.,..^+.", @six_col.read_bases)
-    assert_equal("<<<+;<<<<<<<<<<<=<;<;7<&", @six_col.read_quals)
-  end
-  
-  def test_new_from_10_column
-    assert_equal("seq2", @ten_col.ref_name)
-    assert_equal(151, @ten_col.pos)
-    assert_equal("G", @ten_col.ref_base)
-    assert_equal("G", @ten_col.consensus)
-    assert_equal(36, @ten_col.consensus_quality)
-    assert_equal(0, @ten_col.snp_quality)
-    assert_equal(99, @ten_col.rms_mapq)
-    assert_equal(12, @ten_col.coverage)
-    assert_equal("...........A", @ten_col.read_bases)
-    assert_equal(":9<;;7=<<<<<", @ten_col.read_quals)
-  end
-  
-  def test_non_refs
-    assert_equal({:A => 1, :C => 0, :T => 0, :G => 0}, @ten_col.non_refs)
-    assert_equal({:A => 0, :C => 0, :T => 0, :G => 0}, @six_col.non_refs)
-  end
-  
-  def test_consensus
-    assert_equal("G", @snp.consensus)
-    assert_equal("ACGT", @snp_2.consensus)
-    assert_equal("A", @snp_3.consensus)
-  end
-  
-  def test_non_ref_count
-    assert_equal(13,@snp.non_ref_count)
-    assert_equal(18,@snp_2.non_ref_count)
-    assert_equal(18,@snp_3.non_ref_count)
-  end
-  
-  def test_ref_count
-    assert_equal(11,@snp.ref_count)
-    assert_equal(6,@snp_2.ref_count)
-    assert_equal(6,@snp_3.ref_count)
-  end
-  
-  def test_ref_plus_non_ref_equal_to_coverage
-    assert_equal(@snp.coverage,@snp.ref_count + @snp.non_ref_count)
-   assert_equal(@snp_2.coverage,@snp_2.ref_count + @snp_2.non_ref_count)
-   assert_equal(@snp_3.coverage,@snp_3.ref_count + @snp_3.non_ref_count)
-  end
- 
-end