bio-samtools 2.0.4 → 2.0.5

data/test/old_test_basic.rb

@@ -1,433 +0,0 @@
-$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
-$: << File.expand_path('.')
-require 'rubygems'
-require 'ffi'
-require "test/unit"
-require "bio/db/sam"
-require "bio/db/sam/sam"
-require "bio/db/pileup"
-require "bio/db/vcf"
-
-class TestBioDbSam < Test::Unit::TestCase
-
-  #Set up the paths
-  def setup
-    @test_folder                = "test/samples/small"
-    @testTAMFile                = @test_folder + "/test.tam"
-    @testBAMFile                = @test_folder + "/testu.bam"
-    @testReference              = @test_folder + "/test_chr.fasta"
-    
-  end
-  
-  #Removing the index files
-  def teardown
-    begin
-      File.delete(@testReference + ".fai")
-      #p "deleted: " + @testReference + ".fai "
-    rescue
-    end
-    begin
-      File.delete(@testBAMFile + ".fai")
-      #p "deleted: " + @testBAMFile + ".bai "
-    rescue
-    end
-  end
-
-  def default_test
-    #puts $LOAD_PATH
-    assert(true, "Unit test test")
-  end
-
-  def test_openSAMFile
-    bamfile                      = Bio::DB::SAM::Tools.samopen(@testTAMFile,"r",nil)
-    Bio::DB::SAM::Tools.samclose(bamfile)
-    assert(true, "file open and closed")
-  end
-
-  def test_new_class_empty
-    begin
-      bam                        = Bio::DB::Sam.new({})
-      assert(false, "Should fail while opening without parameters")
-    rescue Bio::DB::SAMException => e
-      #puts e.message
-      assert(true, e.message)
-    end
-  end
-
-  def test_new_class_empty_invalid_path
-    begin
-      sam                        = Bio::DB::Sam.new({:bam=>"INVALID"})
-      sam.open
-      sam.close
-      assert(false, "Should fail with an invalid path")
-    rescue Bio::DB::SAMException => e
-      #puts e.message
-      assert(true, e.message)
-    end
-  end
-
-  def test_class_text_read_no_faidx
-    sam                          = Bio::DB::Sam.new({:tam=>@testTAMFile})
-    sam.open
-    sam.close
-    assert(true, "file open and closed with the class")
-  end
-
-  def test_class_text_read_no_close
-
-    fam                          = Bio::DB::Sam.new({:tam=>@testTAMFile})
-    fam.open
-    fam                          = nil   
-    ObjectSpace.garbage_collect
-
-    assert(true, "file openend but not closed")
-  end
-
-  def test_class_binary_read_no_close
-
-    Bio::DB::Sam.new({:bam=>@testBAMFile}).open
-    ObjectSpace.garbage_collect
-    assert(true, "BINARY file openend but not closed")  
-  end
-
-  def test_read_coverage
-     sam       = Bio::DB::Sam.new({:bam=>@testBAMFile, :fasta=>@testReference})
-     sam.open
-  	File.open( @test_folder +"/ids2.txt", "r") do |file|
-  	  #puts "file opened"
-  	  file.each_line{|line|
-        fetching = line.split(' ')[0]
-        #puts "fetching: " + fetching
-  	    sam.load_reference
-    	  seq = sam.fetch_reference(fetching, 0, 16000)
-  #	  puts seq 
-  #	  puts seq.length
-  	  als = sam.fetch(fetching, 0, seq.length) 
-     #      p als
-  	  if als.length() > 0 then
-  	      # p fetching
-          #      p als
-  	    end
-           }
-
-  	end
-    sam.close
-   assert(true, "Finish")
-  end
-#  def test_read_TAM_as_BAM
-#    begin
-#      sam                          = Bio::DB::Sam.new({:bam=>@testTAMFile})
-#      sam.open
-#      sam.close
-#      assert(false, "Should raise an exception for reading a BAM as TAM") 
-#    rescue Bio::DB::SAMException => e
-#      assert(true, "Properly handled")
-#    end 
-#  end
-
-# def test_read_BAM_as_TAM
-#    begin
-#      sam                          = Bio::DB::Sam.new({:tam=>@testBAMFile})
-#      sam.open
-#      sam.close
-#      assert(false, "Should raise an exception for reading a BAM as TAM") 
-#    rescue Bio::DB::SAMException => e
-#      assert(true, "Properly handled")
-#    end 
-#  end
-
-  def test_bam_load_index
-    sam       = Bio::DB::Sam.new({:bam=>@testBAMFile})
-    sam.open
-    index = sam.load_index
-    sam.close
-    assert(true, "BAM index loaded")
-    #  attach_function :bam_index_build, [ :string ], :int
-    #  attach_function :bam_index_load, [ :string ], :pointer
-    #  attach_function :bam_index_destroy, [ :pointer ], :void
-  end
-
-  def test_tam_load_index
-    begin
-      sam       = Bio::DB::Sam.new({:tam=>@testTAMFile})
-      sam.open
-      sam.load_index
-      sam.close
-      assert(false, "TAM index loaded")
-    rescue Bio::DB::SAMException => e
-      assert(true, "Unable to load an index for a TAM file")
-    end
-  end
-
-  def test_read_segment
-    sam       = Bio::DB::Sam.new({:bam=>@testBAMFile})
-    sam.open
-    als = sam.fetch("chr_1", 0, 500)
-    #p als 
-    sam.close
-    assert(true, "Seems it ran the query")
-    #node_7263       238     60 has 550+, query from 0 to 500, something shall come.... 
-  end
-
-=begin ##these tests are correct-ish but the functionality isnt implemented yet ... 
-  def test_read_invalid_reference
-    sam       = Bio::DB::Sam.new({:bam=>@testBAMFile})
-    sam.open
-    begin
-      als = sam.fetch("Chr1", 0, 500)
-      #p als 
-      sam.close
-      assert(false, "Seems it ran the query")
-    rescue Bio::DB::SAMException => e
-      #p e
-      assert(true, "Exception generated and catched")
-    end
-  end
-
-  def test_read_invalid_reference_start_coordinate
-    sam       = Bio::DB::Sam.new({:bam=>@testBAMFile})
-    sam.open
-    begin
-      als = sam.fetch("chr", -1, 500)
-      #p als 
-      sam.close
-      assert(false, "Seems it ran the query")
-    rescue Bio::DB::SAMException => e
-      #p e
-      assert(true, "Exception generated and catched")
-    end
-  end
-
-  def test_read_invalid_reference_end_coordinate
-    sam       = Bio::DB::Sam.new({:bam=>@testBAMFile})
-    sam.open
-    begin
-      als = sam.fetch("chr", 0, 50000)
-      #p als 
-      sam.close
-      assert(false, "Seems it ran the query")
-    rescue  Bio::DB::SAMException => e
-      #p e
-      assert(true, "Exception generated and catched")
-    end
-  end
- 
-  def test_read_invalid_reference_swaped_coordinates
-    sam       = Bio::DB::Sam.new({:bam=>@testBAMFile})
-    sam.open
-    begin
-      als = sam.fetch("chr", 500, 0)
-      #p als 
-      sam.close
-      assert(false, "Seems it ran the query")
-    rescue  Bio::DB::SAMException => e
-      #p e
-      assert(true, "Exception generated and catched")
-    end
-  end
-=end 
-  def test_fasta_load_index
-    sam = Bio::DB::Sam.new({:fasta=>@testReference})
-    sam.load_reference
-    seq = sam.fetch_reference("chr_1", 0, 500)
-    #p seq 
-    sam.close
-    assert(true, "The reference was loaded")
-  end
-  
-  def test_fasta_load_index
-    sam = Bio::DB::Sam.new({:fasta=>@testReference})
-    sam.load_reference
-    begin
-      seq = sam.fetch_reference("chr1", 0, 500)
-      #p "Error seq:"+ seq 
-      sam.close
-      assert(false, "The reference was loaded")
-    rescue Bio::DB::SAMException => e
-      #p e
-      assert(true,  "The references was not loaded")
-    end
-  end
-  
-  def test_load_feature
-    
-    fs = Feature.find_by_bam("chr_1", 0, 500,@testBAMFile)
-    
-    #p fs
-    assert(true, "Loaded as features")
-  end
-  
-  def test_avg_coverage
-    sam = Bio::DB::Sam.new(:fasta=>@testReference, :bam=>@testBAMFile )
-    sam.open
-    cov = sam.average_coverage("chr_1", 60, 30)
-    #p "Coverage: " + cov.to_s
-    sam.close
-    assert(true, "Average coverage ran")
-    assert(3 == cov, "The coverage is 3")
-  end
-  
-
-  def test_chromosome_coverage
-    sam = Bio::DB::Sam.new({:fasta=>@testReference, :bam=>@testBAMFile })
-    sam.open
-    covs = sam.chromosome_coverage("chr_1", 0, 60)
-    #p "Coverage: "
-    #p covs
-    #puts "POS\tCOV"
-    covs.each_with_index{ |cov, i| puts "#{i}\t#{cov}" }
-    sam.close
-    assert(true, "Average coverage ran")
-    #assert(3 == cov, "The coverage is 3")
-  end
-  
-  #test whether the call to mpileup works and returns 10 objects of class pileup
-  def test_mpileup
-    sam = Bio::DB::Sam.new(:fasta=>@testReference, :bam=>@testBAMFile )
-    pileup_list = []
-    sam.mpileup(:region => "chr_1:100-109") do |pile|
-      #next unless pile.ref_name == 'chr_1' ##required because in the test environment stdout gets mixed in with the captured stdout in the function and non pileup lines are passed...
-      pileup_list << pile
-    end
-    assert_equal(10,pileup_list.length)
-    pileup_list.each  do |p|
-      assert_kind_of(Bio::DB::Pileup, p)
-    end
-  end
-  
-  #test whether the call to experimental mpileup_plus returns vcf or pileup objects appropriately
-  #return ten objects of each class according to set of :g option
-  def test_mpileup_plus
-    sam = Bio::DB::Sam.new(:fasta=>@testReference, :bam=>@testBAMFile)
-    list = []
-    sam.mpileup_plus(:region => "chr_1:100-109") do |pile|
-      list << pile
-    end
-    assert_equal(10,list.length)
-    list.each {|p| assert_kind_of(Bio::DB::Pileup, p)}
-    vcf_list = []
-    sam.mpileup_plus(:region => "chr_1:100-109", :g => true) do |vcf|
-      vcf_list << vcf
-    end
-    assert_equal(10,vcf_list.length)
-    vcf_list.each {|p| assert_kind_of(Bio::DB::Vcf, p)}
-  end
-  
-  # test whether command line calls to mpileup are correctly escaped
-  def test_mpileup_escaping
-    test_dir = File.join('test','samples','pipe_char')
-    sam = Bio::DB::Sam.new(
-      :fasta => File.join(test_dir,'test_chr.fasta'),
-      :bam => File.join(test_dir, 'test.bam')
-    )
-    pileup_list = []
-    sam.mpileup(:region => "gi|123|chr_1:100-109") do |pile|
-      pileup_list << pile
-    end
-    assert_equal(10,pileup_list.length)
-    pileup_list.each  do |p|
-      assert_kind_of(Bio::DB::Pileup, p)
-    end
-  end
-  
-  # test whether command line calls to mpileup are correctly escaped
-  def test_mpileup_error_reporting
-    test_dir = File.join('test','samples','pipe_char')
-    sam = Bio::DB::Sam.new(
-      :fasta => File.join(test_dir,'does_not_exist.fasta'),
-      :bam => File.join(test_dir, 'test.bam')
-    )
-    assert_raise Bio::DB::SAMException do
-      pileup_list = []
-      sam.mpileup(:region => "gi|123|chr_1:100-109") do |pile|
-        pileup_list << pile
-      end
-    end
-  end
-
-  #test whether the call to mpileup returns a vcf object if :g => true is used on the command-line
-#  def test_vcf
-
-#    sam = Bio::DB::Sam.new(:fasta=>@testReference, :bam=>@testBAMFile )
-#        sam.mpileup(:region => "chr_1:100-109", :u => true ) do |p|
-#        $stderr.puts "p is #{p}"
-#        assert_kind_of(String,p)
-#    end
-#  end
-  def test_indexstats
-
-    sam = Bio::DB::Sam.new(:bam => @testBAMFile, :fasta => @testReference)
-    assert_equal({"chr_1"=>{:length=>69930, :mapped_reads=>0, :unmapped_reads=>0},
-                  "*"=>{:length=>0, :mapped_reads=>0, :unmapped_reads=>0}
-                 }, sam.index_stats)
-  end
-  
-  def test_each_reference
-    sam = Bio::DB::Sam.new(:bam => @testBAMFile, :fasta => @testReference)
-    sam.each_reference do |name, length|
-      next if name == '*'
-      assert_equal name, "chr_1"
-      assert_equal length, 69930
-    end
-  end
-  
-  def test_view
-    sam = Bio::DB::Sam.new(:bam => @testBAMFile, :fasta => @testReference)
-    sam.open 
-    count = 0
-    sam.view() do |aln|
-      count = count +1
-    end
-    assert_equal count, 9
-  end
-  
-  def test_view_b
-    sam = Bio::DB::Sam.new(:bam =>"/Users/macleand/Desktop/AT1/realigned.bam", :fasta => "/Users/macleand/src/data/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/assemblies/gDNA/KW1_assembly_version1/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa")
-    sam.open 
-    count = 0
-    sam.view_b do |aln|
-
-      count = count +1
-    end
-    puts "count is: #{count}"
-    assert_equal count, 9
-  end
-  
-#  def test_view_big
-#    puts "...woot"
-#    sam = Bio::DB::Sam.new(:bam => "/Users/macleand/Desktop/AT1/realigned.bam", :fasta => "/Users/macleand/src/data/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/assemblies/gDNA/KW1_assembly_version1/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa")
-#    sam.open
-#    sam.view do |aln|
-#      puts aln
-#    end
-#  end
-  
-end
-
-class Feature 
-attr_reader :start, :end, :strand, :sequence, :quality
-
-def initialize(a={})
-  #p a
-  @start = a[:start]
-  @end = a[:enf]
-  @strand = a[:strand]
-  @sequence = a[:sequence]
-  @quality = a[:quality]
-end
-
-def self.find_by_bam(reference,start,stop,bam_file_path)
-  
-  sam = Bio::DB::Sam.new({:bam=>bam_file_path})
-  features = []
-  sam.open
-  
-  fetchAlignment = Proc.new do |a|
-    a.query_strand ? strand = '+'  : strand = '-'
-    features << Feature.new({:start=>a.pos,:end=>a.calend,:strand=>strand,:sequence=>a.seq,:quality=>a.qual})
-  end
-  sam.fetch_with_function(reference, start, stop, fetchAlignment)
-  sam.close
-  features
-end
-end

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