bio-samtools 2.0.4 → 2.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: fb06f8ed5dc89daa39e4b30bd58d5c7bb87f1f27
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data/Gemfile

@@ -15,7 +15,7 @@ group :development do
   gem "jeweler"
   gem "rcov", ">=0", :platforms => :ruby_18
   gem "simplecov", ">= 0",   :platforms => :ruby_19
-
+  gem "ruby-prof"
   gem 'rdoc'
   gem 'test-unit'
 end

data/README.md

@@ -68,6 +68,7 @@ See more detail on doc/tutorial.html or doc/tutorial.pdf for a walkthrough tutor
 	
 	[Answer] This appears to be a bug in RubyGems that doesn't affect the running of the tools. It will keep happening until someone updates RubyGems. If it really bugs you, downgrade RubyGems.
 
+
 ## Contributing to bio-samtools
  
 * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
@@ -86,16 +87,16 @@ Try [Ricardo.Ramirez-Gonzalez@tgac.ac.uk](Ricardo.Ramirez-Gonzalez@tgac.ac.uk)
  and [dan.maclean@tsl.ac.uk](dan.maclean@tsl.ac.uk)
 
 ### Important Notes
-* Libraries (libbam) are downloaded, compiled and installed inside the gem at install time on the host system
+* samtools is downloaded, compiled and installed inside the gem at install time on the host system
 
-    `openssl dgst libbam.so.1` MD5 is c45cfccfb41ffeb2730ee4b227d244c4
+* If you use this tool for publication, please cite http://dx.doi.org/10.1186/1751-0473-7-6
 
 ### Important Notes for developers
 
-Remember that you must compile and install the right libbam library for you host system. In order to do that there are three possible solutions:
+Remember that you must compile and install samtools for you host system. In order to do that there are two possible solutions:
 
-* download, compile and install the library in bioruby-samtools-your_clone/lib/bio/db/sam/external/libbam.xxxxx by yourself
-* install the gem and then grab the compiled library `cp 'locate libbam.1.dylib' bioruby-samtools-your_clone/lib/bio/db/sam/external` (library name is an example)
+* download, compile and install the library in bioruby-samtools-your_clone/lib/bio/db/sam/external/samtools and
+ bioruby-samtools-your_clone/lib/bio/db/sam/external/bcftools by yourself
 * in your bioruby-samtools-your_clone create the Rakefile typing `cd ext; ruby mkrf_conf.rb; rake -f Rakefile`
 
 The latest I think is the easiest way, cause you are replicating the automatic process.

data/VERSION

@@ -1 +1 @@
-2.0.4
+2.0.5

data/bio-samtools.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 2.0.4 ruby lib
+# stub: bio-samtools 2.0.5 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools"
-  s.version = "2.0.4"
+  s.version = "2.0.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = "2014-04-28"
+  s.date = "2014-05-31"
   s.description = "Binder of samtools for ruby, on the top of FFI. \n\n  This project was born from the need to add support of BAM files to \n  the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
   s.email = "ilpuccio.febo@gmail.com"
   s.extensions = ["ext/mkrf_conf.rb"]
@@ -94,12 +94,11 @@ Gem::Specification.new do |s|
     "lib/bio/db/sam.rb",
     "lib/bio/db/sam/external/COPYING",
     "lib/bio/db/sam/external/VERSION",
-    "lib/bio/db/sam/faidx_old.rb",
     "lib/bio/db/sam/library.rb",
     "lib/bio/db/vcf.rb",
     "test/.gitignore",
     "test/helper.rb",
-    "test/old_test_basic.rb",
+    "test/samples/.gitignore",
     "test/samples/small/dupes.bam",
     "test/samples/small/dupes.sam",
     "test/samples/small/ids2.txt",
@@ -133,12 +132,15 @@ Gem::Specification.new do |s|
     "test/samples/small/test_cov.svg",
     "test/samples/small/testu.bam",
     "test/samples/small/testu.bam.bai",
-    "test/svg",
     "test/test_bio-samtools.rb",
     "test/test_pileup.rb",
     "test/test_sam.rb",
     "test/test_vcf.rb",
+    "tutorial/images/out.svg",
+    "tutorial/images/out2.svg",
+    "tutorial/images/out3.svg",
     "tutorial/tutorial.html",
+    "tutorial/tutorial.md",
     "tutorial/tutorial.pdf"
   ]
   s.homepage = "http://github.com/helios/bioruby-samtools"
@@ -159,6 +161,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<jeweler>, [">= 0"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<ruby-prof>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, [">= 0"])
       s.add_development_dependency(%q<test-unit>, [">= 0"])
     else
@@ -171,6 +174,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, [">= 0"])
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<ruby-prof>, [">= 0"])
       s.add_dependency(%q<rdoc>, [">= 0"])
       s.add_dependency(%q<test-unit>, [">= 0"])
     end
@@ -184,6 +188,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<jeweler>, [">= 0"])
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<ruby-prof>, [">= 0"])
     s.add_dependency(%q<rdoc>, [">= 0"])
     s.add_dependency(%q<test-unit>, [">= 0"])
   end

data/lib/bio/db/fastadb.rb

@@ -69,7 +69,7 @@ module Bio::DB::Fasta
   class Region
     BASE_COUNT_ZERO =  {:A => 0, :C => 0, :G => 0,  :T => 0}
     attr_accessor :entry, :start, :end, :orientation
-    attr_accessor :pileup, :average_coverage, :snps, :reference, :base_ratios, :consensus, :coverages, :bases, :total_cov, :called
+    attr_accessor :pileup, :average_coverage, :reference, :base_ratios, :consensus, :coverages, :bases, :total_cov, :called
 
     #TODO: Debug, as it hasnt been tested in the actual code. 
     def base_ratios_for_base(base)

data/lib/bio/db/sam.rb

@@ -1,3 +1,4 @@
+require 'open3'
 module Bio
   class DB
     class Sam
@@ -63,6 +64,8 @@ module Bio
       def view(opts={},&block)
         region = String.new
         if opts[:chr] and opts[:start] and opts[:stop]
+          has_e = self.has_entry? opts[:chr]
+          raise Exception.new(), "[view] The sequence #{opts[:chr]} is not in the bam file" unless self.has_entry? opts[:chr] 
           region = "#{opts[:chr]}:#{opts[:start]}-#{opts[:stop]}"
           [:chr, :start, :stop].each {|o| opts.delete(o)}
         end
@@ -89,6 +92,7 @@ module Bio
       #* stop - the stop position for the subsequence
       #* &block - the the block of code to execute
       def fetch(chr, start,stop, &block)
+       
         view(
         :chr => chr,
         :start => start,
@@ -136,7 +140,7 @@ module Bio
         :number_of_intervals => 10,
         :font_size => 14
         )
-        data_track = p.add_track(:glyph => :histogram, 
+        default_options = {:glyph => :histogram, 
         :stroke_color => 'black',
         :fill_color => 'gold',
         :track_height => 150,
@@ -144,7 +148,10 @@ module Bio
         :label => true, 
         :stroke_width => '1', 
         :x_round => 1,
-        :y_round => 1 )
+        :y_round => 1 }
+        opts = default_options.merge(opts)
+        
+        data_track = p.add_track(opts)
         index = 0;        
         result.each_slice(bin) {|slice| 
           #result.each_with_index {|val, index|
@@ -243,11 +250,14 @@ module Bio
 
         opts[:f] = @fasta
 
-
+        #TOODO: reduce the string handling
         query = opts[:r].to_s
         query = opts[:r].to_region.to_s if opts[:r].respond_to?(:to_region)
+        if not query.nil? and query.size > 0
+          raise Exception.new(), "The sequence #{query} is not in the bam file"  unless has_region? query 
+        end
         opts[:r] = query
-
+        
         if opts[:six]
           opts["6"] = nil
           opts.delete(:six)
@@ -258,7 +268,7 @@ module Bio
         if opts[:u]
           command = command + " | #{@bcftools} view -cg -"
         end
-
+        
         klass = opts[:u] ? Bio::DB::Vcf : Bio::DB::Pileup
         @last_command = command
         yield_from_pipe(command, klass, :text, &block)
@@ -271,6 +281,7 @@ module Bio
       #* stop - [INT] the stop position for the subsequence
       #* as_bio - boolean stating if the returned object should be a Bio::Sequence::NA object
       def fetch_reference(chr,start,stop, opts={:as_bio => false})
+        raise Exception.new(), "The sequence #{chr} is not in the bam file" unless has_entry? chr
         seq = ""
         unless @fasta #We return a string of Ns if we don't know the reference. 
           seq = "n" * (stop-start) 
@@ -344,38 +355,54 @@ module Bio
 
       #Retrieve and print stats in the index file. The output is TAB delimited with each line consisting of reference sequence name, sequence length, number of mapped reads and number unmapped reads.
       def index_stats
+       return @stats if @stats
         stats = {}   
-        command = form_opt_string(@samtools, "idxstats #{@bam}", {}, [])
+        command = form_opt_string(@samtools, "idxstats", {}, [])
         @last_command = command
-        puts command if $VERBOSE
         yield_from_pipe(command, String, :text, true, "#") do |line|
           info = line.chomp.split(/\t/)
           stats[ info[0] ] = {:length => info[1].to_i, :mapped_reads => info[2].to_i, :unmapped_reads => info[3].to_i }
         end
-        stats
+        @stats = stats
+        return @stats
       end
 
       alias_method :idxstats, :index_stats
       
       #Retrive a hash with all the regions, with the region id as index or runs the function on each region
       def each_region
-        stats=index_stats unless @stats
+        index_stats 
         if @regions 
-          return @regionss unless block_given? 
+          return @regions unless block_given? 
         else
           @regions = Hash.new
         end
-        stats.each do |k,v|
-          reg = Bio::DB::Fasta::Region
+        index_stats.each do |k,v|
+          reg = Bio::DB::Fasta::Region.new
           reg.entry = k
           reg.start = 1
           reg.end = v[:length]
           reg.orientation = :forward
-          
+          @regions << reg unless @regions[k]
           yield reg if block_given?
         end
         @regions
       end
+      
+      #Tells if the bam file contains the entry. It has to be indexed.
+      def has_entry?(entry)
+         index_stats.has_key?(entry)
+    #    puts "#{entry} #{@stats.inspect}"
+      #  index_stats
+      end
+      
+      def has_region?(region)
+        index_stats
+        reg=Bio::DB::Fasta::Region::parse_region(region)
+        return 0 unless has_entry? (reg.entry) 
+         len = @stats[reg.entry][:length]
+         reg.start > 0 and reg.end <= len
+      end
 
       #Merge multiple sorted alignments
       #* n - sort by read names
@@ -431,7 +458,7 @@ module Bio
         opts.delete(:bams)
         options = commandify(opts, [:h] )
         command = "#{@samtools} cat #{options} -o #{out} #{bam_list}"
-        puts command
+        puts command if $VERBOSE
         @last_command = command
         system(command)
 
@@ -617,7 +644,7 @@ module Bio
       #
       #TODO: It may be good to load partially the pileup
       def mpileup_cached (opts={})      
-        raise SAMException.new(), "A region must be provided" unless opts[:r] or opts[:region]
+        raise Exception.new(), "A region must be provided" unless opts[:r] or opts[:region]
         @cached_regions = Hash.new unless @cached_regions
         region = opts[:r] ? opts[:r] : opts[:region]
         @cached_regions[region.to_s] = fetch_region(opts) unless @cached_regions[region.to_s]
@@ -666,10 +693,23 @@ module Bio
         fetch_with_function(chromosome, qstart, qstart+len,  print_fastq)
         out.close if fastq_filename
       end
+      
+       # checks existence of files in instance
+      def files_ok?
+        [@fasta, @sam, @bam].flatten.compact.each {|f| return false unless File.exists? f }
+        true
+      end
+      
+      #Returns true if the .bai exists. It doesn't validate if it is valid. 
+      def indexed?
+        File.exists? @bam and File.exists? "#{@bam}.bai"
+      end
+        
       private
       #Returns Process::Status with the execution status. If run in a $VERBOSE environment, stderr of the process
       #is forwarded to the default stdout
       def yield_from_pipe(command, klass, type=:text, skip_comments=true, comment_char="#", &block)
+        puts "[yield_from_pipe] #{command}" if $VERBOSE
         stdin, pipe, stderr, wait_thr = Open3.popen3(command)
         pid = wait_thr[:pid]  # pid of the started process.       
         if type == :text
@@ -711,15 +751,6 @@ module Bio
         end
         list.join(" ")
       end
-
-      # checks existence of files in instance
-      def files_ok?
-        [@fasta, @sam, @bam].flatten.compact.each {|f| return false unless File.exists? f }
-        true
-      end
-
-
-
     end
   end
 end

data/test/samples/.gitignore

@@ -0,0 +1 @@
+svgenes/

data/test/test_sam.rb

@@ -3,12 +3,16 @@ $: << File.expand_path('.')
 require 'rubygems'
 require 'bio/db/sam'
 require "test/unit"
+#gem 'ruby-prof'
 gem 'test-unit'
+#require "ruby-prof"
 
 
 class TestBioDbSam < Test::Unit::TestCase
+#  include RubyProf::Test
   
   class << self
+
     def shutdown
       File.delete("test/samples/small/different_index.bam.bai")
       File.delete("test/samples/small/dupes_rmdup.bam")
@@ -46,9 +50,12 @@ class TestBioDbSam < Test::Unit::TestCase
       puts "bam index exists....deleting..."
       File.delete(test_bai_file)
     end
-     #index the bam file
+ 
+    #No bam file 
+    assert_equal(@sam.indexed?, false)
+    #index the bam file
     @sam.index()
-    
+    assert_equal(@sam.indexed?, true)
     #make sure the .bai file exists
     assert_nothing_thrown do
       File.open(test_bai_file, "r")
@@ -73,11 +80,18 @@ class TestBioDbSam < Test::Unit::TestCase
   end
   
   def test_fetch
+#puts    @sam.inspect
+    i = 0
+    @sam.index
     @sam.fetch("chr_1", 10,1000) do |sam|
       #test that all the objects are Bio::DB::Alignment objects
       assert_equal(sam.class, Bio::DB::Alignment)
       assert_equal(sam.rname, "chr_1")
+      i += 1
     end
+    assert(i>0)
+    assert_equal(i,9)
+    
   end
   
   def test_fetch_with_function
@@ -170,6 +184,7 @@ class TestBioDbSam < Test::Unit::TestCase
   
   def test_mpileup
     #create an mpileup
+  #  @sam.index
     @sam.mpileup(:g => false) do |pileup|
       #test that all the objects are Bio::DB::Pileup objects
       assert_kind_of(Bio::DB::Pileup, pileup)
@@ -266,7 +281,8 @@ class TestBioDbSam < Test::Unit::TestCase
     bam_files = [bam_to_merge1, bam_to_merge2]
     
     merged_bam_file = @test_folder + "/maps_merged.bam"
-    
+    File.delete merged_bam_file if File.exists?(merged_bam_file)
+#    File.delete("test/samples/small/maps_merged.bam")
     @sam.merge(:out=>merged_bam_file, :bams=>bam_files, :n=>true)
     merged_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => merged_bam_file)
     no_reads_mapped = 0;
@@ -286,7 +302,7 @@ class TestBioDbSam < Test::Unit::TestCase
     bam_files = [bam1, bam2]
     
     cat_bam_file = @test_folder + "/maps_cated.bam"
-    
+    File.delete cat_bam_file if File.exists?(cat_bam_file)
     @sam.merge(:out=>cat_bam_file, :bams=>bam_files)
     cated_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => cat_bam_file)
     

data/tutorial/images/out.svg

@@ -0,0 +1,75 @@
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+<text x="3" y="60" fill="black" transform="" style="font-family:monospace;">read coverage</text>
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