bio-samtools-server 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e23edcddef2395d0d46cb0d405c9931280af98ee
-  data.tar.gz: e2887c08e5853df572e72f32008c4e3266a46849
+  metadata.gz: c918eeecb592ab3dfd5263d500924d5125741161
+  data.tar.gz: cf157144793f62bbdaade370d637962525d80405
 SHA512:
-  metadata.gz: 590478424e3e6613786cfd4c3b114bc3b904bfd90440c6783e4f9d36c9c8595d6c30432986591d853639ec3ef24d9b1c1702036ac815e232438191afcea44519
-  data.tar.gz: 4cc09d1c5ca6c921730b0e8626cc7ade786afb1705f84a10f1e05bb5b12aa160ea2f03fbd2438e658c1cbca3464a06c45e97f3a0a92e86f5d74a92065225aa4d
+  metadata.gz: 9c9207d1efb79e1f8899bdc71010d154e927395ab61e026906333a334946ff714ca7edd28ecaef52425b1881f6fd3d583804408f166918bca323b8978bde7dc5
+  data.tar.gz: 60f92d49a1485bb1e92914f04617a1c6d48b9ef14ce542d4998e95b2235043f235efc15d3e07e022f51eb6b634f12f6d2db09c6b9ca6694168b19623f7b1004f

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bin/bam-server.rb

@@ -21,6 +21,10 @@ OptionParser.new do |opts|
    opts.on("-f", "--bam FOLDER", "Folder containing the BAM files") do |o|
      options[:folder] = o
    end   
+
+   opts.on("-b", "--biojs FOLDER", "Folder containing the compiled biojs module (optinal)") do |o|
+   	options[:biojs] = o
+   end
    
 end.parse!  
    

data/lib/bio-samtools-server.rb

@@ -9,4 +9,5 @@
 # In this file only require other files. Avoid other source code.
 require 'bio-samtools'
 require 'bio-samtools-server/samtools-server.rb'
+require 'bio-samtools-server/samtools-extensions.rb'
 

data/lib/bio-samtools-server/samtools-extensions.rb

@@ -0,0 +1,25 @@
+class Bio::DB::Fasta::Region
+	def to_wig(opts={})
+		step_size = opts[:step_size] ? opts[:step_size] : 1
+		
+		out = StringIO.new
+		out << "fixedStep chrom=#{self.entry} span=#{step_size}\n"
+		return out.string if self.pileup.size == 0
+		current_start = self.pileup[0].pos
+		current_acc = 0.0
+		current_end = current_start + step_size
+
+		self.pileup.each do |pile|
+
+			if pile.pos >= current_end
+				out << current_start << " " << (current_acc/step_size).to_s << "\n"
+				current_start = pile.pos
+				current_acc = 0.0
+				current_end = current_start + step_size
+			end
+			current_acc += pile.coverage
+
+		end
+		out.string
+	end
+end

data/lib/bio-samtools-server/samtools-server.rb

@@ -24,23 +24,60 @@ module Bio::WS
       return @bam_files[bam] 
     end
       
-    get '/' do
-      folder = settings.folder.to_s
+    get '/biojs/*' do
+      file=params[:splat]
+      biojs_path = "#{self.settings.biojs.to_s}"
+      File.read(File.join(biojs_path, file))
+    end
       
+    get '/alignment' do
       bam = params[:bam]
       region = params[:region]
       ref = params[:ref]
-      
-#      "Hello World from MyApp in separate file! #{ self.settings.folder.to_s} #{bam} #{region}"
-      #self.settings.folder.to_s
+      reg = Bio::DB::Fasta::Region.parse_region(region)
       stream do |out|
-        get_bam(bam, ref).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")
+        get_bam(bam, ref).fetch(reg.entry, reg.start, reg.end) do |sam|
           out << "#{sam.sam_string}\n"
         end
       end
     end
+
+    get '/wig' do
+      bam = params[:bam]
+      region = params[:region]
+      ref = params[:ref]
+      step_size = 1
+      step_size = params[:step_size].to_i if params[:step_size]
+      step_size = 1 if step_size < 1
+      reg = Bio::DB::Fasta::Region.parse_region(region)
+      stream do |out|
+         pile_region = get_bam(bam, ref).fetch_region({:region=>reg}) 
+         out << pile_region.to_wig({:step_size=>step_size})
+      end
+    end
+
+    get '/reference' do
+      bam = params[:bam]
+      region = params[:region]
+      ref = params[:ref]
+      reg = Bio::DB::Fasta::Region.parse_region(region)
+      stream do |out|
+         ref = get_bam(bam, ref).fetch_reference(reg.entry, reg.start, reg.end)
+          out << "#{ref}\n"
+       end
+      
+    end
+  
+    get '/list' do
+       bam = params[:bam]
+       ref = params[:ref]
+       stream do |out|
+         get_bam(bam, ref).each_region do |reg|
+          out <<  "#{reg.to_s}\n"
+         end
+       end
+       
+    end
+    
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools-server
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - homonecloco
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-27 00:00:00.000000000 Z
+date: 2014-05-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-samtools
@@ -142,6 +142,7 @@ files:
 - VERSION
 - bin/bam-server.rb
 - lib/bio-samtools-server.rb
+- lib/bio-samtools-server/samtools-extensions.rb
 - lib/bio-samtools-server/samtools-server.rb
 - test/helper.rb
 - test/test_bio-samtools-server.rb