bio-samtools 2.6.0 → 2.6.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 72a3a3a4e3c01d54205edb87755569d0a3299e7b
-  data.tar.gz: 92ba63563ff1d9f0e3b5009ee6f1eea0ce0b3064
+  metadata.gz: 94952e1666a5c9bb480bc7e2d0636e8a7e581927
+  data.tar.gz: e6958ffe7198152b72f47bbdda23df054e723150
 SHA512:
-  metadata.gz: cbe47a74c33a88e075528be9f295d2e389df16209ca7c5a1ffce47481db4e14dbe799672e7204f578041d35bcb3cacc48b890e86cb506b68b0a2e39d47181c62
-  data.tar.gz: 355d19cc987094262d5b925c4fce99d3334ca9de58bd6b550a2507a10903e3206f0500417413adbd0377dd69a5696a3fb4c27bb4970d8a3642a2978cab905413
+  metadata.gz: 0a3ded21f99ebfb2b1de0ad8d9d819d4c9de0e74719b446fbffdba394100c1970458fc020c564583f0a5eeb60d0b368db75c0b96c1362173121d24819fb7b0d7
+  data.tar.gz: 7cf4e0fac18c81ce20a31588f98452a34ed9d25916048c9c1fbe562129ff96c15ab880c9f4e6299f442935db72b716ff7c1fa7e109fe6ccbdc558c11bb71b719

data/VERSION

@@ -1 +1 @@
-2.6.0
+2.6.1

data/bio-samtools.gemspec

@@ -2,12 +2,12 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 2.6.0 ruby lib
+# stub: bio-samtools 2.6.1 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools".freeze
-  s.version = "2.6.0"
+  s.version = "2.6.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]

data/lib/bio/db/fastadb.rb

@@ -64,6 +64,7 @@ module Bio::DB::Fasta
       #puts "line pffset: #{line_offset}"
       #puts self.inspect
       pointer = offset + (line_length * lines_for_offset) + line_offset - 1
+      pointer
     end
 
     def get_full_region
@@ -181,7 +182,7 @@ module Bio::DB::Fasta
 
   #Class that holds the fasta file. It is used as a database. 
   class FastaFile
-    attr_reader :index, :fasta_path
+    attr_reader :fasta_path
 
     #Initialize the fasta file. If the fai file doesn't exists, it is generated at startup
     #* fasta path to the fasta file
@@ -190,6 +191,8 @@ module Bio::DB::Fasta
       #puts "The arguments are: '#{fasta}':'#{samtools}'"
       @fasta_path = fasta
       @samtools = samtools  
+      @index = nil
+      @fasta_file = nil
       @samtools = File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools') if samtools == true
       raise FastaDBException.new(), "No path for the refernce fasta file. " if @fasta_path.nil?
       @fai_file = @fasta_path + ".fai" 
@@ -249,7 +252,7 @@ module Bio::DB::Fasta
       query = region.to_s
       query = region.to_region.to_s if region.respond_to?(:to_region) 
       command = "#{@samtools} faidx #{@fasta_path} '#{query}'"
-      puts command  if $VERBOSE
+      puts "Running: #{command}"  if $VERBOSE
       @last_command = command
       seq = ""
       yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}
@@ -295,7 +298,7 @@ module Bio::DB::Fasta
     #is forwarded to the default stdout
     def yield_from_pipe(command, klass, type=:text, skip_comments=true, comment_char="#", &block)
       stdin, pipe, stderr, wait_thr = Open3.popen3(command)
-      pid = wait_thr[:pid]  # pid of the started process.       
+      #pid = wait_thr[:pid]  # pid of the started process.       
       if type == :text
         while (line = pipe.gets)
           next if skip_comments and line[0] == comment_char

data/lib/bio/db/pileup.rb

@@ -27,13 +27,19 @@
 module Bio
   class DB
     class Pileup
-      attr_accessor :ref_name, :pos, :ref_base, :coverage, :read_bases, :read_quals, :consensus, :consensus_quality, :snp_quality, :rms_mapq, :ar1, :ar2, :ar3, :indel_1, :indel_2
+      attr_accessor :ref_name, :pos, :ref_base, :coverage, :read_bases, :read_quals, :consensus_quality, :snp_quality, :rms_mapq, :ar1, :ar2, :ar3, :indel_1, :indel_2
       
       #creates the Pileup object
       #    pile_up_line = "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
       #    pile = Bio::DB::Pileup.new(pile_up_line)
       def initialize(pile_up_line)
         cols = pile_up_line.split(/\t/)
+        @consensus = nil
+        @consensus_quality = nil
+        @read_quals = nil
+        @bases = nil
+        @allele_frequency = nil
+        @consensus_iuap = nil
         if cols.length == 6 ##should only be able to get 6 lines from mpileup
           @ref_name, @pos, @ref_base, @coverage, @read_bases, @read_quals = cols
         elsif (10..13).include?(cols.length) ##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...

data/lib/bio/db/sam.rb

@@ -20,10 +20,16 @@ module Bio
       def initialize(args)
         @fasta = args[:fasta]
         @bam = args[:bam]
+        @bams = nil
+        @sam = nil
+        @files = nil 
+        @cached_regions = nil
+        @stats = nil
         @samtools = args[:samtools] || File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')
         @bcftools = args[:bcftools] || File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','bcftools')
 
         @files = [@files] if @files.instance_of?(String)
+       
 
         @last_command = nil
         raise ArgumentError, "Need Fasta and at least one BAM or SAM" if not @fasta or not @bam
@@ -67,7 +73,7 @@ module Bio
         region = String.new
         if opts[:chr] and opts[:start] and opts[:stop]
           has_e = self.has_entry? opts[:chr]
-          raise SamException.new(), "[view] The sequence #{opts[:chr]} is not in the bam file" unless self.has_entry? opts[:chr]
+          raise SamException.new(), "[view] The sequence #{opts[:chr]} is not in the bam file" unless has_e
           region = "#{opts[:chr]}:#{opts[:start]}-#{opts[:stop]}"
           [:chr, :start, :stop].each {|o| opts.delete(o)}
         end
@@ -712,13 +718,13 @@ module Bio
 
        # checks existence of files in instance
       def files_ok?
-        [@fasta, @sam, @bam].flatten.compact.each {|f| return false unless File.exists? f }
+        [@fasta, @sam, @bam].flatten.compact.each {|f| return false unless File.exist? 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"
+        File.exists? @bam and File.exist? "#{@bam}.bai"
       end
 
       private
@@ -727,7 +733,7 @@ module Bio
       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.
+        #pid = wait_thr[:pid]  # pid of the started process.
         if type == :text
           while (line = pipe.gets)
             next if skip_comments and line[0] == comment_char

data/test/test_fastadb.rb

@@ -24,7 +24,7 @@ class TestBioDbfastaDB < Test::Unit::TestCase
         	samtools: true
     	)
 	end
-     class << self    
+    class << self    
         def shutdown
             File.delete("test/samples/small/test_fastadb.fasta.fai")
         end
@@ -43,7 +43,7 @@ class TestBioDbfastaDB < Test::Unit::TestCase
 
 
 
-	def test_fetch_reference
+    def test_fetch_reference
     	#this is the first 70 nucleotides of the test seqeunce
     	@fasta_samtools.faidx()
 
@@ -73,15 +73,17 @@ GGAAACCCGAGGAATCAGAGAGGAGTGTTGACAGTGTAGCACGGGATG",
             "chr_2:765-770" => Bio::DB::Fasta::FastaDBException,
 
     	}
+
     	test_regions.each_pair do |region, expected_eception|  
             assert_raise expected_eception do
-                seq_fetched = @fasta_samtools.fetch_sequence(region)
+                #seq_fetched =
+                @fasta_samtools.fetch_sequence(region)
             end
 
             assert_raise expected_eception do
-    	       seq_fetched_local = @fasta_local.fetch_sequence(region)
+    	       #seq_fetched_local = 
+               @fasta_local.fetch_sequence(region)
     	   end
         end
     end
-
 end

data/test/test_sam.rb

@@ -178,7 +178,7 @@ class TestBioDbSam < Test::Unit::TestCase
   end
    
   def test_index_stats
-    puts "Stats: #{@sam.index_stats.inspect}"
+    #puts "Stats: #{@sam.index_stats.inspect}"
     @sam.index_stats.each_pair do |seq, stat|
       assert_send([['chr_1' , '*'], :member?, seq])
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 2.6.0
+  version: 2.6.1
 platform: ruby
 authors:
 - Ricardo Ramirez-Gonzalez