bio-pileup_iterator 0.0.3 → 0.0.4

data/.travis.yml

@@ -3,7 +3,7 @@ rvm:
   - 1.9.2
   - 1.9.3
   - jruby-19mode # JRuby in 1.9 mode
-  - rbx-19mode
+##  - rbx-19mode #This fails because of ffi problems (at least)
 #  - 1.8.7
 #  - jruby-18mode # JRuby in 1.8 mode
 #  - rbx-18mode

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.4

data/lib/bio/db/pileup_iterator.rb

@@ -1,12 +1,8 @@
-
+require 'pp'
 
 class Bio::DB::Pileup
   # Bio::DB::PileupIterator::PileupRead objects that occur at this position
   attr_accessor :reads
-  
-  def num_deletions
-    return read_bases.gsub(/[^\*]/,'').length
-  end
 end
 
 class Bio::DB::PileupIterator
@@ -21,6 +17,7 @@ class Bio::DB::PileupIterator
   # Known problems:
   # * Doesn't record start or ends of each read
   # * Doesn't lookahead to determine the sequence of each read (though it does give the preceding bases)
+  # * Doesn't record the mapping quality of each read
   def each
     current_ordered_reads = []
     log = Bio::Log::LoggerPlus['bio-pileup_iterator']
@@ -35,6 +32,7 @@ class Bio::DB::PileupIterator
       log.debug "new column's read_bases: #{bases.inspect}" if log.debug?
       log.debug "pileup entry parsed: #{pileup.inspect}" if log.debug?
       while bases.length > 0
+        log.debug "==== new read within a single pileup being parsed. Starting with #{bases}" if log.debug?
         
         # Firstly, what is the current read we are working with
         current_read = current_ordered_reads[current_read_index]
@@ -47,9 +45,11 @@ class Bio::DB::PileupIterator
         matches = nil
         
         # if starting, remove it
+        log.debug "before read start removal, pileup is #{bases}, read is #{current_read}" if log.debug?
         matched_string = ''
-        if bases[0..1]=='^]'
-          matched_string += bases[0]
+        if bases[0]=='^'
+          # Match the ^ and the mapping quality
+          matched_string += bases[0..1]
           bases = bases[2...bases.length]
         end
         log.debug "after read start removal, pileup is #{bases}" if log.debug?
@@ -58,15 +58,28 @@ class Bio::DB::PileupIterator
         if matches = bases.match(/^([ACGTNacgtn\.\,\*])/)
           matched_string += bases[0]
           if matches[1] == '.'
-            raise if !current_read.direction.nil? and current_read.direction != PileupRead::FORWARD_DIRECTION
+            if !current_read.direction.nil? and current_read.direction != PileupRead::FORWARD_DIRECTION
+              pp current_read
+              raise "Unexpectedly found direction #{current_read.direction}, expected #{PileupRead::FORWARD_DIRECTION}, in starting at '#{bases}'(EndOfLine) in '#{line}', in the read above"
+            end
             current_read.direction = PileupRead::FORWARD_DIRECTION
             current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
           elsif matches[1] == ','
-            raise if !current_read.direction.nil? and current_read.direction != PileupRead::REVERSE_DIRECTION
+            if !current_read.direction.nil? and current_read.direction != PileupRead::REVERSE_DIRECTION
+              pp current_read
+              raise "Unexpectedly found direction #{current_read.direction}, expected #{PileupRead::REVERSE_DIRECTION}, in starting at '#{bases}'(EndOfLine) in '#{line}', in the read above"
+            end
             current_read.direction = PileupRead::REVERSE_DIRECTION
             current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
           else
-            # Could sanity check the direction here by detecting case, but eh
+            if current_read.direction.nil? and matches[1] != '*'
+              # Could sanity check the direction here by detecting case, but eh
+              if matches[1].upcase == matches[1] or matches[1]== '.'
+                current_read.direction = PileupRead::FORWARD_DIRECTION
+              else
+                current_read.direction = PileupRead::REVERSE_DIRECTION
+              end
+            end
             current_read.sequence = "#{current_read.sequence}#{matches[1]}"
           end
           # remove the matched base

data/test/test_bio-pileup_iterator.rb

@@ -223,4 +223,49 @@ class TestBioPileupIterator < Test::Unit::TestCase
     assert_equal 10, piles[0].coverage
     assert_equal 10, piles[0].reads.length
   end
+  
+  def test_optional_mapping_quality
+    line = "gi|308171891|ref|NC_014551.1|\t2\tA\t2\t^:,^~,\t!!\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a #parse, it should fail otherwise
+    assert_equal 2, piles[0].coverage
+    assert_equal 2, piles[0].reads.length
+    assert_equal 'A', piles[0].reads[0].sequence
+    assert_equal '-', piles[0].reads[0].direction
+    
+    line_without_mapping_quality = "gi|308171891|ref|NC_014551.1|\t2\tA\t2\t^,^,\t!!\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a #parse, it should fail otherwise
+    assert_equal 2, piles[0].coverage
+    assert_equal 2, piles[0].reads.length
+    assert_equal 'A', piles[0].reads[0].sequence
+    assert_equal '-', piles[0].reads[0].direction
+  end
+  
+  def test_when_read_mapping_quality_is_dot
+    lines = "gi|308171891|ref|NC_014551.1|\t2\tA\t2\t^:,^~,\t!!\n"+
+      "gi|308171891|ref|NC_014551.1|\t3\tT\t4\t,,^!.^.,\t!!!!\n"+ # This is the line that is really being tested
+      "gi|308171891|ref|NC_014551.1|\t4\tT\t4\t,,.,\t!!!!\n"
+    piles = Bio::DB::PileupIterator.new(lines).to_a #parse, it should fail otherwise
+    assert_equal 2, piles[0].coverage
+    assert_equal 4, piles[2].coverage
+    assert_equal 2, piles[0].reads.length
+    assert_equal 'ATT', piles[0].reads[0].sequence
+    assert_equal '-', piles[0].reads[0].direction
+  end
+  
+  def test_n
+    lines = "gi|308171891|ref|NC_014551.1|\t111565\tN\t7\taaAaAAA\t~~~~~~~\n"
+    piles = Bio::DB::PileupIterator.new(lines).to_a #parse, it should fail otherwise
+    assert_equal 1, piles.length
+    assert_equal 7, piles[0].coverage
+    assert_equal 'a', piles[0].reads[1].sequence
+    assert_equal 'N', piles[0].ref_base
+  end
+
+  def test_direction_without_starting_a_read
+    lines = "contig00074\t4243\tN\t8\tg$GGGgGgg\t~~~~~~~~\n"
+    
+    piles = Bio::DB::PileupIterator.new(lines).to_a
+    assert_equal '-', piles[0].reads[0].direction
+    assert_equal '+', piles[0].reads[1].direction
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-pileup_iterator
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-15 00:00:00.000000000 Z
+date: 2012-11-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &79398350 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *79398350
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &79397770 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +37,15 @@ dependencies:
         version: 0.5.3
   type: :runtime
   prerelease: false
-  version_requirements: *79397770
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.3
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &79397240 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +53,15 @@ dependencies:
         version: 1.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *79397240
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &79396870 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +69,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79396870
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &79396550 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +85,15 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *79396550
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &79396200 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +101,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *79396200
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &79395820 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +117,15 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *79395820
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &79481120 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +133,15 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *79481120
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &79480630 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -109,7 +149,12 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *79480630
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 description: Iterate through a samtools pileup file
 email: donttrustben near gmail.com
 executables: []
@@ -144,7 +189,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 421311475
+      hash: -965124785
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -153,7 +198,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.17
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Iterate through a samtools pileup file