bio-cigar 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 95056409b5f06d3c60a738740f27c4835a414335
+  data.tar.gz: 7882ac6d35a76b43ac78af2218faf7a46a7542eb
+SHA512:
+  metadata.gz: 5fca372c6030c01121adddbb273bc9fdca7eb25579ea15c5957842a592c7ce337c1b2eab749f511aa73c100d815c3dd02101285daf346629c36625e893c1cac0
+  data.tar.gz: d5e72661f94fb60bb8c1afec10d8cce76cac22e0e6edf3483a1003cacfb6cef70f006c0fd5dd185f110b67384603e9154881c845a836a4b0c299a6fb70492ee7

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio-samtools', '>=0.6.2'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", ">= 2.8.0"
+  gem "rdoc", ">= 3.12"
+  gem "jeweler"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Ben J Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-cigar
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-cigar.png)](http://travis-ci.org/wwood/bioruby-cigar)
+
+Parser for the cigar sequence alignment format.
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-cigar
+```
+
+## Usage
+
+```ruby
+require 'bio-cigar'
+
+# An example from http://davetang.org/wiki/tiki-index.php?page=SAM
+# CIGAR: 3S8M1D6M4S
+cigar_string = '3S8M1D6M4S'
+cigar = Bio::Cigar.new(cigar_string) #=> Bio::Cigar object
+
+# REF:     TCGCCCGTCTAGCATACGC
+# READ: gggGTGTAACC-GACTAGgggg
+# MATCH:---001000000010010----
+ref =   'TCGCCCGTCTAGCATACGCCCGTCTAGCATACGC'
+query = 'gggGTGTAACCGACTAGgggg'
+answer = cigar.percent_identity(ref, query)
+answer.should == [
+  20.0, #20% Identity
+  3, #3 matches
+  12 #12 mismatches
+]
+```
+It can also be used directly on SAM format alignments (```Bio::DB::Alignment``` objects),
+which are produced by ```bio-samtools```:
+```ruby
+sam = Bio::DB::Alignment.new
+sam.cigar = '196M54S'
+sam.pos = 1150
+sam.seq = 'ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT'
+ref = 'GAGCGAACGTTAGCGGCGGGCTTAACACATGCAAGTCGAACGAGAATGAAGGAGCAATCCTTCTAGTAAAGTGGCGGACGGGTGCGTAACACGTGGATAATCTACCTTCCGGCGGGGGACAACAGTTCGAAAGGACTGCTAATACCGCGTACGTCGGCGAGAGCTCAGGCTCTTGTCGGGAAAGATGGCCAATCCTTGGAAGCTGTCACCGGAAGATGAATCCGCGGCCCATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTAAGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGCGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCCACGCCGCGTGAGTGATGAAGGCCTTCGGGTCGTAAAGCTCTGTGGGGAGGGACGAACAAGTGCGTATCGAATAAATACGTGCCCTGACGGTACCTCCTTAGCAAGCACCGGCTAACCATGTGCCAGCAGCCGCGGTAATACATGGGGTGCAAACGTTGCTCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTCGCTTAAGTCGGATGTGAAATCCCTCGGCTTAACTGAGGAAGTGCATCCGAGACTGAATGGCTAGAGTACGAAAGAGGGTCGNNNNNTTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAACACCGGCGGCGAAGGCGGCGACCTGGTTCGAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATGCTAGATGTTTCTGGTATTGACCCCGGAGGCGTCGTAGCTAACGCGATAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTCAATTTGACGCAACGCGAAGAACCTTACCTGGGTTGGAACCCTCCAGAAGTCCGCAGAGATGTGGATGTGCTCGCAAGAGAACTGGATGTCCAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTGCTAACAGTTCGGCTGAGCACTCTAACGAGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGTCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCTAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCGCTAGTAATCCCTGATCAGCAGGCAGGGGTGAATACGTTCCCGGGCC'
+sam.percent_identity(ref).should == [
+  98.46938775510205,
+  193,
+  3
+]
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-cigar
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+This software is currently unpublished.
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-cigar)
+
+## Copyright
+
+Copyright (c) 2013 Ben J Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-cigar"
+  gem.homepage = "http://github.com/wwood/bioruby-cigar"
+  gem.license = "MIT"
+  gem.summary = %Q{A parser for CIGAR format alignments}
+  gem.description = %Q{A parser for CIGAR format alignments.}
+  gem.email = "donttrustben@gmail.com"
+  gem.authors = ["Ben J Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-cigar #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-cigar.rb

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+
+require 'bio-cigar/cigar'
+require 'bio-cigar/sam'
+

data/lib/bio-cigar/cigar.rb

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+module Bio
+  class Cigar
+    attr_accessor :cigar_string
+
+    def initialize(cigar_string)
+      @cigar_string = cigar_string
+    end
+
+    def percent_identity(reference_sequence_string, query_sequence_string)
+      num_match = 0
+      num_mismatch = 0
+
+      ref_index = 0
+      query_index = 0
+      each_alignment_chunk do |type, count|
+        case type
+        when 'M'
+          (0...count).each do |i|
+            if reference_sequence_string[ref_index+i] == query_sequence_string[query_index+i]
+              num_match += 1
+            else
+              num_mismatch += 1
+            end
+          end
+          ref_index += count
+          query_index += count
+        when 'I'
+          # Extra characters in the query sequence
+          num_mismatch += count
+          query_index += count
+        when 'D'
+          num_mismatch += count
+          ref_index += count
+        when 'S'
+          #ref_index += count
+          query_index += count
+        when 'H'
+          query_index += count
+        else
+          raise "Cigar string not parsed correctly. Unrecognised alignment type #{type}"
+        end
+      end
+
+      percent = num_match.to_f/(num_match+num_mismatch)*100
+      return percent, num_match, num_mismatch
+    end
+
+    # Yield the type and count for each different part of the
+    # cigar string e.g.
+    #
+    #    cigar = Bio::Cigar.new('1S3M')
+    #    cigar.each_alignment_chunk do |type, count|
+    #        type #=> first 'S', second 'M' (as strings)
+    #        type #=> first 1, second 3 (as integers)
+    #    end
+    def each_alignment_chunk
+      leftover = @cigar_string
+      while matches = leftover.match(/^(\d+)([MSIHD])(.*)/)
+        yield matches[2], matches[1].to_i
+        leftover = matches[3]
+      end
+      unless leftover.length == 0
+        raise "Incorrect parsing of cigar string #{@cigar_string}, at the end left with #{leftover}"
+      end
+    end
+  end
+end

data/lib/bio-cigar/sam.rb

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+require 'bio-samtools'
+
+class Bio::DB::Alignment
+  # Work out the percent identity given of the query sequence
+  # against the reference sequence, using the CIGAR string as
+  # the alignment
+  def percent_identity(reference_sequence)
+    return Bio::Cigar.new(self.cigar).percent_identity(
+      reference_sequence[self.pos-1...reference_sequence.length],
+      self.seq
+    )
+  end
+end

data/spec/bio-cigar_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioCigar" do
+  it "should do as in the README" do
+    cigar_string = '3S8M1D6M4S'
+    cigar = Bio::Cigar.new(cigar_string) #=> Bio::Cigar object
+    cigar.should be_kind_of(Bio::Cigar)
+
+    # REF:  GTGTCGCCCGTCTAGCATACGC
+    # READ: gggGTGTAACC-GACTAGgggg
+    # MATCH:---001000000010010----
+    ref =     'TCGCCCGTCTAGCATACGC'
+    query = 'gggGTGTAACCGACTAGgggg'
+    cigar.percent_identity(ref, query).should == [20.0, 3, 12] #=> 20.0 (3/15 is 20% identity)
+  end
+
+  it 'should alignment chunk right' do
+    cigar_string = '3S8M1D6M4S'
+    types = []
+    counts = []
+    cigar = Bio::Cigar.new(cigar_string)
+    cigar.each_alignment_chunk do |type, count|
+      types.push type
+      counts.push count
+    end
+    types.should == %w(S M D M S)
+    counts.should == [3,8,1,6,4]
+    cigar_string.should == '3S8M1D6M4S' #shouldn't modify the passed string
+  end
+
+  it 'should work on real data' do
+    # SAM:
+    # 790     16      2303416 1150    1       196M54S *       0       0       ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT      *       AS:i:184
+    ref = 'GAGCGAACGTTAGCGGCGGGCTTAACACATGCAAGTCGAACGAGAATGAAGGAGCAATCCTTCTAGTAAAGTGGCGGACGGGTGCGTAACACGTGGATAATCTACCTTCCGGCGGGGGACAACAGTTCGAAAGGACTGCTAATACCGCGTACGTCGGCGAGAGCTCAGGCTCTTGTCGGGAAAGATGGCCAATCCTTGGAAGCTGTCACCGGAAGATGAATCCGCGGCCCATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTAAGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGCGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCCACGCCGCGTGAGTGATGAAGGCCTTCGGGTCGTAAAGCTCTGTGGGGAGGGACGAACAAGTGCGTATCGAATAAATACGTGCCCTGACGGTACCTCCTTAGCAAGCACCGGCTAACCATGTGCCAGCAGCCGCGGTAATACATGGGGTGCAAACGTTGCTCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTCGCTTAAGTCGGATGTGAAATCCCTCGGCTTAACTGAGGAAGTGCATCCGAGACTGAATGGCTAGAGTACGAAAGAGGGTCGNNNNNTTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAACACCGGCGGCGAAGGCGGCGACCTGGTTCGAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATGCTAGATGTTTCTGGTATTGACCCCGGAGGCGTCGTAGCTAACGCGATAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTCAATTTGACGCAACGCGAAGAACCTTACCTGGGTTGGAACCCTCCAGAAGTCCGCAGAGATGTGGATGTGCTCGCAAGAGAACTGGATGTCCAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTGCTAACAGTTCGGCTGAGCACTCTAACGAGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGTCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCTAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCGCTAGTAATCCCTGATCAGCAGGCAGGGGTGAATACGTTCCCGGGCC'
+    query = 'ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT'
+    pos = 1150
+
+    ref_seq = ref[pos-1...ref.length]
+    Bio::Cigar.new('196M54S').percent_identity(ref_seq, query).should == [
+      98.46938775510205,
+      193,
+      3
+    ]
+  end
+
+  it 'should monkey patch SAM alignments' do
+    sam = Bio::DB::Alignment.new
+    sam.cigar = '196M54S'
+    sam.pos = 1150
+    sam.seq = 'ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT'
+    ref = 'GAGCGAACGTTAGCGGCGGGCTTAACACATGCAAGTCGAACGAGAATGAAGGAGCAATCCTTCTAGTAAAGTGGCGGACGGGTGCGTAACACGTGGATAATCTACCTTCCGGCGGGGGACAACAGTTCGAAAGGACTGCTAATACCGCGTACGTCGGCGAGAGCTCAGGCTCTTGTCGGGAAAGATGGCCAATCCTTGGAAGCTGTCACCGGAAGATGAATCCGCGGCCCATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTAAGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGCGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCCACGCCGCGTGAGTGATGAAGGCCTTCGGGTCGTAAAGCTCTGTGGGGAGGGACGAACAAGTGCGTATCGAATAAATACGTGCCCTGACGGTACCTCCTTAGCAAGCACCGGCTAACCATGTGCCAGCAGCCGCGGTAATACATGGGGTGCAAACGTTGCTCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTCGCTTAAGTCGGATGTGAAATCCCTCGGCTTAACTGAGGAAGTGCATCCGAGACTGAATGGCTAGAGTACGAAAGAGGGTCGNNNNNTTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAACACCGGCGGCGAAGGCGGCGACCTGGTTCGAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATGCTAGATGTTTCTGGTATTGACCCCGGAGGCGTCGTAGCTAACGCGATAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTCAATTTGACGCAACGCGAAGAACCTTACCTGGGTTGGAACCCTCCAGAAGTCCGCAGAGATGTGGATGTGCTCGCAAGAGAACTGGATGTCCAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTGCTAACAGTTCGGCTGAGCACTCTAACGAGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGTCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCTAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCGCTAGTAATCCCTGATCAGCAGGCAGGGGTGAATACGTTCCCGGGCC'
+    sam.percent_identity(ref).should == [
+      98.46938775510205,
+      193,
+      3
+    ]
+  end
+
+  it 'should work on real data 2' do
+    #SRR400867.981	0	3225199 9	4	10S240M *	0	0	TCAGAGCTACAAGAGTTTGATCGTGGCTCAGAAGGAACGCTAGCTATATGCTTAACACATGCAAGTCGAACGTTGTTTTCGGGGAGCTGGGCAGAAGGAAAAGAGGCTCCTAGCGTGAAGGTAGCTTGTCTCGCCCAGGAGGTGGGAACAGTTGAAAACAAAGTGGCGAACGGGTGCGTAATGCGTGGGAATCTGCCGAACAGTTCGGGCCAAATCCTGAAGAAAGCTAAAAAGCGCTGTTTGATGAGCC	*	AS:i:236	XS:i:232	XF:i:3	XE:i:2	NM:i:1
+    ref = 'CTCAAAAGAAGAGTTTGATCCTGGCTCAGAAGGAACGCTAGCTATATGCTTAACACATGCAAGTCGAACGTTGTTTTCGGGGAGCTGGGCAGAAGGAAAAGAGGCTCCTAGCGTGAAGGTAGCTTGTCTCGCCCAGGAGGTGGGAACAGTTGAAAACAAAGTGGCGAACGGGTGCGTAATGCGTGGGAATCTGCCGAACAGTTCGGGCCAAATCCTGAAGAAAGCTAAAAAGCGCTGTTTGATGAGCCTGCGTAGTATTAGGTAGTTGGTCAGGTAAAGGCTGACCAAGCCAATGATGCTTAGCTGGTCTTTTCGGATGATCAGCCACACTGGGACTGAGACACGGCCCGGACTCCCACGGGGGGCAGCAGTGGGGAATCTTGGACAATGGGCGAAAGCCCGATCCAGCAATATCGCGTGAGTGAAGAAGGGCAATGCCGCTTGTAAAGCTCTTTCGTCGAGTGCGCGATCACGACAGGACTCGAGGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGGGGGGGCAAGTGTTCTTCGGAATGACTGGGCGTAAAGGGCACGTAGGCGGTGAATCGGGTTGAAAGTGAAAGTCGCCAAAAACTGGTGGAATGCTCTCGAAACCAATTCACTTGAGTGAGACAGAGGAGAGTGGAATTTCGTGTGTAGGGGTGAAATCCGCAGATCTACGAAGGAAGGCCAAAAGCGAAGGCAGCTCTCTGGGTCCCTACCGACGCTGGAGTGCGAAAGCATGGGGAGCGAACGGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGAGTGTTCGCCCTTGGTCTACGTGGATCAGGGGCCCAGCTAACGCGTGAAACACTCCGCCTGGGGAGTACGGTCGCAAGACCGAAACTCAAAGGAATTGACGGGGGCCTGCACAAGCGGTGGAGCATGTGGTTTAATTCGATACAACGCGCAAAACCTTACCAGCCCTTGAAATATGAAAAAGAAAACCAGTCCTTAACGGGATGGTACTTACTTTCATACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTTGGTCAAGTCCTATAACGAGCGAAACCCTCGTTTTGTGTTGCTGAGACATGCGCCTAAGGATAAAGTCTTTGCAACCGAAGTGAGCCGAGGAGCCGAGTGACGCGCCAGCGCTACTAATTTATTTAGTGCCAGCACGTAGCTGTGCTGTCAGTAAGAAGGGAGCCGGCGCCTTTCGAATTCGAAGCACTTTCTAGTGTGCGCTCTTTTTTGATTGCAGCTAGCGAGCAAGAAAACGGATGCGCGTTAGCCTTTATTAGTAATAGTAATGGAGGCTTTCTTTTTTTCAGCTCAATCCCTTGCTTCTTGCTTTACTAAATAGAAAGGGCTTTTCTCGCTTTTTTAGTAAAGTCCAGTTTTTGGCCTTATCTTGCAGGTGACGACGACGTCGAGTTGGCGGCGGAGAAAGACTCGGCATTCAGGCGAGCCGCCCGGTGGTGTGGTACGTAGTGGGTTTAGTACGCCCCGCCAAAACGGCTCCGAAAGAAACTAAAAGGTGCATGCCGCACTCACGAGGGACTGCCAGTGATATACTGGAGGAAGGTGGGGATGACGTCAAGTCCGCATGCCCTTATGGGCTGGGCCACACACGTGCTACAATGGCAATTACAATGGGAAGCAAGGCTGTAAGGCGGAGCGAATCCGGAAAGATTGCCTCAGTTCGGATTGTTCTCTGCAACTCGGGAACATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATATGTACCCGGGCCCTGTACACACCGCCCGTCACACCCTGGGAATTGGTTTCGCCCGAAGCATCGGACCAATGATCACCCATGACTTCTGTGTACCACTAGTGCCACAAAGGCTTTTGGTGGTCTTCTTGGCGCATACCACGGTGGGGTCTTCGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGTGGCTGGAT'
+    sam = Bio::DB::Alignment.new
+    sam.cigar = '10S240M'
+    sam.pos = 9
+    sam.seq = 'TCAGAGCTACAAGAGTTTGATCGTGGCTCAGAAGGAACGCTAGCTATATGCTTAACACATGCAAGTCGAACGTTGTTTTCGGGGAGCTGGGCAGAAGGAAAAGAGGCTCCTAGCGTGAAGGTAGCTTGTCTCGCCCAGGAGGTGGGAACAGTTGAAAACAAAGTGGCGAACGGGTGCGTAATGCGTGGGAATCTGCCGAACAGTTCGGGCCAAATCCTGAAGAAAGCTAAAAAGCGCTGTTTGATGAGCC'
+    sam.percent_identity(ref)[0].should == 99.58333333333333
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,12 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-cigar'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,142 @@
+--- !ruby/object:Gem::Specification
+name: bio-cigar
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-02-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.6.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.6.2
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+description: A parser for CIGAR format alignments.
+email: donttrustben@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-cigar.rb
+- lib/bio-cigar/cigar.rb
+- lib/bio-cigar/sam.rb
+- spec/bio-cigar_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-cigar
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: A parser for CIGAR format alignments
+test_files: []