bio-mummer 0.1.0

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Files changed (18) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.travis.yml +14 -0
  4. data/Gemfile +15 -0
  5. data/LICENSE.txt +20 -0
  6. data/README.md +44 -0
  7. data/README.rdoc +48 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/lib/bio-mummer.rb +12 -0
  11. data/lib/bio-mummer/mummer.rb +126 -0
  12. data/test/data/out.delta +41 -0
  13. data/test/data/query.fasta +401 -0
  14. data/test/data/reference.fasta +401 -0
  15. data/test/data/reference.gff +91 -0
  16. data/test/helper.rb +38 -0
  17. data/test/test_bio-mummer.rb +57 -0
  18. metadata +147 -0
data/test/helper.rb ADDED
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+ require 'simplecov'
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+ require 'bio'
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+
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+ module SimpleCov::Configuration
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+ def clean_filters
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+ @filters = []
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+ end
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+ end
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+
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+ SimpleCov.configure do
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+ clean_filters
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+ load_profile 'test_frameworks'
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+ end
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+
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+ ENV["COVERAGE"] && SimpleCov.start do
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+ add_filter "/.rvm/"
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+ end
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'minitest/autorun'
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+ require 'shoulda'
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+
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ require 'bio-mummer'
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+
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+ class MiniTest::Test
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+ end
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+
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+ MiniTest.autorun
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+
data/test/test_bio-mummer.rb ADDED
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+ require 'helper'
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+
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+ class TestBioMummer < MiniTest::Test
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+
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+ def setup
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+ @report = BioMummer::DeltaFile.open("test/data/out.delta")
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+ end
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+
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+ should "open and close a delta file" do
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+ assert_kind_of BioMummer::DeltaFile, @report
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+ end
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+
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+ should "have enumerable alignments" do
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+ assert_equal "reference", @report.alignments.first.refname
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+ assert_kind_of Fixnum, @report.alignments.first.refstart
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+ assert_equal 1, @report.alignments.first.refstart
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+ assert_equal 2435, @report.alignments.first.refstop
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+ assert_equal 1, @report.alignments.first.querystart
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+ assert_equal 2435, @report.alignments.first.querystop
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+ end
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+
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+ should "do basic coordinate transforms on the positive strand" do
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+ a = BioMummer::Alignment.new('ref', 'query', 101, 150, 201, 248, true, [5,-2,3,1,1,-4])
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+ assert_equal 201, a.ref_to_query(101)
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+ assert_equal 202, a.ref_to_query(102)
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+ assert_equal 203, a.ref_to_query(103)
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+ assert_equal 204, a.ref_to_query(104)
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+ assert_equal nil, a.ref_to_query(105)
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+ assert_equal 205, a.ref_to_query(106)
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+ assert_equal 207, a.ref_to_query(107)
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+ assert_equal 208, a.ref_to_query(108)
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+ assert_equal nil, a.ref_to_query(109)
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+ assert_equal nil, a.ref_to_query(110)
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+ assert_equal nil, a.ref_to_query(111)
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+ assert_equal 209, a.ref_to_query(112)
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+ assert_equal 217, a.ref_to_query(119)
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+ assert_equal 248, a.ref_to_query(150)
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+ end
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+
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+ should "do basic coordinate transforms on the negative strand" do
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+ a = BioMummer::Alignment.new('ref', 'query', 101, 118, 201, 216, false, [5,-2,3,1,1,-4])
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+ assert_equal 216, a.ref_to_query(101)
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+ assert_equal 201, a.ref_to_query(118)
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+ end
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+
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+ should "transpose a given region if it maps cleanly onto a nucmer alignment" do
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+ query_seqs = Hash[Bio::FlatFile.open("test/data/query.fasta").map{ |e| [e.entry_id, e.naseq] }]
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+ ref_cds_start = 26255
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+ ref_cds_stop = 26285
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+ ref_cds_source = 'reference'
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+
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+ query_name, query_start, query_stop, query_strand = @report.transpose_region(ref_cds_source, ref_cds_start, ref_cds_stop)
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+ query = query_seqs[query_name].subseq(query_start, query_stop)
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+ assert_equal Bio::Sequence::AA.new("MAEPSGYSVQ"), query.complement.translate
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+ end
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+ end
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+
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-mummer
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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+ platform: ruby
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+ authors:
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+ - robsyme
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2015-02-10 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: shoulda
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
17
+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - '>='
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+ - !ruby/object:Gem::Version
26
+ version: '0'
27
+ - !ruby/object:Gem::Dependency
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+ name: simplecov
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+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - '>='
32
+ - !ruby/object:Gem::Version
33
+ version: '0'
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
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+ - - '>='
39
+ - !ruby/object:Gem::Version
40
+ version: '0'
41
+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
45
+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 2.0.0
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+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ~>
53
+ - !ruby/object:Gem::Version
54
+ version: 2.0.0
55
+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - '>='
60
+ - !ruby/object:Gem::Version
61
+ version: 1.0.21
62
+ type: :development
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - '>='
67
+ - !ruby/object:Gem::Version
68
+ version: 1.0.21
69
+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - '>='
74
+ - !ruby/object:Gem::Version
75
+ version: 1.4.2
76
+ type: :development
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - '>='
81
+ - !ruby/object:Gem::Version
82
+ version: 1.4.2
83
+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - ~>
88
+ - !ruby/object:Gem::Version
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+ version: '3.12'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
94
+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ description: Help for working with the output of the .delta files produced by nucmer
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+ and promer
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+ email: rob.syme@gmail.com
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files:
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+ - LICENSE.txt
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+ - README.md
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+ - README.rdoc
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+ files:
107
+ - .document
108
+ - .travis.yml
109
+ - Gemfile
110
+ - LICENSE.txt
111
+ - README.md
112
+ - README.rdoc
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+ - Rakefile
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+ - VERSION
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+ - lib/bio-mummer.rb
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+ - lib/bio-mummer/mummer.rb
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+ - test/data/out.delta
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+ - test/data/query.fasta
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+ - test/data/reference.fasta
120
+ - test/data/reference.gff
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+ - test/helper.rb
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+ - test/test_bio-mummer.rb
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+ homepage: http://github.com/robsyme/bioruby-mummer
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
129
+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
132
+ requirements:
133
+ - - '>='
134
+ - !ruby/object:Gem::Version
135
+ version: '0'
136
+ required_rubygems_version: !ruby/object:Gem::Requirement
137
+ requirements:
138
+ - - '>='
139
+ - !ruby/object:Gem::Version
140
+ version: '0'
141
+ requirements: []
142
+ rubyforge_project:
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+ rubygems_version: 2.0.14
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+ signing_key:
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+ specification_version: 4
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+ summary: Helper methods for reading .delta files
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+ test_files: []