Microhomology 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +17 -0
- data/.rspec +2 -0
- data/.travis.yml +5 -0
- data/Gemfile +4 -0
- data/Guardfile +70 -0
- data/LICENSE.txt +22 -0
- data/README.md +156 -0
- data/Rakefile +7 -0
- data/examples/crispr_example.rb +26 -0
- data/examples/talen_example.rb +24 -0
- data/lib/microhomology.rb +135 -0
- data/lib/microhomology/strategies.rb +4 -0
- data/lib/microhomology/version.rb +3 -0
- data/microhomology.gemspec +30 -0
- data/microhomology.png +0 -0
- data/spec/microhomology_helper.rb +10 -0
- data/spec/spec_helper.rb +99 -0
- metadata +189 -0
checksums.yaml
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SHA1:
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metadata.gz: 82171a97b2db1812ff28de4c26ea59553418e012
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data.tar.gz: 631e0439c1cf32ff546a14cd5aa8f5d1d7d6f4e7
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SHA512:
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metadata.gz: 0980e8500d877fd6200611b3da128feaa5aa3cf9a90971206c5c4823e90b77db6d08c9fc71dba546781325689b84037578fb624b63b2eb982b80c08ffb39989e
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data.tar.gz: a7bb1ed83705c59873633c87dc01977c5d711d5b2e31c2aa9fdd929a300975d9793be5c48d8dfa2f029c3b49a23c42db28b830537b0d674c8f3be9a316b315af
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data/.gitignore
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data/.rspec
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data/.travis.yml
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data/Gemfile
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data/Guardfile
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# A sample Guardfile
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# More info at https://github.com/guard/guard#readme
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## Uncomment and set this to only include directories you want to watch
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# directories %w(app lib config test spec features) \
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# .select{|d| Dir.exists?(d) ? d : UI.warning("Directory #{d} does not exist")}
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## Note: if you are using the `directories` clause above and you are not
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## watching the project directory ('.'), then you will want to move
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## the Guardfile to a watched dir and symlink it back, e.g.
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#
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# $ mkdir config
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# $ mv Guardfile config/
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# $ ln -s config/Guardfile .
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#
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# and, you'll have to watch "config/Guardfile" instead of "Guardfile"
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# Note: The cmd option is now required due to the increasing number of ways
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# rspec may be run, below are examples of the most common uses.
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# * bundler: 'bundle exec rspec'
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# * bundler binstubs: 'bin/rspec'
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# * spring: 'bin/rspec' (This will use spring if running and you have
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# installed the spring binstubs per the docs)
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# * zeus: 'zeus rspec' (requires the server to be started separately)
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# * 'just' rspec: 'rspec'
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guard :rspec, cmd: "bundle exec rspec" do
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require "guard/rspec/dsl"
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dsl = Guard::RSpec::Dsl.new(self)
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# Feel free to open issues for suggestions and improvements
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# RSpec files
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rspec = dsl.rspec
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watch(rspec.spec_helper) { rspec.spec_dir }
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watch(rspec.spec_support) { rspec.spec_dir }
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watch(rspec.spec_files)
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# Ruby files
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ruby = dsl.ruby
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dsl.watch_spec_files_for(ruby.lib_files)
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# Rails files
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rails = dsl.rails(view_extensions: %w(erb haml slim))
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dsl.watch_spec_files_for(rails.app_files)
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dsl.watch_spec_files_for(rails.views)
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watch(rails.controllers) do |m|
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[
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rspec.spec.("routing/#{m[1]}_routing"),
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rspec.spec.("controllers/#{m[1]}_controller"),
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rspec.spec.("acceptance/#{m[1]}")
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]
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end
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# Rails config changes
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watch(rails.spec_helper) { rspec.spec_dir }
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watch(rails.routes) { "#{rspec.spec_dir}/routing" }
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watch(rails.app_controller) { "#{rspec.spec_dir}/controllers" }
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# Capybara features specs
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watch(rails.view_dirs) { |m| rspec.spec.("features/#{m[1]}") }
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watch(rails.layouts) { |m| rspec.spec.("features/#{m[1]}") }
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# Turnip features and steps
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watch(%r{^spec/acceptance/(.+)\.feature$})
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watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$}) do |m|
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Dir[File.join("**/#{m[1]}.feature")][0] || "spec/acceptance"
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end
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end
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data/LICENSE.txt
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Copyright (c) 2015 Chris Mikelson
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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By [Chris Mikelson](http://chrismikelson.com)
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[](https://travis-ci.org/cmike444/microhomology)
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Quickly perform microhomology to speed up genetic engineering.
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With only a few lines of code, researchers can...
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* Identify microhomology canidate sites in a gene
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* Perform microhomology on sites using multiple strategies
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* Get forward and reverse sequences for each strategy's results
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* Get forward and reverse oligo sequences for each strategy's results
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This gem uses [BioRuby](https://rubygems.org/gems/bio) to easily obtain compliment pairs and traverse forward or reverse strands.
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem 'microhomology'
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```
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Or install it yourself via Command Line Interface:
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```ruby
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$ gem install microhomology
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```
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## Usage
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>**Note:** This currently relies on the Ensembl REST API for it's data. DNA can only be obtained by using a valid Ensembl Gene ID. Additional options for obtaining DNA via other sources such as text files, formated files or 3rd Party API's is intended to be added at a later date.
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## The DNA
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The DNA from Ensembl is masked to differentiate between Introns and Exons.
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>**Note:** The default is to scan only exons when using a microhomology strategy. Adding options to choose between exons, introns or include both is intended to be added at a later date.
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```ruby
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mh = Microhomology::Crispr.new('ENSDARG00000061303', [3, 6, 9])
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```
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```ruby
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mh.dna
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# TTTGCTGTGGTTTCACTCCTTCagaaggtcttatttgttttcttccag
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```
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```ruby
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mh.introns
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# agaaggtcttatttgttttcttccag
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```
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```ruby
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mh.exons
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# TTTGCTGTGGTTTCACTCCTTC
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```
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#### CRIPSR
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Perform microhomology on a DNA sequence using the [CRISPR](https://www.youtube.com/watch?v=2pp17E4E-O8) technique. This class takes two inputs, an Ensembl Gene ID _(string)_ and the microhomology strategies _(array)_. Using the DNA returned from Ensembl and the [CRISPR algorithm](lib/microhomology/strategies.rb), the DNA is scanned to identify target sites on both forward and reverse strands. Once target sites are identified, microhomology is performed according to each strategy in the array.
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```ruby
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mh = Microhomology::Crispr.new('ENSDARG00000061303', [6, 12, 24, 48, 96])
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mh.results
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```
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```javascript
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{
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"target": "GGCCGATTCATTAATGCAGCTGG",
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"first": 155,
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"last": 178,
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"microhomology": [
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{
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"strategy": "mh6",
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"forward_strand": "TAATGC",
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"reverse_strand": "ATTACG",
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"mh6_oligo_forward": "TAATGCAGCTGG",
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"mh6_oligo_reverse": "ATTACGTCGACC"
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},
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{
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"strategy": "mh9",
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"forward_strand": "CATTAATGC",
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"reverse_strand": "GTAATTACG",
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"mh9_oligo_forward": "CATTAATGCAGCTGG",
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"mh9_oligo_reverse": "GTAATTACGTCGACC"
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},
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{
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"strategy": "mh12",
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"forward_strand": "ATTCATTAATGC",
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"reverse_strand": "TAAGTAATTACG",
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"mh12_oligo_forward": "ATTCATTAATGCAGCTGG",
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"mh12_oligo_reverse": "TAAGTAATTACGTCGACC"
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},
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{
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"strategy": "mh24",
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"forward_strand": "GCGCGTTGGCCGATTCATTAATGC",
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"reverse_strand": "CGCGCAACCGGCTAAGTAATTACG",
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"mh24_oligo_forward": "GCGCGTTGGCCGATTCATTAATGCAGCTGG",
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"mh24_oligo_reverse": "CGCGCAACCGGCTAAGTAATTACGTCGACC"
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},
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{
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"strategy": "mh48",
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"forward_strand": "CCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGC",
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"reverse_strand": "GGTTATGCGTTTGGCGGAGAGGGGCGCGCAACCGGCTAAGTAATTACG",
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"mh48_oligo_forward": "CCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGG",
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"mh48_oligo_reverse": "GGTTATGCGTTTGGCGGAGAGGGGCGCGCAACCGGCTAAGTAATTACGTCGACC"
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}
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]
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}
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```
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See an [CRISPR example](examples/crispr_example.rb) that prints out results to the console.
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#### TALEN
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Perform microhomology on a DNA sequence using the [TALEN](https://en.wikipedia.org/wiki/Transcription_activator-like_effector_nuclease) technique. This class takes one input, an Ensembl Gene ID _(string)_. Using the DNA returned from Ensembl and the [TALEN algorithm](lib/microhomology/strategies.rb), the DNA is scanned to identify target sites on both forward and reverse strands. Once target sites are identified, microhomology is performed.
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```ruby
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mh = Microhomology::Talen.new('ENSDARG00000061303')
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mh.results
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```
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```javascript
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{
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"target": "TTGCTGTGGTTTCACTCCTTCATCTTCTTGAAGGAGCTCAACCTCCA",
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"first": 1,
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"last": 48,
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"microhomology": [
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{
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"forward_strand": "TTGCTGTGGTTTCACTCCTTCATCTTCTTGAAGGAGCTCAACCTCCA",
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"reverse_strand": "AACGACACCAAAGTGAGGAAGTAGAAGAACTTCCTCGAGTTGGAGGT",
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"oligo_forward": "TTGCTGTGGTTTCACTCTTCTTGACCTTCATAGGAGCTCAACCTCCA",
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"oligo_reverse": "AACGACACCAAAGTGAGAAGAACTGGAAGTATCCTCGAGTTGGAGGT"
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},
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]
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}
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```
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See an [TALEN example](examples/talen_example.rb) that prints out results to the console.
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## Roadmap
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Changes to this gem will be ongoing. If you would like to contribute, please follow the process below.
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* Better integration with Rails
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* Additional DNA data source options
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* Intron and Exon options
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## Contributing
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1. Fork it ( http://github.com/<my-github-username>/microhomology/fork )
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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require 'rubygems'
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require 'microhomology'
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mh = Microhomology::Crispr.new('ENSDARG00000061303', [6, 12, 24, 48, 96])
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puts ' '
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puts mh.key # The Ensembl Gene ID
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puts mh.dna # The DNA data
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puts mh.introns # The DNA data (only introns)
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puts mh.exons # The DNA data (only exons)
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puts mh.strategies # The microhomology strategies
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mh.results.each do |target|
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puts ' '
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puts "Target: " + target['target'] # Identified target site
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puts "First: " + target['first'].to_s # Position (from left) of first base pair
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puts "Last: " + target['last'].to_s # Position (from left) of last base pair
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target['microhomology'].each do |result|
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puts " "
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puts " Strategy: " + result["strategy"].to_s # Microhomology strategy
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puts " Forward: " + result["forward_strand"] # Forward Strand
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puts " Reverse: " + result["reverse_strand"] # Reverse Strand
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puts " Oligo Forward: " + result["oligo_forward"] # Oligo Forward Strand
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puts " Oligo Reverse: " + result["oligo_reverse"] # Oligo Reverse Strand
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end
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end
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require 'rubygems'
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require 'microhomology'
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mh = Microhomology::Talen.new('ENSDARG00000061303')
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puts ' '
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puts mh.key # The Ensembl Gene ID
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puts mh.dna # The DNA data
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puts mh.introns # The DNA data (only introns)
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puts mh.exons # The DNA data (only exons)
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mh.results.each do |target|
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puts ' '
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puts "Target: " + target['target'] # Identified target site
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puts "First: " + target['first'].to_s # Position (from left) of first base pair
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puts "Last: " + target['last'].to_s # Position (from left) of last base pair
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target['microhomology'].each do |result|
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puts " "
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puts " Forward: " + result["forward_strand"] # Forward Strand
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puts " Reverse: " + result["reverse_strand"] # Reverse Strand
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puts " Oligo Forward: " + result["oligo_forward"] # Oligo Forward Strand
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puts " Oligo Reverse: " + result["oligo_reverse"] # Oligo Reverse Strand
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end
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end
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require "microhomology/version"
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require "microhomology/strategies"
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require 'bio'
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require 'json'
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require "open-uri"
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module Microhomology
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class Crispr
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attr_accessor :key, :strategies, :dna, :results
|
11
|
+
|
12
|
+
def initialize(key, strategies)
|
13
|
+
@key = key
|
14
|
+
@strategies = strategies
|
15
|
+
@dna = open(get_ensembl_url).read
|
16
|
+
@results = perform_microhomology
|
17
|
+
end
|
18
|
+
|
19
|
+
def get_ensembl_url
|
20
|
+
"http://rest.ensembl.org/sequence/id/#{self.key}?content-type=text/plain;mask_feature=true"
|
21
|
+
end
|
22
|
+
|
23
|
+
def get_bio_sequence
|
24
|
+
Bio::Sequence::NA.new(self.dna)
|
25
|
+
end
|
26
|
+
|
27
|
+
def exons
|
28
|
+
self.dna.scan /[A-Z]+/
|
29
|
+
end
|
30
|
+
|
31
|
+
def introns
|
32
|
+
self.dna.scan /[a-z]+/
|
33
|
+
end
|
34
|
+
|
35
|
+
def perform_microhomology
|
36
|
+
targets = []
|
37
|
+
self.dna.scan(Microhomology::CRISPR) do |crispr|
|
38
|
+
# Compile first set of data to JSON
|
39
|
+
targets << {
|
40
|
+
"target" => crispr,
|
41
|
+
"first" => Regexp.last_match.offset(0).first,
|
42
|
+
"last" => Regexp.last_match.offset(0).last,
|
43
|
+
"microhomology" => []
|
44
|
+
}
|
45
|
+
end
|
46
|
+
|
47
|
+
if targets
|
48
|
+
targets.each do |target|
|
49
|
+
|
50
|
+
self.strategies.each do |strategy|
|
51
|
+
# Double strand break based on polarity
|
52
|
+
if target["target"][0] == "G"
|
53
|
+
mh_last_char = target["last"] - 7
|
54
|
+
else
|
55
|
+
mh_last_char = target["first"] + 5
|
56
|
+
end
|
57
|
+
mh_first_char = mh_last_char - (strategy - 1)
|
58
|
+
|
59
|
+
target["microhomology"] << {
|
60
|
+
"strategy" => "#{strategy}",
|
61
|
+
"forward_strand" => get_bio_sequence[mh_first_char..mh_last_char].upcase,
|
62
|
+
"reverse_strand" => get_bio_sequence[mh_first_char..mh_last_char].complement.reverse.upcase,
|
63
|
+
"oligo_forward" => get_bio_sequence[mh_first_char...target["last"]].upcase,
|
64
|
+
"oligo_reverse" => get_bio_sequence[mh_first_char...target["last"]].complement.reverse.upcase
|
65
|
+
}
|
66
|
+
end
|
67
|
+
end
|
68
|
+
targets
|
69
|
+
else
|
70
|
+
"Sorry, no CRISPR targets found."
|
71
|
+
end
|
72
|
+
end
|
73
|
+
end
|
74
|
+
|
75
|
+
class Talen
|
76
|
+
attr_accessor :key, :dna, :results
|
77
|
+
|
78
|
+
def initialize(key)
|
79
|
+
@key = key
|
80
|
+
@dna = open(get_ensembl_url).read
|
81
|
+
@results = perform_microhomology
|
82
|
+
end
|
83
|
+
|
84
|
+
def get_ensembl_url
|
85
|
+
"http://rest.ensembl.org/sequence/id/#{self.key}?content-type=text/plain;mask_feature=true"
|
86
|
+
end
|
87
|
+
|
88
|
+
def exons
|
89
|
+
self.dna.scan /[A-Z]+/
|
90
|
+
end
|
91
|
+
|
92
|
+
def introns
|
93
|
+
self.dna.scan /[a-z]+/
|
94
|
+
end
|
95
|
+
|
96
|
+
def perform_microhomology
|
97
|
+
targets = []
|
98
|
+
self.dna.scan(Microhomology::TALEN) do |talen|
|
99
|
+
targets << {
|
100
|
+
"target" => talen,
|
101
|
+
"first" => Regexp.last_match.offset(0).first,
|
102
|
+
"last" => Regexp.last_match.offset(0).last,
|
103
|
+
"microhomology" => []
|
104
|
+
}
|
105
|
+
end
|
106
|
+
|
107
|
+
if targets
|
108
|
+
targets.each do |target|
|
109
|
+
|
110
|
+
talen_site = Bio::Sequence::NA.new(target['target'])
|
111
|
+
talen_site_complement = talen_site.complement.reverse
|
112
|
+
|
113
|
+
talen1 = talen_site[0..15]
|
114
|
+
spacer1 = talen_site[16..22]
|
115
|
+
spacer2 = talen_site[23..30]
|
116
|
+
talen2 = talen_site[31..47]
|
117
|
+
|
118
|
+
talen_forward = Bio::Sequence::NA.new("#{talen1}#{spacer2}#{spacer1}#{talen2}")
|
119
|
+
talen_reverse = talen_forward.complement.reverse
|
120
|
+
|
121
|
+
target["microhomology"] << {
|
122
|
+
"forward_strand" => "#{talen_site.upcase}",
|
123
|
+
"reverse_strand" => "#{talen_site_complement.upcase}",
|
124
|
+
"oligo_forward" => "#{talen_forward.upcase}",
|
125
|
+
"oligo_reverse" => "#{talen_reverse.upcase}"
|
126
|
+
}
|
127
|
+
end
|
128
|
+
targets
|
129
|
+
else
|
130
|
+
"Sorry, no TALEN targets found."
|
131
|
+
end
|
132
|
+
end
|
133
|
+
|
134
|
+
end
|
135
|
+
end
|
@@ -0,0 +1,30 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'microhomology/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "Microhomology"
|
8
|
+
spec.version = Microhomology::VERSION
|
9
|
+
spec.authors = ["Chris Mikelson"]
|
10
|
+
spec.email = ["chrismikelson@gmail.com"]
|
11
|
+
spec.summary = %q{Perform simultaneous microhomology strategies with ease using CRISPR or TALEN techniques.}
|
12
|
+
spec.description = %q{Simultaneously perform custom microhomoly strategies for genetic engineering and bioinformatics.}
|
13
|
+
spec.homepage = "https://github.com/cmike444/microhomology"
|
14
|
+
spec.license = "MIT"
|
15
|
+
|
16
|
+
spec.files = `git ls-files -z`.split("\x0")
|
17
|
+
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
18
|
+
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
19
|
+
spec.require_paths = ["lib"]
|
20
|
+
|
21
|
+
spec.add_development_dependency "bundler", "~> 1.5"
|
22
|
+
spec.add_development_dependency "rake", '~> 0'
|
23
|
+
spec.add_development_dependency "rspec"
|
24
|
+
spec.add_development_dependency "guard"
|
25
|
+
spec.add_development_dependency "guard-rspec"
|
26
|
+
spec.add_development_dependency "coveralls"
|
27
|
+
|
28
|
+
spec.add_runtime_dependency "json", '~> 1.8', '>= 1.8.3'
|
29
|
+
spec.add_runtime_dependency "bio", '~> 1.5', '>= 1.5.0'
|
30
|
+
end
|
data/microhomology.png
ADDED
Binary file
|
@@ -0,0 +1,10 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
describe Microhomology do
|
4
|
+
context "on new crispr" do
|
5
|
+
it "adds key to ensembl url" do
|
6
|
+
crispr = Microhomology::Crispr.new('ENSDARG00000061303', [6, 12, 24, 48, 96])
|
7
|
+
expect(crispr.get_ensembl_url).to eq "http://rest.ensembl.org/sequence/id/ENSDARG00000061303?content-type=text/plain;mask_feature=true"
|
8
|
+
end
|
9
|
+
end
|
10
|
+
end
|
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1,99 @@
|
|
1
|
+
# This file was generated by the `rspec --init` command. Conventionally, all
|
2
|
+
# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
|
3
|
+
# The generated `.rspec` file contains `--require spec_helper` which will cause
|
4
|
+
# this file to always be loaded, without a need to explicitly require it in any
|
5
|
+
# files.
|
6
|
+
#
|
7
|
+
# Given that it is always loaded, you are encouraged to keep this file as
|
8
|
+
# light-weight as possible. Requiring heavyweight dependencies from this file
|
9
|
+
# will add to the boot time of your test suite on EVERY test run, even for an
|
10
|
+
# individual file that may not need all of that loaded. Instead, consider making
|
11
|
+
# a separate helper file that requires the additional dependencies and performs
|
12
|
+
# the additional setup, and require it from the spec files that actually need
|
13
|
+
# it.
|
14
|
+
#
|
15
|
+
# The `.rspec` file also contains a few flags that are not defaults but that
|
16
|
+
# users commonly want.
|
17
|
+
#
|
18
|
+
# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
|
19
|
+
|
20
|
+
require 'microhomology'
|
21
|
+
|
22
|
+
RSpec.configure do |config|
|
23
|
+
# rspec-expectations config goes here. You can use an alternate
|
24
|
+
# assertion/expectation library such as wrong or the stdlib/minitest
|
25
|
+
# assertions if you prefer.
|
26
|
+
config.expect_with :rspec do |expectations|
|
27
|
+
# This option will default to `true` in RSpec 4. It makes the `description`
|
28
|
+
# and `failure_message` of custom matchers include text for helper methods
|
29
|
+
# defined using `chain`, e.g.:
|
30
|
+
# be_bigger_than(2).and_smaller_than(4).description
|
31
|
+
# # => "be bigger than 2 and smaller than 4"
|
32
|
+
# ...rather than:
|
33
|
+
# # => "be bigger than 2"
|
34
|
+
expectations.include_chain_clauses_in_custom_matcher_descriptions = true
|
35
|
+
end
|
36
|
+
|
37
|
+
# rspec-mocks config goes here. You can use an alternate test double
|
38
|
+
# library (such as bogus or mocha) by changing the `mock_with` option here.
|
39
|
+
config.mock_with :rspec do |mocks|
|
40
|
+
# Prevents you from mocking or stubbing a method that does not exist on
|
41
|
+
# a real object. This is generally recommended, and will default to
|
42
|
+
# `true` in RSpec 4.
|
43
|
+
mocks.verify_partial_doubles = true
|
44
|
+
end
|
45
|
+
|
46
|
+
# The settings below are suggested to provide a good initial experience
|
47
|
+
# with RSpec, but feel free to customize to your heart's content.
|
48
|
+
=begin
|
49
|
+
# These two settings work together to allow you to limit a spec run
|
50
|
+
# to individual examples or groups you care about by tagging them with
|
51
|
+
# `:focus` metadata. When nothing is tagged with `:focus`, all examples
|
52
|
+
# get run.
|
53
|
+
config.filter_run :focus
|
54
|
+
config.run_all_when_everything_filtered = true
|
55
|
+
|
56
|
+
# Allows RSpec to persist some state between runs in order to support
|
57
|
+
# the `--only-failures` and `--next-failure` CLI options. We recommend
|
58
|
+
# you configure your source control system to ignore this file.
|
59
|
+
config.example_status_persistence_file_path = "spec/examples.txt"
|
60
|
+
|
61
|
+
# Limits the available syntax to the non-monkey patched syntax that is
|
62
|
+
# recommended. For more details, see:
|
63
|
+
# - http://myronmars.to/n/dev-blog/2012/06/rspecs-new-expectation-syntax
|
64
|
+
# - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
|
65
|
+
# - http://myronmars.to/n/dev-blog/2014/05/notable-changes-in-rspec-3#new__config_option_to_disable_rspeccore_monkey_patching
|
66
|
+
config.disable_monkey_patching!
|
67
|
+
|
68
|
+
# This setting enables warnings. It's recommended, but in some cases may
|
69
|
+
# be too noisy due to issues in dependencies.
|
70
|
+
config.warnings = true
|
71
|
+
|
72
|
+
# Many RSpec users commonly either run the entire suite or an individual
|
73
|
+
# file, and it's useful to allow more verbose output when running an
|
74
|
+
# individual spec file.
|
75
|
+
if config.files_to_run.one?
|
76
|
+
# Use the documentation formatter for detailed output,
|
77
|
+
# unless a formatter has already been configured
|
78
|
+
# (e.g. via a command-line flag).
|
79
|
+
config.default_formatter = 'doc'
|
80
|
+
end
|
81
|
+
|
82
|
+
# Print the 10 slowest examples and example groups at the
|
83
|
+
# end of the spec run, to help surface which specs are running
|
84
|
+
# particularly slow.
|
85
|
+
config.profile_examples = 10
|
86
|
+
|
87
|
+
# Run specs in random order to surface order dependencies. If you find an
|
88
|
+
# order dependency and want to debug it, you can fix the order by providing
|
89
|
+
# the seed, which is printed after each run.
|
90
|
+
# --seed 1234
|
91
|
+
config.order = :random
|
92
|
+
|
93
|
+
# Seed global randomization in this process using the `--seed` CLI option.
|
94
|
+
# Setting this allows you to use `--seed` to deterministically reproduce
|
95
|
+
# test failures related to randomization by passing the same `--seed` value
|
96
|
+
# as the one that triggered the failure.
|
97
|
+
Kernel.srand config.seed
|
98
|
+
=end
|
99
|
+
end
|
metadata
ADDED
@@ -0,0 +1,189 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: Microhomology
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Chris Mikelson
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2015-09-27 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ~>
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.5'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ~>
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.5'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
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:
|
38
|
+
- - ~>
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rspec
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - '>='
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - '>='
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: guard
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - '>='
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - '>='
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: guard-rspec
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - '>='
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: '0'
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - '>='
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: '0'
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: coveralls
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - '>='
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: '0'
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - '>='
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: '0'
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: json
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - ~>
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: '1.8'
|
104
|
+
- - '>='
|
105
|
+
- !ruby/object:Gem::Version
|
106
|
+
version: 1.8.3
|
107
|
+
type: :runtime
|
108
|
+
prerelease: false
|
109
|
+
version_requirements: !ruby/object:Gem::Requirement
|
110
|
+
requirements:
|
111
|
+
- - ~>
|
112
|
+
- !ruby/object:Gem::Version
|
113
|
+
version: '1.8'
|
114
|
+
- - '>='
|
115
|
+
- !ruby/object:Gem::Version
|
116
|
+
version: 1.8.3
|
117
|
+
- !ruby/object:Gem::Dependency
|
118
|
+
name: bio
|
119
|
+
requirement: !ruby/object:Gem::Requirement
|
120
|
+
requirements:
|
121
|
+
- - ~>
|
122
|
+
- !ruby/object:Gem::Version
|
123
|
+
version: '1.5'
|
124
|
+
- - '>='
|
125
|
+
- !ruby/object:Gem::Version
|
126
|
+
version: 1.5.0
|
127
|
+
type: :runtime
|
128
|
+
prerelease: false
|
129
|
+
version_requirements: !ruby/object:Gem::Requirement
|
130
|
+
requirements:
|
131
|
+
- - ~>
|
132
|
+
- !ruby/object:Gem::Version
|
133
|
+
version: '1.5'
|
134
|
+
- - '>='
|
135
|
+
- !ruby/object:Gem::Version
|
136
|
+
version: 1.5.0
|
137
|
+
description: Simultaneously perform custom microhomoly strategies for genetic engineering
|
138
|
+
and bioinformatics.
|
139
|
+
email:
|
140
|
+
- chrismikelson@gmail.com
|
141
|
+
executables: []
|
142
|
+
extensions: []
|
143
|
+
extra_rdoc_files: []
|
144
|
+
files:
|
145
|
+
- .gitignore
|
146
|
+
- .rspec
|
147
|
+
- .travis.yml
|
148
|
+
- Gemfile
|
149
|
+
- Guardfile
|
150
|
+
- LICENSE.txt
|
151
|
+
- README.md
|
152
|
+
- Rakefile
|
153
|
+
- examples/crispr_example.rb
|
154
|
+
- examples/talen_example.rb
|
155
|
+
- lib/microhomology.rb
|
156
|
+
- lib/microhomology/strategies.rb
|
157
|
+
- lib/microhomology/version.rb
|
158
|
+
- microhomology.gemspec
|
159
|
+
- microhomology.png
|
160
|
+
- spec/microhomology_helper.rb
|
161
|
+
- spec/spec_helper.rb
|
162
|
+
homepage: https://github.com/cmike444/microhomology
|
163
|
+
licenses:
|
164
|
+
- MIT
|
165
|
+
metadata: {}
|
166
|
+
post_install_message:
|
167
|
+
rdoc_options: []
|
168
|
+
require_paths:
|
169
|
+
- lib
|
170
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
171
|
+
requirements:
|
172
|
+
- - '>='
|
173
|
+
- !ruby/object:Gem::Version
|
174
|
+
version: '0'
|
175
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
176
|
+
requirements:
|
177
|
+
- - '>='
|
178
|
+
- !ruby/object:Gem::Version
|
179
|
+
version: '0'
|
180
|
+
requirements: []
|
181
|
+
rubyforge_project:
|
182
|
+
rubygems_version: 2.2.1
|
183
|
+
signing_key:
|
184
|
+
specification_version: 4
|
185
|
+
summary: Perform simultaneous microhomology strategies with ease using CRISPR or TALEN
|
186
|
+
techniques.
|
187
|
+
test_files:
|
188
|
+
- spec/microhomology_helper.rb
|
189
|
+
- spec/spec_helper.rb
|