Microhomology 0.1.0
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- 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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![Microhomology Logo](https://raw.github.com/cmike444/microhomology/master/microhomology.png)
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By [Chris Mikelson](http://chrismikelson.com)
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[![Build Status](https://travis-ci.org/cmike444/microhomology.svg?branch=master)](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
ADDED
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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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|
+
|
9
|
+
class Crispr
|
10
|
+
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
|