muscle_bio 0.2.0 → 0.3.0
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 +4 -4
- data/Gemfile.lock +1 -1
- data/README.md +6 -17
- data/lib/muscle_bio.rb +9 -1
- data/lib/muscle_bio/version.rb +1 -1
- data/muscle_bio.gemspec +1 -1
- metadata +3 -2
checksums.yaml
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SHA1:
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metadata.gz:
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metadata.gz: aa933fcac87a7b3662ee990c35d61d1df51a26ba
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data.tar.gz: 3b87a66959ff6d3dd2811290507fb40f022555f4
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metadata.gz: e75e2958cb504d8d394af1817471c814c5cf24daa215dea5de4a82100d456add5b47efe073c9bc5eca2a17748c39dc20101cf91190917bfc2e537a5a903ab20e
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data.tar.gz: b9c12e81029f8d2b707712bf364232ada0315466974758c5ad195574b688ee8580ed6832acbdf3ccd6580f3f3b111ce53dd9c3197944f0c07e14ac34d932d757
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data/Gemfile.lock
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data/README.md
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# MuscleBio
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TODO: Delete this and the text above, and describe your gem
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Supported on Mac, Linux, and Windows.
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## Installation
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@@ -22,22 +20,13 @@ Or install it yourself as:
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## Usage
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## Development
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After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
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To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
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## Contributing
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require 'muscle_bio'
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MuscleBio.run('muscle -in ../sample/sequence.fasta -out ../sample/sequence.afa')
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#pass string in as your current Muscle command
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The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
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MuscleBio.init(fileIn, fileOut, maxIters)
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#maxIters is optional
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data/lib/muscle_bio.rb
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file = File.join( File.dirname(__FILE__), 'runnable/'+file)
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cmd = cmd.sub 'sudo ', ''
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cmd = cmd.sub 'muscle', file
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cmd = 'sudo ' + cmd
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cmd = 'sudo ' + cmd + " -quiet"
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`#{cmd}`
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end
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def self.init(fileIn, fileOut, maxIters = nil)
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cmd = "muscle -in " + fileIn + " -out " + fileOut
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if maxIters != nil
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cmd += " -maxiters " + maxIters
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end
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self.run(cmd)
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end
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end
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data/lib/muscle_bio/version.rb
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data/muscle_bio.gemspec
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@@ -10,7 +10,7 @@ Gem::Specification.new do |spec|
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spec.email = ["clarkmu@gmail.com"]
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spec.summary = %q{Run Muscle from Ruby gem}
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spec.description = %q{Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/}
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spec.description = %q{Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/. For instructions on how to use, see https://github.com/clarkmu/muscle_bio}
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spec.homepage = "http://swanstrom.web.unc.edu/"
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spec.license = "MIT"
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metadata
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--- !ruby/object:Gem::Specification
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name: muscle_bio
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.3.0
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platform: ruby
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authors:
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- Michael Clark
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.0'
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description: Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle
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description: Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/. For
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instructions on how to use, see https://github.com/clarkmu/muscle_bio
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email:
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- clarkmu@gmail.com
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executables: []
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