muscle_bio 0.2.0 → 0.3.0

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@@ -1,7 +1,7 @@
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  PATH
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  remote: .
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  specs:
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- muscle_bio (0.1.0)
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+ muscle_bio (0.3.0)
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  GEM
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  remote: https://rubygems.org/
data/README.md CHANGED
@@ -1,8 +1,6 @@
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  # MuscleBio
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- Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/muscle_bio`. To experiment with that code, run `bin/console` for an interactive prompt.
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-
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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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- TODO: Write usage instructions here
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-
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- ## Development
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-
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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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-
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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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-
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- ## Contributing
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+ require 'muscle_bio'
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- Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/muscle_bio. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
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+ MuscleBio.run('muscle -in ../sample/sequence.fasta -out ../sample/sequence.afa')
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- ## License
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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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- ## Code of Conduct
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+ MuscleBio.init(fileIn, fileOut, maxIters)
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- Everyone interacting in the MuscleBio project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/muscle_bio/blob/master/CODE_OF_CONDUCT.md).
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+ #maxIters is optional
@@ -8,8 +8,16 @@ module MuscleBio
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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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+
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  end
@@ -1,3 +1,3 @@
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  module MuscleBio
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- VERSION = "0.2.0"
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+ VERSION = "0.3.0"
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  end
@@ -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 CHANGED
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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: 0.2.0
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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
@@ -52,7 +52,8 @@ dependencies:
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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: []