muscle_bio 0.2.0 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: aa933fcac87a7b3662ee990c35d61d1df51a26ba
+  data.tar.gz: 3b87a66959ff6d3dd2811290507fb40f022555f4
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    muscle_bio (0.1.0)
+    muscle_bio (0.3.0)
 
 GEM
   remote: https://rubygems.org/

data/README.md

@@ -1,8 +1,6 @@
 # MuscleBio
 
-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.
-
-TODO: Delete this and the text above, and describe your gem
+Supported on Mac, Linux, and Windows.
 
 ## Installation
 
@@ -22,22 +20,13 @@ Or install it yourself as:
 
 ## Usage
 
-TODO: Write usage instructions here
-
-## Development
-
-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.
-
-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).
-
-## Contributing
+require 'muscle_bio'
 
-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.
+MuscleBio.run('muscle -in ../sample/sequence.fasta -out ../sample/sequence.afa')
 
-## License
+#pass string in as your current Muscle command
 
-The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
 
-## Code of Conduct
+MuscleBio.init(fileIn, fileOut, maxIters)
 
-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).
+#maxIters is optional

data/lib/muscle_bio.rb

@@ -8,8 +8,16 @@ module MuscleBio
   	file = File.join( File.dirname(__FILE__), 'runnable/'+file)
   	cmd = cmd.sub 'sudo ', ''
   	cmd = cmd.sub 'muscle', file
-  	cmd = 'sudo ' + cmd
+  	cmd = 'sudo ' + cmd + " -quiet"
 	`#{cmd}`
   end
 
+  def self.init(fileIn, fileOut, maxIters = nil)
+  	cmd = "muscle -in " + fileIn + " -out " + fileOut
+  	if maxIters != nil
+  		cmd += " -maxiters " + maxIters
+  	end
+  	self.run(cmd)
+  end
+
 end

data/lib/muscle_bio/version.rb

@@ -1,3 +1,3 @@
 module MuscleBio
-  VERSION = "0.2.0"
+  VERSION = "0.3.0"
 end

data/muscle_bio.gemspec

@@ -10,7 +10,7 @@ Gem::Specification.new do |spec|
   spec.email         = ["clarkmu@gmail.com"]
 
   spec.summary       = %q{Run Muscle from Ruby gem}
-  spec.description   = %q{Multiple Sequence Alignment for Ruby scripts.  Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/}
+  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}
   spec.homepage      = "http://swanstrom.web.unc.edu/"
   spec.license       = "MIT"
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: muscle_bio
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - Michael Clark
@@ -52,7 +52,8 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.0'
-description: Multiple Sequence Alignment for Ruby scripts.  Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/
+description: 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
 email:
 - clarkmu@gmail.com
 executables: []