muscle_bio 0.1.0 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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+SHA256:
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data/.gitignore

@@ -11,4 +11,5 @@
 .rspec_status
 
 .DS_STORE
-*.gem
+*.gem
+.DS_Store

data/Gemfile.lock

@@ -0,0 +1,35 @@
+PATH
+  remote: .
+  specs:
+    muscle_bio (0.5.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    diff-lcs (1.3)
+    rake (13.0.1)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.4)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.2)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 2.0)
+  muscle_bio!
+  rake (~> 13.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   2.2.32

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-Intel64, Mac-AMR64, Linux, and Windows. Support Muscle 5.1.
 
 ## Installation
 
@@ -22,22 +20,16 @@ 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
+```{ruby}
+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.
-
-## License
-
-The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
-
-## Code of Conduct
+MuscleBio.exec(
+               '/sample/sequence.fasta', # input file
+               '/sample/sequence.afa', # output file
+               :PPP # choose from :PPP or :Super5
+               )
+```
 
-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).
+### Version history
+  * v0.5.0 - update Muscle to version 5.1.
+  * v0.4.0 - Muscle 3.8.1

data/lib/muscle_bio/version.rb

@@ -1,3 +1,3 @@
 module MuscleBio
-  VERSION = "0.1.0"
+  VERSION = "0.5.0"
 end

data/lib/muscle_bio.rb

@@ -1,26 +1,34 @@
 require "muscle_bio/version"
 
 module MuscleBio
-  def self.run(cmd)
-
-  	file = ""
 
-  	if (/darwin/ =~ RUBY_PLATFORM) != nil 
-  		file = "muscle_mac_64"
-  	elsif (/cygwin|mswin|mingw|bccwin|wince|emx/ =~ RUBY_PLATFORM) != nil
-  		file = "muscle_windows_32.exe"
-  	else
-  		file = "muscle_linux_64"
-  	end
+  def self.run(cmd)
+    case RUBY_PLATFORM
+    when /arm64/
+      file = "muscle5.1.macos_arm64"
+    when /x86.*darwin/
+      file = "muscle5.1.macos_intel64"
+    when /cygwin|mswin|mingw|bccwin|wince|emx/
+      file = "muscle5.1.win64.exe"
+    else
+      file = "muscle5.1.linux_intel64"
+    end
 
   	file = File.join( File.dirname(__FILE__), 'runnable/'+file)
+  	cmd = file + "\s" + cmd + " -quiet"
+	  `#{cmd}`
+  end
 
-  	cmd = cmd.sub 'sudo ', ''
-  	cmd = cmd.sub 'muscle', file
-  	# cmd = 'sudo ' + cmd
-
-  	# puts cmd
-
-	`#{cmd}`
+  ### two algorithms to choose, :PPP or Super5
+  def self.exec(fileIn, fileOut, algorithm = :PPP)
+    if algorithm == :PPP
+      cmd = "-align " + fileIn + " -output " + fileOut
+    elsif algorithm == :Super5
+      cmd = "-super5 " + fileIn + " -output " + fileOut
+    else
+      raise "algorithm not found. Muscle aborted."
+    end
+  	self.run(cmd)
   end
-end
+
+end

data/muscle_bio.gemspec

@@ -9,9 +9,9 @@ Gem::Specification.new do |spec|
   spec.authors       = ["Michael Clark"]
   spec.email         = ["clarkmu@gmail.com"]
 
-  spec.summary       = %q{}
-  spec.description   = %q{}
-  spec.homepage      = ""
+  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/.  For instructions on how to use, see https://github.com/clarkmu/muscle_bio}
+  spec.homepage      = "http://swanstrom.web.unc.edu/"
   spec.license       = "MIT"
 
   # Specify which files should be added to the gem when it is released.
@@ -24,6 +24,6 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_development_dependency "bundler", "~> 2.0"
-  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rake", "~> 13.0"
   spec.add_development_dependency "rspec", "~> 3.0"
 end

data/sample/sample_seq.afa

@@ -0,0 +1,48 @@
+>test5
+A-TTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCA
+GTGTTTGCAATAAAGAAAAAGGA-CAGTACTAAGTGGAGAAAATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAG
+ACTTCTGGGAGGTTCAATTAGGAATACCACACCCGGCAGGGTTAAGAAAGAAAAAATCAGTAACAGTATTAGATGTGGGG
+GATG-CATATTTTTCAGTTCCCTTAGATAA-----------AGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCA
+TGACAAAAATTTTA-GAGCCTTTCAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGACTTGTATGTAGG
+CTCTGACTTAGAAGTAGAGCAACATAGAGCAAAAATAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACAC
+CAGACAAAAAGCATCAGAAAGAACCTCCCTTCCA---TTGGA--T-GGGTT-ATGAACTCCATCCT
+>test4
+GACAAGTAGACTGTAGCCCAGGAATAT-----GGCAACTAGATTGTACACATTTAGAAGGAAAAAT----------TATC
+CTGGTAGCAGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAGAGACA-GGGAGTGAAACAGCACACT
+TCCTCT------TAAAATTAGCAGGAAGA------------------------TGGCCAGTAAAAACAATACATACAGAC
+AATGGCAGCAATTTCACCAGTGCTACAGTGAAGGCCGCATGCTGGTGGGCAGGGATCA----------------------
+-AACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGT---------------------------------
+---------------------------------------------------------------------AGAATCTATGA
+ATA----AAG-AATTAAAGAAAA--TCATAGGACAAGTAAGAGATCAGGCTGAACATCTTAAGACA
+>test6
+CCTCAAATCACTCTT-----------T-----GGCAA---------------------------CG----------ACCC
+CTCGTCACAGTAAAGATAGGGGGTCAGCTAAAGGAGGCTCTATTAGATACAGGAGCA-------GATGATACAGTTTTAG
+AAGAAA------TGTATTTGCCAGGAAAA------------------------TGGAAACCAAAAATGAT----AGGGGG
+AATTGGAGGTTTTATCAAAGTAAGACAATATG-ATCAGATATTAG-----------------------------------
+---TAGAAATTTGT----GGACATAAAGCAATAGGTACAGTATTAAT---------------------------------
+---------------------------------------------------------------------AGGACCTACAC
+CTGTCAACAT-AATTGGAAGAAA--TCTGTTGAC---TCAGA--T-TGGTT-GCACTCTAAACTTT
+>test1
+GACAGGTAGACTGTAGCCCAGGAATAT-----GGCAACTAGATTGTACACATCTAGAAGGAAAAAT----------TATC
+CTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGGAGACA-GGACAGGAAACAGCATACT
+TCCTCT------TAAAATTAGCAGGAAGA------------------------TGGCCAGTAAAAACAATACATACAGAC
+AATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGTGGGCAGGGATTA----------------------
+-CACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGT---------------------------------
+---------------------------------------------------------------------AGAATCTATGA
+ATA----AAG-AATTAAAGAAAA--TTATAGGACAAGTGAGAGATCAGGCTGAACATCTTAAGACA
+>test2
+GACAAGTAGACTGTAGCCCAGGAATAT-----GGCAACTAGATTGCACACATTTAGAAGGAAAAAT----------TATC
+CTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAGACA-GGGAGTGAAACAGCATACT
+TCCTCT------TAAAGTTGGCAGGAAGA------------------------TGGCCAGTAAAAACAATACATACAGAC
+AATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGTGGGCAGGGATCA----------------------
+-AGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGT---------------------------------
+---------------------------------------------------------------------AGAATCTATGA
+ATA----AAG-AATTAAAGAAGA--TCATAGGACAAGTAAGAGATCAGGCTGAACATCTTAAAACA
+>test3
+GACAAGTAGACTGTAGCCCAGGAATAT-----GGCAACTAGATTGTACACATCTAGAAGGAAAAAT----------TATC
+CTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACA-GGACAGGAAACAGCATACT
+TCCTCT------TAAAATTAGCAGGAAGA------------------------TGGCCAGTAAAAACAATACATACAGAT
+AATGGCAGTAATTTCACCAGTACTACAGTTAAGGCCGCATGCTGGTGGGCAGGGATCA----------------------
+-AACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGT---------------------------------
+---------------------------------------------------------------------AGAATCTATGA
+ATA----AAG-AATTAAAGAAAA--TTATAGGGCAAGTAAGAGATCAGGCTGAACATCTTAAGACA

data/sample/sample_seq.fasta

@@ -0,0 +1,48 @@
+>test1
+GACAGGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATCTAGAAGGAAAAA
+TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGG
+AGACAGGACAGGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
+CAATACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGT
+GGGCAGGGATTACACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
+AATCTATGAATAAAGAATTAAAGAAAATTATAGGACAAGTGAGAGATCAGGCTGAACATC
+TTAAGACA
+>test2
+GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGCACACATTTAGAAGGAAAAA
+TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAG
+AGACAGGGAGTGAAACAGCATACTTCCTCTTAAAGTTGGCAGGAAGATGGCCAGTAAAAA
+CAATACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGT
+GGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
+AATCTATGAATAAAGAATTAAAGAAGATCATAGGACAAGTAAGAGATCAGGCTGAACATC
+TTAAAACA
+>test3
+GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATCTAGAAGGAAAAA
+TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAG
+AAACAGGACAGGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
+CAATACATACAGATAATGGCAGTAATTTCACCAGTACTACAGTTAAGGCCGCATGCTGGT
+GGGCAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
+AATCTATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGATCAGGCTGAACATC
+TTAAGACA
+>test4
+GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAA
+TTATCCTGGTAGCAGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAG
+AGACAGGGAGTGAAACAGCACACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
+CAATACATACAGACAATGGCAGCAATTTCACCAGTGCTACAGTGAAGGCCGCATGCTGGT
+GGGCAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
+AATCTATGAATAAAGAATTAAAGAAAATCATAGGACAAGTAAGAGATCAGGCTGAACATC
+TTAAGACA
+>test5
+ATTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGA
+AAATCCATACAATACTCCAGTGTTTGCAATAAAGAAAAAGGACAGTACTAAGTGGAGAAA
+ATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAGACTTCTGGGAGGTTCAATTAGG
+AATACCACACCCGGCAGGGTTAAGAAAGAAAAAATCAGTAACAGTATTAGATGTGGGGGA
+TGCATATTTTTCAGTTCCCTTAGATAAAGGGATGGAAAGGATCACCAGCAATATTCCAAA
+GTAGCATGACAAAAATTTTAGAGCCTTTCAGAAAACAAAATCCAGACATAGTTATCTATC
+AATACATGGATGACTTGTATGTAGGCTCTGACTTAGAAGTAGAGCAACATAGAGCAAAAA
+TAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACACCAGACAAAAAGCATC
+AGAAAGAACCTCCCTTCCATTGGATGGGTTATGAACTCCATCCT
+>test6
+CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAGTAAAGATAGGGGGTCAGCTAAAG
+GAGGCTCTATTAGATACAGGAGCAGATGATACAGTTTTAGAAGAAATGTATTTGCCAGGA
+AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT
+CAGATATTAGTAGAAATTTGTGGACATAAAGCAATAGGTACAGTATTAATAGGACCTACA
+CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTCTAAACTTT

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: muscle_bio
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.5.0
 platform: ruby
 authors:
 - Michael Clark
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2019-06-11 00:00:00.000000000 Z
+date: 2022-02-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -30,14 +30,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -52,7 +52,8 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.0'
-description: ''
+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: []
@@ -65,6 +66,7 @@ files:
 - ".travis.yml"
 - CODE_OF_CONDUCT.md
 - Gemfile
+- Gemfile.lock
 - LICENSE.txt
 - README.md
 - Rakefile
@@ -73,15 +75,18 @@ files:
 - lib/.DS_Store
 - lib/muscle_bio.rb
 - lib/muscle_bio/version.rb
-- lib/runnable/muscle_linux_64
-- lib/runnable/muscle_mac_64
-- lib/runnable/muscle_windows_32.exe
+- lib/runnable/muscle5.1.linux_intel64
+- lib/runnable/muscle5.1.macos_arm64
+- lib/runnable/muscle5.1.macos_intel64
+- lib/runnable/muscle5.1.win64.exe
 - muscle_bio.gemspec
-homepage: ''
+- sample/sample_seq.afa
+- sample/sample_seq.fasta
+homepage: http://swanstrom.web.unc.edu/
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -96,9 +101,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.2.3
-signing_key: 
+rubygems_version: 3.2.29
+signing_key:
 specification_version: 4
-summary: ''
+summary: Run Muscle from Ruby gem
 test_files: []