muscle_bio 0.1.0 → 0.2.0

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Files changed (9) hide show
  1. checksums.yaml +4 -4
  2. data/.DS_Store +0 -0
  3. data/Gemfile.lock +35 -0
  4. data/lib/muscle_bio.rb +5 -16
  5. data/lib/muscle_bio/version.rb +1 -1
  6. data/muscle_bio.gemspec +3 -3
  7. data/sample/sample_seq.afa +60 -0
  8. data/sample/sample_seq.fasta +48 -0
  9. metadata +7 -4
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data/.DS_Store CHANGED
Binary file
data/Gemfile.lock ADDED
@@ -0,0 +1,35 @@
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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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+
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+ GEM
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+ remote: https://rubygems.org/
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+ specs:
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+ diff-lcs (1.3)
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+ rake (10.4.2)
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+ rspec (3.8.0)
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+ rspec-core (~> 3.8.0)
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+ rspec-expectations (~> 3.8.0)
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+ rspec-mocks (~> 3.8.0)
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+ rspec-core (3.8.0)
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+ rspec-support (~> 3.8.0)
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+ rspec-expectations (3.8.4)
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+ diff-lcs (>= 1.2.0, < 2.0)
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+ rspec-support (~> 3.8.0)
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+ rspec-mocks (3.8.0)
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+ diff-lcs (>= 1.2.0, < 2.0)
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+ rspec-support (~> 3.8.0)
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+ rspec-support (3.8.2)
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+
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+ PLATFORMS
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+ ruby
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+
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+ DEPENDENCIES
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+ bundler (~> 2.0)
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+ muscle_bio!
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+ rake (~> 10.0)
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+ rspec (~> 3.0)
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+
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+ BUNDLED WITH
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+ 2.0.1
data/lib/muscle_bio.rb CHANGED
@@ -1,26 +1,15 @@
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  require "muscle_bio/version"
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  module MuscleBio
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- def self.run(cmd)
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-
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- file = ""
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-
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- if (/darwin/ =~ RUBY_PLATFORM) != nil
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- file = "muscle_mac_64"
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- elsif (/cygwin|mswin|mingw|bccwin|wince|emx/ =~ RUBY_PLATFORM) != nil
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- file = "muscle_windows_32.exe"
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- else
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- file = "muscle_linux_64"
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- end
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+ def self.run(cmd)
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+ file = (/darwin/ =~ RUBY_PLATFORM) != nil ? "muscle_mac_64" :
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+ (/cygwin|mswin|mingw|bccwin|wince|emx/ =~ RUBY_PLATFORM) != nil ? "muscle_windows_32.exe" : "muscle_linux_64"
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  file = File.join( File.dirname(__FILE__), 'runnable/'+file)
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-
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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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-
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- # puts cmd
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-
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+ cmd = 'sudo ' + cmd
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  `#{cmd}`
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  end
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+
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  end
data/lib/muscle_bio/version.rb CHANGED
@@ -1,3 +1,3 @@
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  module MuscleBio
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- VERSION = "0.1.0"
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+ VERSION = "0.2.0"
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  end
data/muscle_bio.gemspec CHANGED
@@ -9,9 +9,9 @@ Gem::Specification.new do |spec|
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  spec.authors = ["Michael Clark"]
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  spec.email = ["clarkmu@gmail.com"]
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- spec.summary = %q{}
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- spec.description = %q{}
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- spec.homepage = ""
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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.homepage = "http://swanstrom.web.unc.edu/"
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  spec.license = "MIT"
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  # Specify which files should be added to the gem when it is released.
data/sample/sample_seq.afa ADDED
@@ -0,0 +1,60 @@
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+ >test1
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+ -----------------------------------------------------------G
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+ ACAGGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
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+ ---ACTAGATTGTACACATCTAGAAGGAAAAATT---------------ATCCTGGTAGC
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+ AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGGAGACAGGACAGGA
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+ AACAGCATAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
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+ ATACAGACAATGGCAGCAATTTCA---CCAGTACTACAGTTAAGGCCGCCTGTTGGTGGG
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+ CAGGGATTACACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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+ CTATGAATAAAGAATTAAAGAAAAT------------------------TATAGGACAAG
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+ TGAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
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+ >test3
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+ -----------------------------------------------------------G
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+ ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
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+ ---ACTAGATTGTACACATCTAGAAGGAAAAATT---------------ATCCTGGTAGC
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+ AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGACAGGA
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+ AACAGCATAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
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+ ATACAGATAATGGCAGTAATTTCA---CCAGTACTACAGTTAAGGCCGCATGCTGGTGGG
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+ CAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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+ CTATGAATAAAGAATTAAAGAAAAT------------------------TATAGGGCAAG
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+ TAAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
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+ >test2
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+ -----------------------------------------------------------G
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+ ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
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+ ---ACTAGATTGCACACATTTAGAAGGAAAAATT---------------ATCCTGGTAGC
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+ AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAGACAGGGAGTGA
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+ AACAGCATAC-------TTCCTCTTAAAGTTGGCAGGAAGATGGCCAGTAAAAACAATAC
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+ ATACAGACAATGGCAGCAATTTCA---CCAGTACTACAGTTAAGGCCGCCTGTTGGTGGG
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+ CAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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+ CTATGAATAAAGAATTAAAGAAGAT------------------------CATAGGACAAG
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+ TAAGAGATCAGGCTGAACAT--CTTAAAACA----------------------
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+ >test4
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+ -----------------------------------------------------------G
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+ ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
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+ ---ACTAGATTGTACACATTTAGAAGGAAAAATT---------------ATCCTGGTAGC
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+ AGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAGAGACAGGGAGTGA
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+ AACAGCACAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
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+ ATACAGACAATGGCAGCAATTTCA---CCAGTGCTACAGTGAAGGCCGCATGCTGGTGGG
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+ CAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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+ CTATGAATAAAGAATTAAAGAAAAT------------------------CATAGGACAAG
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+ TAAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
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+ >test5
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+ ATTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGA
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+ AAATCCATACAATACTCCAGTGTTTGCAATAAAGAAAAAGGACAGTACTAAGTGGAGAAA
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+ ATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAGACTTCTGGGAGGTTCAATTAGG
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+ AATAC-CACACCCGGCAGGGTTAAGAAAGAAAAAATCAGT--AACAGTATTAGATGTGGG
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+ GGATGCATATTTTTCAGTTCCCTTAGATAAAGGGATGGAAAGGATCACCAGCAATATTCC
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+ A-AAGTAGCATGACAAAAATTTTAGAGCCTTTCAGAAAACAAAATCCAGACATAGTTATC
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+ TATCAATACATGGATGACTTGTATGTAGGCTCTGACTTAGAAGTAGAGCAACA-TAGAGC
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+ --AAAAATAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACACCAGACAA-
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+ -AAAGCATCAGAAAGAACCTCCCTTCCATTGGATGGGTTATGAACTCCATCCT
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+ >test6
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+ -------------------------------------------CCTCAAATCACTCTTTG
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+ GCAACGACCCCTCGTCACAGT-----------AAAGATAGGGGG----------------
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+ ---------------TCAGCTAAAGGAG---------------------GCTCTATTAG-
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+ --------------------ATACAGGAGCAGATGATA------------CAGTTTTAGA
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+ AGAAATGTAT-------------------TTGCCAGGAAAATGGAAACCAAAAATGAT--
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+ --AGGGGGAATTGGAGGTTTTATC---AAAGTAAGACAA-TATGATCAGATATTAGTA--
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+ -------------GAAATTTG----TGGACATAAAGCAATAGGTACAGTATTAATAGGAC
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+ CTA----------------------------------------------CACCTGTCAA-
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+ --CATAATTGGAAGAAATCT--GTTGACTCAGATTGGTTGCACTCTAAACTTT
data/sample/sample_seq.fasta ADDED
@@ -0,0 +1,48 @@
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+ >test1
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+ GACAGGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATCTAGAAGGAAAAA
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+ TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGG
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+ AGACAGGACAGGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
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+ CAATACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGT
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+ GGGCAGGGATTACACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
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+ AATCTATGAATAAAGAATTAAAGAAAATTATAGGACAAGTGAGAGATCAGGCTGAACATC
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+ TTAAGACA
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+ >test2
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+ GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGCACACATTTAGAAGGAAAAA
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+ TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAG
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+ AGACAGGGAGTGAAACAGCATACTTCCTCTTAAAGTTGGCAGGAAGATGGCCAGTAAAAA
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+ CAATACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGT
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+ GGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
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+ AATCTATGAATAAAGAATTAAAGAAGATCATAGGACAAGTAAGAGATCAGGCTGAACATC
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+ TTAAAACA
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+ >test3
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+ GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATCTAGAAGGAAAAA
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+ TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAG
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+ AAACAGGACAGGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
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+ CAATACATACAGATAATGGCAGTAATTTCACCAGTACTACAGTTAAGGCCGCATGCTGGT
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+ GGGCAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
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+ AATCTATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGATCAGGCTGAACATC
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+ TTAAGACA
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+ >test4
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+ GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAA
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+ TTATCCTGGTAGCAGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAG
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+ AGACAGGGAGTGAAACAGCACACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
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+ CAATACATACAGACAATGGCAGCAATTTCACCAGTGCTACAGTGAAGGCCGCATGCTGGT
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+ GGGCAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
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+ AATCTATGAATAAAGAATTAAAGAAAATCATAGGACAAGTAAGAGATCAGGCTGAACATC
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+ TTAAGACA
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+ >test5
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+ ATTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGA
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+ AAATCCATACAATACTCCAGTGTTTGCAATAAAGAAAAAGGACAGTACTAAGTGGAGAAA
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+ ATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAGACTTCTGGGAGGTTCAATTAGG
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+ AATACCACACCCGGCAGGGTTAAGAAAGAAAAAATCAGTAACAGTATTAGATGTGGGGGA
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+ TGCATATTTTTCAGTTCCCTTAGATAAAGGGATGGAAAGGATCACCAGCAATATTCCAAA
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+ GTAGCATGACAAAAATTTTAGAGCCTTTCAGAAAACAAAATCCAGACATAGTTATCTATC
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+ AATACATGGATGACTTGTATGTAGGCTCTGACTTAGAAGTAGAGCAACATAGAGCAAAAA
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+ TAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACACCAGACAAAAAGCATC
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+ AGAAAGAACCTCCCTTCCATTGGATGGGTTATGAACTCCATCCT
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+ >test6
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+ CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAGTAAAGATAGGGGGTCAGCTAAAG
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+ GAGGCTCTATTAGATACAGGAGCAGATGATACAGTTTTAGAAGAAATGTATTTGCCAGGA
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+ AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT
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+ CAGATATTAGTAGAAATTTGTGGACATAAAGCAATAGGTACAGTATTAATAGGACCTACA
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+ CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTCTAAACTTT
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 0.1.0
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+ version: 0.2.0
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  platform: ruby
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  authors:
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  - Michael Clark
@@ -52,7 +52,7 @@ 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: ''
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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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  email:
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  - clarkmu@gmail.com
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  executables: []
@@ -65,6 +65,7 @@ files:
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  - ".travis.yml"
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  - CODE_OF_CONDUCT.md
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  - Gemfile
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+ - Gemfile.lock
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  - LICENSE.txt
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  - README.md
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  - Rakefile
@@ -77,7 +78,9 @@ files:
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  - lib/runnable/muscle_mac_64
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  - lib/runnable/muscle_windows_32.exe
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  - muscle_bio.gemspec
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- homepage: ''
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+ - sample/sample_seq.afa
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+ - sample/sample_seq.fasta
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+ homepage: http://swanstrom.web.unc.edu/
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84
  licenses:
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  - MIT
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  metadata: {}
@@ -100,5 +103,5 @@ rubyforge_project:
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  rubygems_version: 2.5.2.3
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  signing_key:
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105
  specification_version: 4
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- summary: ''
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+ summary: Run Muscle from Ruby gem
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  test_files: []