muscle_bio 0.1.0 → 0.2.0
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- checksums.yaml +4 -4
- data/.DS_Store +0 -0
- data/Gemfile.lock +35 -0
- data/lib/muscle_bio.rb +5 -16
- data/lib/muscle_bio/version.rb +1 -1
- data/muscle_bio.gemspec +3 -3
- data/sample/sample_seq.afa +60 -0
- data/sample/sample_seq.fasta +48 -0
- metadata +7 -4
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 27aa0358df79d390e3ca21f2dd17b76057528b5e
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data.tar.gz: ed573ec60398e0b2af16edafeec7125c5876832e
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 5d2d0fdf747ea6de8fb8aed3d19c9885396ef2b25d2190c05f2ab81515a2fca4dd86c0240bed8f69c8fc6603f92ee58edd3c928e8ae728cde1e811c1cc54131a
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7
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data.tar.gz: 25cf67384b8d0154484238f9ae40631ad7c0cb43861b6ebb76ab8ce1e4727a28aef40ab6ebcd769249260195d2d00af5b4057d86b40f880bba34342dc3ef4b7c
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data/.DS_Store
CHANGED
Binary file
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data/Gemfile.lock
ADDED
@@ -0,0 +1,35 @@
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1
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PATH
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remote: .
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specs:
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4
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muscle_bio (0.1.0)
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5
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+
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6
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GEM
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7
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remote: https://rubygems.org/
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specs:
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9
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diff-lcs (1.3)
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10
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rake (10.4.2)
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11
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rspec (3.8.0)
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12
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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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PLATFORMS
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ruby
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+
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28
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DEPENDENCIES
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29
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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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35
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+
2.0.1
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data/lib/muscle_bio.rb
CHANGED
@@ -1,26 +1,15 @@
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1
1
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require "muscle_bio/version"
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2
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3
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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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7
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-
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8
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if (/darwin/ =~ RUBY_PLATFORM) != nil
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9
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file = "muscle_mac_64"
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10
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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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12
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-
else
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file = "muscle_linux_64"
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-
end
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15
4
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5
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+
def self.run(cmd)
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6
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file = (/darwin/ =~ RUBY_PLATFORM) != nil ? "muscle_mac_64" :
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7
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(/cygwin|mswin|mingw|bccwin|wince|emx/ =~ RUBY_PLATFORM) != nil ? "muscle_windows_32.exe" : "muscle_linux_64"
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16
8
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file = File.join( File.dirname(__FILE__), 'runnable/'+file)
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-
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9
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cmd = cmd.sub 'sudo ', ''
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10
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cmd = cmd.sub 'muscle', file
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-
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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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12
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`#{cmd}`
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25
13
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end
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+
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15
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end
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data/lib/muscle_bio/version.rb
CHANGED
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.
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@@ -0,0 +1,60 @@
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1
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>test1
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2
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-----------------------------------------------------------G
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3
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ACAGGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
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4
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---ACTAGATTGTACACATCTAGAAGGAAAAATT---------------ATCCTGGTAGC
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5
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+
AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGGAGACAGGACAGGA
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6
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+
AACAGCATAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
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7
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+
ATACAGACAATGGCAGCAATTTCA---CCAGTACTACAGTTAAGGCCGCCTGTTGGTGGG
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8
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CAGGGATTACACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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9
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+
CTATGAATAAAGAATTAAAGAAAAT------------------------TATAGGACAAG
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10
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TGAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
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11
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>test3
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12
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+
-----------------------------------------------------------G
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13
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+
ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
|
14
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+
---ACTAGATTGTACACATCTAGAAGGAAAAATT---------------ATCCTGGTAGC
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15
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+
AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGACAGGA
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16
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+
AACAGCATAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
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17
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+
ATACAGATAATGGCAGTAATTTCA---CCAGTACTACAGTTAAGGCCGCATGCTGGTGGG
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18
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+
CAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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19
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+
CTATGAATAAAGAATTAAAGAAAAT------------------------TATAGGGCAAG
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20
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+
TAAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
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21
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+
>test2
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22
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+
-----------------------------------------------------------G
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23
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+
ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
|
24
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+
---ACTAGATTGCACACATTTAGAAGGAAAAATT---------------ATCCTGGTAGC
|
25
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+
AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAGACAGGGAGTGA
|
26
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+
AACAGCATAC-------TTCCTCTTAAAGTTGGCAGGAAGATGGCCAGTAAAAACAATAC
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27
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+
ATACAGACAATGGCAGCAATTTCA---CCAGTACTACAGTTAAGGCCGCCTGTTGGTGGG
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28
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+
CAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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29
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+
CTATGAATAAAGAATTAAAGAAGAT------------------------CATAGGACAAG
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30
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+
TAAGAGATCAGGCTGAACAT--CTTAAAACA----------------------
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31
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>test4
|
32
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+
-----------------------------------------------------------G
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33
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ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
|
34
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+
---ACTAGATTGTACACATTTAGAAGGAAAAATT---------------ATCCTGGTAGC
|
35
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+
AGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAGAGACAGGGAGTGA
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36
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+
AACAGCACAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
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37
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+
ATACAGACAATGGCAGCAATTTCA---CCAGTGCTACAGTGAAGGCCGCATGCTGGTGGG
|
38
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+
CAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
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39
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+
CTATGAATAAAGAATTAAAGAAAAT------------------------CATAGGACAAG
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40
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+
TAAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
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41
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+
>test5
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42
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+
ATTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGA
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43
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AAATCCATACAATACTCCAGTGTTTGCAATAAAGAAAAAGGACAGTACTAAGTGGAGAAA
|
44
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+
ATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAGACTTCTGGGAGGTTCAATTAGG
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45
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+
AATAC-CACACCCGGCAGGGTTAAGAAAGAAAAAATCAGT--AACAGTATTAGATGTGGG
|
46
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+
GGATGCATATTTTTCAGTTCCCTTAGATAAAGGGATGGAAAGGATCACCAGCAATATTCC
|
47
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+
A-AAGTAGCATGACAAAAATTTTAGAGCCTTTCAGAAAACAAAATCCAGACATAGTTATC
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48
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+
TATCAATACATGGATGACTTGTATGTAGGCTCTGACTTAGAAGTAGAGCAACA-TAGAGC
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49
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+
--AAAAATAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACACCAGACAA-
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50
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+
-AAAGCATCAGAAAGAACCTCCCTTCCATTGGATGGGTTATGAACTCCATCCT
|
51
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+
>test6
|
52
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+
-------------------------------------------CCTCAAATCACTCTTTG
|
53
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GCAACGACCCCTCGTCACAGT-----------AAAGATAGGGGG----------------
|
54
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+
---------------TCAGCTAAAGGAG---------------------GCTCTATTAG-
|
55
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+
--------------------ATACAGGAGCAGATGATA------------CAGTTTTAGA
|
56
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+
AGAAATGTAT-------------------TTGCCAGGAAAATGGAAACCAAAAATGAT--
|
57
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+
--AGGGGGAATTGGAGGTTTTATC---AAAGTAAGACAA-TATGATCAGATATTAGTA--
|
58
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+
-------------GAAATTTG----TGGACATAAAGCAATAGGTACAGTATTAATAGGAC
|
59
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+
CTA----------------------------------------------CACCTGTCAA-
|
60
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+
--CATAATTGGAAGAAATCT--GTTGACTCAGATTGGTTGCACTCTAAACTTT
|
@@ -0,0 +1,48 @@
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1
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+
>test1
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2
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+
GACAGGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATCTAGAAGGAAAAA
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3
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+
TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGG
|
4
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+
AGACAGGACAGGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
|
5
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+
CAATACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGT
|
6
|
+
GGGCAGGGATTACACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
|
7
|
+
AATCTATGAATAAAGAATTAAAGAAAATTATAGGACAAGTGAGAGATCAGGCTGAACATC
|
8
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+
TTAAGACA
|
9
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+
>test2
|
10
|
+
GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGCACACATTTAGAAGGAAAAA
|
11
|
+
TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAG
|
12
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+
AGACAGGGAGTGAAACAGCATACTTCCTCTTAAAGTTGGCAGGAAGATGGCCAGTAAAAA
|
13
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+
CAATACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGT
|
14
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+
GGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
|
15
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+
AATCTATGAATAAAGAATTAAAGAAGATCATAGGACAAGTAAGAGATCAGGCTGAACATC
|
16
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+
TTAAAACA
|
17
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+
>test3
|
18
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+
GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATCTAGAAGGAAAAA
|
19
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+
TTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAG
|
20
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+
AAACAGGACAGGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
|
21
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+
CAATACATACAGATAATGGCAGTAATTTCACCAGTACTACAGTTAAGGCCGCATGCTGGT
|
22
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+
GGGCAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
|
23
|
+
AATCTATGAATAAAGAATTAAAGAAAATTATAGGGCAAGTAAGAGATCAGGCTGAACATC
|
24
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+
TTAAGACA
|
25
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+
>test4
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26
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+
GACAAGTAGACTGTAGCCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAA
|
27
|
+
TTATCCTGGTAGCAGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAG
|
28
|
+
AGACAGGGAGTGAAACAGCACACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAA
|
29
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+
CAATACATACAGACAATGGCAGCAATTTCACCAGTGCTACAGTGAAGGCCGCATGCTGGT
|
30
|
+
GGGCAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAG
|
31
|
+
AATCTATGAATAAAGAATTAAAGAAAATCATAGGACAAGTAAGAGATCAGGCTGAACATC
|
32
|
+
TTAAGACA
|
33
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+
>test5
|
34
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+
ATTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGA
|
35
|
+
AAATCCATACAATACTCCAGTGTTTGCAATAAAGAAAAAGGACAGTACTAAGTGGAGAAA
|
36
|
+
ATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAGACTTCTGGGAGGTTCAATTAGG
|
37
|
+
AATACCACACCCGGCAGGGTTAAGAAAGAAAAAATCAGTAACAGTATTAGATGTGGGGGA
|
38
|
+
TGCATATTTTTCAGTTCCCTTAGATAAAGGGATGGAAAGGATCACCAGCAATATTCCAAA
|
39
|
+
GTAGCATGACAAAAATTTTAGAGCCTTTCAGAAAACAAAATCCAGACATAGTTATCTATC
|
40
|
+
AATACATGGATGACTTGTATGTAGGCTCTGACTTAGAAGTAGAGCAACATAGAGCAAAAA
|
41
|
+
TAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACACCAGACAAAAAGCATC
|
42
|
+
AGAAAGAACCTCCCTTCCATTGGATGGGTTATGAACTCCATCCT
|
43
|
+
>test6
|
44
|
+
CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAGTAAAGATAGGGGGTCAGCTAAAG
|
45
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+
GAGGCTCTATTAGATACAGGAGCAGATGATACAGTTTTAGAAGAAATGTATTTGCCAGGA
|
46
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+
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT
|
47
|
+
CAGATATTAGTAGAAATTTGTGGACATAAAGCAATAGGTACAGTATTAATAGGACCTACA
|
48
|
+
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTCTAAACTTT
|
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: muscle_bio
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
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+
version: 0.2.0
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Michael Clark
|
@@ -52,7 +52,7 @@ dependencies:
|
|
52
52
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- - "~>"
|
53
53
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- !ruby/object:Gem::Version
|
54
54
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version: '3.0'
|
55
|
-
description:
|
55
|
+
description: Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/
|
56
56
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email:
|
57
57
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- clarkmu@gmail.com
|
58
58
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executables: []
|
@@ -65,6 +65,7 @@ files:
|
|
65
65
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- ".travis.yml"
|
66
66
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- CODE_OF_CONDUCT.md
|
67
67
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- Gemfile
|
68
|
+
- Gemfile.lock
|
68
69
|
- LICENSE.txt
|
69
70
|
- README.md
|
70
71
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- Rakefile
|
@@ -77,7 +78,9 @@ files:
|
|
77
78
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- lib/runnable/muscle_mac_64
|
78
79
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- lib/runnable/muscle_windows_32.exe
|
79
80
|
- muscle_bio.gemspec
|
80
|
-
|
81
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+
- sample/sample_seq.afa
|
82
|
+
- sample/sample_seq.fasta
|
83
|
+
homepage: http://swanstrom.web.unc.edu/
|
81
84
|
licenses:
|
82
85
|
- MIT
|
83
86
|
metadata: {}
|
@@ -100,5 +103,5 @@ rubyforge_project:
|
|
100
103
|
rubygems_version: 2.5.2.3
|
101
104
|
signing_key:
|
102
105
|
specification_version: 4
|
103
|
-
summary:
|
106
|
+
summary: Run Muscle from Ruby gem
|
104
107
|
test_files: []
|