muscle_bio 0.4.0 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 8836c15a40b87918d321842dea3a197ba82f9d15
-  data.tar.gz: 8f4bdc93effa4fdce1fddeda15396dd1185bd8b7
+SHA256:
+  metadata.gz: b9bddb09f6263aafe70d7212d7b44b2340c68f8bc097ea8136761951f073ed9d
+  data.tar.gz: 50c6af382b99e721b3640c45e2b5cd293bff404ec3cfa627e986d30ef2f4194f
 SHA512:
-  metadata.gz: d5f881d227141eafda1e9d1f3f77adc0b7b7d7b19da1f94cb50ce4a203a66ecc30ab73d6d0d2fd768d44cade9c4e634756b513f6326f0b3b962d8308182baf9c
-  data.tar.gz: e9db0d200636a410c095fffdc89e2610967b4b4b52bb25f8a556c3bd925d7c84b19fd1c98897f0884b4f9c5a529b79e0103e60e6a692a96dec70cb141bb54a69
+  metadata.gz: eab1345502bcf4f7dc1650309bf8022bed9156535e34815a70ac4ca1da2f210989527ef85b136d8f52383fd1f07971a93ba60761cefad43d0b0472246f632f87
+  data.tar.gz: a15e9eb67ef7da31d0161cbd6cc5b5bd02f10779a7ff3580da2fc57f8335be688bf7b8f219ab6167e21a62b4e01976c8a7c553818ffab8f8e91a7c1ba70cb064

data/.gitignore

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

data/Gemfile.lock

@@ -1,13 +1,13 @@
 PATH
   remote: .
   specs:
-    muscle_bio (0.3.0)
+    muscle_bio (0.5.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
     diff-lcs (1.3)
-    rake (10.4.2)
+    rake (13.0.1)
     rspec (3.8.0)
       rspec-core (~> 3.8.0)
       rspec-expectations (~> 3.8.0)
@@ -28,8 +28,8 @@ PLATFORMS
 DEPENDENCIES
   bundler (~> 2.0)
   muscle_bio!
-  rake (~> 10.0)
+  rake (~> 13.0)
   rspec (~> 3.0)
 
 BUNDLED WITH
-   2.0.1
+   2.2.32

data/README.md

@@ -1,6 +1,6 @@
 # MuscleBio
 
-Supported on Mac, Linux, and Windows.
+Supported on Mac-Intel64, Mac-AMR64, Linux, and Windows. Support Muscle 5.1.
 
 ## Installation
 
@@ -20,13 +20,16 @@ Or install it yourself as:
 
 ## Usage
 
+```{ruby}
 require 'muscle_bio'
 
-MuscleBio.run('muscle -in ../sample/sequence.fasta -out ../sample/sequence.afa')
-
-#pass string in as your current Muscle command
-
-
-MuscleBio.init(fileIn, fileOut, maxIters)
+MuscleBio.exec(
+               '/sample/sequence.fasta', # input file
+               '/sample/sequence.afa', # output file
+               :PPP # choose from :PPP or :Super5
+               )
+```
 
-#maxIters is optional
+### 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 = "0.4.0"
+  VERSION = "0.5.0"
 end

data/lib/muscle_bio.rb

@@ -2,25 +2,33 @@ require "muscle_bio/version"
 
 module MuscleBio
 
-  def self.run(cmd, useSudo = false)
-  	file = (/darwin/ =~ RUBY_PLATFORM) != nil ? "muscle_mac_64" :
-  		(/cygwin|mswin|mingw|bccwin|wince|emx/ =~ RUBY_PLATFORM) != nil ? "muscle_windows_32.exe" : "muscle_linux_64"
-  	file = File.join( File.dirname(__FILE__), 'runnable/'+file)
-  	cmd = cmd.sub 'sudo ', ''
-  	cmd = cmd.sub 'muscle', file
-  	cmd = cmd + " -quiet"
-    if useSudo
-      cmd = 'sudo ' + cmd
+  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
-	`#{cmd}`
+
+  	file = File.join( File.dirname(__FILE__), 'runnable/'+file)
+  	cmd = file + "\s" + cmd + " -quiet"
+	  `#{cmd}`
   end
 
-  def self.init(fileIn, fileOut, maxIters = nil)
-  	cmd = "muscle -in " + fileIn + " -out " + fileOut
-  	if maxIters != nil
-  		cmd += " -maxiters " + maxIters
-  	end
+  ### 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

@@ -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

@@ -1,60 +1,48 @@
->test1
------------------------------------------------------------G
-ACAGGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
----ACTAGATTGTACACATCTAGAAGGAAAAATT---------------ATCCTGGTAGC
-AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCGGAGACAGGACAGGA
-AACAGCATAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
-ATACAGACAATGGCAGCAATTTCA---CCAGTACTACAGTTAAGGCCGCCTGTTGGTGGG
-CAGGGATTACACAGGAATTTGGTATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
-CTATGAATAAAGAATTAAAGAAAAT------------------------TATAGGACAAG
-TGAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
->test3
------------------------------------------------------------G
-ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
----ACTAGATTGTACACATCTAGAAGGAAAAATT---------------ATCCTGGTAGC
-AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGACAGGA
-AACAGCATAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
-ATACAGATAATGGCAGTAATTTCA---CCAGTACTACAGTTAAGGCCGCATGCTGGTGGG
-CAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
-CTATGAATAAAGAATTAAAGAAAAT------------------------TATAGGGCAAG
-TAAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
->test2
------------------------------------------------------------G
-ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
----ACTAGATTGCACACATTTAGAAGGAAAAATT---------------ATCCTGGTAGC
-AGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAGACAGGGAGTGA
-AACAGCATAC-------TTCCTCTTAAAGTTGGCAGGAAGATGGCCAGTAAAAACAATAC
-ATACAGACAATGGCAGCAATTTCA---CCAGTACTACAGTTAAGGCCGCCTGTTGGTGGG
-CAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
-CTATGAATAAAGAATTAAAGAAGAT------------------------CATAGGACAAG
-TAAGAGATCAGGCTGAACAT--CTTAAAACA----------------------
->test4
------------------------------------------------------------G
-ACAAGTAGACTGTAGCCCA--------------GGAATATGGCA----------------
----ACTAGATTGTACACATTTAGAAGGAAAAATT---------------ATCCTGGTAGC
-AGTACATGTAGCCAGTGGATACATAGAAGCAGAAGTTATTCCAGCAGAGACAGGGAGTGA
-AACAGCACAC-------TTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATAC
-ATACAGACAATGGCAGCAATTTCA---CCAGTGCTACAGTGAAGGCCGCATGCTGGTGGG
-CAGGGATCAAACAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAAT
-CTATGAATAAAGAATTAAAGAAAAT------------------------CATAGGACAAG
-TAAGAGATCAGGCTGAACAT--CTTAAGACA----------------------
 >test5
-ATTAGTAGAAATTTGTGCAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGA
-AAATCCATACAATACTCCAGTGTTTGCAATAAAGAAAAAGGACAGTACTAAGTGGAGAAA
-ATTAGTAGATTTTAGAGAACTGAATAAGAAAACTCAAGACTTCTGGGAGGTTCAATTAGG
-AATAC-CACACCCGGCAGGGTTAAGAAAGAAAAAATCAGT--AACAGTATTAGATGTGGG
-GGATGCATATTTTTCAGTTCCCTTAGATAAAGGGATGGAAAGGATCACCAGCAATATTCC
-A-AAGTAGCATGACAAAAATTTTAGAGCCTTTCAGAAAACAAAATCCAGACATAGTTATC
-TATCAATACATGGATGACTTGTATGTAGGCTCTGACTTAGAAGTAGAGCAACA-TAGAGC
---AAAAATAGAGAACCTAAGAGAACATCTGTTGAAGTGGGGACTTACTACACCAGACAA-
--AAAGCATCAGAAAGAACCTCCCTTCCATTGGATGGGTTATGAACTCCATCCT
+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
--------------------------------------------CCTCAAATCACTCTTTG
-GCAACGACCCCTCGTCACAGT-----------AAAGATAGGGGG----------------
----------------TCAGCTAAAGGAG---------------------GCTCTATTAG-
---------------------ATACAGGAGCAGATGATA------------CAGTTTTAGA
-AGAAATGTAT-------------------TTGCCAGGAAAATGGAAACCAAAAATGAT--
---AGGGGGAATTGGAGGTTTTATC---AAAGTAAGACAA-TATGATCAGATATTAGTA--
--------------GAAATTTG----TGGACATAAAGCAATAGGTACAGTATTAATAGGAC
-CTA----------------------------------------------CACCTGTCAA-
---CATAATTGGAAGAAATCT--GTTGACTCAGATTGGTTGCACTCTAAACTTT
+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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: muscle_bio
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
 platform: ruby
 authors:
 - Michael Clark
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2019-06-21 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
@@ -75,9 +75,10 @@ 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
 - sample/sample_seq.afa
 - sample/sample_seq.fasta
@@ -85,7 +86,7 @@ homepage: http://swanstrom.web.unc.edu/
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -100,9 +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: Run Muscle from Ruby gem
 test_files: []