miga-base 0.3.0.5 → 0.3.0.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
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@@ -148,7 +148,10 @@ module MiGA::DatasetResult
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  result_files_exist?(base, ".nomytaxa.txt")
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  r = MiGA::Result.new("#{base}.json")
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  add_files_to_ds_result(r, name, mytaxa:".mytaxa", blast:".blast",
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- mytaxain:".mytaxain", nomytaxa:".nomytaxa.txt")
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+ mytaxain:".mytaxain", nomytaxa:".nomytaxa.txt",
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+ species:".mytaxa.Species.txt", genus:".mytaxa.Genus.txt",
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+ phylum:".mytaxa.Phylum.txt", innominate:".mytaxa.innominate",
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+ kronain:".mytaxa.krona", krona:".html")
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  else
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  MiGA::Result.new("#{base}.json")
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  end
data/lib/miga/version.rb CHANGED
@@ -10,7 +10,7 @@ module MiGA
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  # - Float representing the major.minor version.
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  # - Integer representing gem releases of the current version.
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  # - Integer representing minor changes that require new version number.
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- VERSION = [0.3, 0, 5]
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+ VERSION = [0.3, 0, 6]
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  ##
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  # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
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  ##
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  # Date of the current gem release.
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- VERSION_DATE = Date.new(2017, 7, 8)
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+ VERSION_DATE = Date.new(2017, 8, 24)
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  ##
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  # Reference of MiGA.
@@ -0,0 +1 @@
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+ utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl
@@ -0,0 +1 @@
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+ utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl
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+ utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl
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+ utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl
@@ -0,0 +1 @@
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+ utils/enveomics/Scripts/lib/../../enveomics.R
metadata CHANGED
@@ -1,103 +1,109 @@
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  --- !ruby/object:Gem::Specification
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  name: miga-base
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  version: !ruby/object:Gem::Version
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- version: 0.3.0.5
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+ version: 0.3.0.6
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  platform: ruby
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  authors:
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  - Luis M. Rodriguez-R
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2017-07-08 00:00:00.000000000 Z
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+ date: 2017-08-24 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rest-client
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.7'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.7'
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  - !ruby/object:Gem::Dependency
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  name: daemons
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.2'
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- - - '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 1.2.4
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.2'
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- - - '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 1.2.4
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  - !ruby/object:Gem::Dependency
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  name: json
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - ">"
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  - !ruby/object:Gem::Version
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  version: '1.8'
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+ - - "<"
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+ - !ruby/object:Gem::Version
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+ version: '3'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - ">"
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  - !ruby/object:Gem::Version
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  version: '1.8'
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+ - - "<"
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+ - !ruby/object:Gem::Version
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+ version: '3'
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  - !ruby/object:Gem::Dependency
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  name: sqlite3
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.3'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.3'
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  - !ruby/object:Gem::Dependency
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  name: rake
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '11'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '11'
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  - !ruby/object:Gem::Dependency
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  name: test-unit
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '3'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '3'
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  description: Microbial Genomes Atlas
@@ -108,6 +114,34 @@ extensions: []
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  extra_rdoc_files:
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  - README.md
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  files:
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+ - Gemfile
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+ - LICENSE
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+ - README.md
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+ - Rakefile
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+ - actions/about.rb
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+ - actions/add.rb
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+ - actions/add_result.rb
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+ - actions/daemon.rb
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+ - actions/date.rb
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+ - actions/files.rb
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+ - actions/find.rb
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+ - actions/get.rb
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+ - actions/init.rb
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+ - actions/ln.rb
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+ - actions/ls.rb
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+ - actions/new.rb
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+ - actions/plugins.rb
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+ - actions/rm.rb
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+ - actions/run.rb
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+ - actions/stats.rb
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+ - actions/tax_dist.rb
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+ - actions/tax_index.rb
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+ - actions/tax_set.rb
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+ - actions/tax_test.rb
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+ - bin/miga
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+ - lib/miga.rb
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+ - lib/miga/_data/aai-intax.tsv.gz
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+ - lib/miga/_data/aai-novel.tsv.gz
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  - lib/miga/common.rb
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  - lib/miga/daemon.rb
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  - lib/miga/dataset.rb
@@ -121,18 +155,6 @@ files:
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  - lib/miga/tax_index.rb
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  - lib/miga/taxonomy.rb
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  - lib/miga/version.rb
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- - lib/miga.rb
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- - test/common_test.rb
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- - test/daemon_test.rb
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- - test/dataset_test.rb
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- - test/metadata_test.rb
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- - test/project_test.rb
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- - test/remote_dataset_test.rb
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- - test/tax_index_test.rb
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- - test/taxonomy_test.rb
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- - test/test_helper.rb
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- - lib/miga/_data/aai-intax.tsv.gz
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- - lib/miga/_data/aai-novel.tsv.gz
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  - scripts/_distances_functions.bash
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  - scripts/_distances_noref_nomulti.bash
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  - scripts/_distances_ref_nomulti.bash
@@ -156,74 +178,23 @@ files:
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  - scripts/subclades.bash
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  - scripts/trimmed_fasta.bash
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  - scripts/trimmed_reads.bash
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+ - test/common_test.rb
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+ - test/daemon_test.rb
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+ - test/dataset_test.rb
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+ - test/metadata_test.rb
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+ - test/project_test.rb
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+ - test/remote_dataset_test.rb
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+ - test/tax_index_test.rb
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+ - test/taxonomy_test.rb
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+ - test/test_helper.rb
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  - utils/adapters.fa
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  - utils/core-pan-plot.R
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- - utils/enveomics/build_enveomics_r.bash
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- - utils/enveomics/enveomics.R/data/growth.curves.rda
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- - utils/enveomics/enveomics.R/data/phyla.counts.rda
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- - utils/enveomics/enveomics.R/DESCRIPTION
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- - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
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- - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
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- - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
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- - utils/enveomics/enveomics.R/man/enve.barplot.Rd
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- - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
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- - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
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- - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
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- - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
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- - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
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- - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
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- - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
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- - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
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- - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
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- - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
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- - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
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- - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
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- - utils/enveomics/enveomics.R/man/enve.tribs.Rd
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- - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
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- - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
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- - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
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- - utils/enveomics/enveomics.R/man/growth.curves.Rd
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- - utils/enveomics/enveomics.R/man/phyla.counts.Rd
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- - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
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- - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
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- - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
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- - utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
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- - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
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- - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
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- - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
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- - utils/enveomics/enveomics.R/man/z$-methods.Rd
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- - utils/enveomics/enveomics.R/NAMESPACE
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- - utils/enveomics/enveomics.R/R/autoprune.R
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- - utils/enveomics/enveomics.R/R/barplot.R
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- - utils/enveomics/enveomics.R/R/cliopts.R
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- - utils/enveomics/enveomics.R/R/df2dist.R
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- - utils/enveomics/enveomics.R/R/growthcurve.R
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- - utils/enveomics/enveomics.R/R/recplot.R
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- - utils/enveomics/enveomics.R/R/recplot2.R
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- - utils/enveomics/enveomics.R/R/tribs.R
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- - utils/enveomics/enveomics.R/R/utils.R
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- - utils/enveomics/enveomics.R/README.md
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- - utils/enveomics/Pipelines/assembly.pbs/kSelector.R
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- - utils/enveomics/Pipelines/assembly.pbs/newbler.pbs
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- - utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl
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- - utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash
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  - utils/enveomics/Scripts/BlastTab.addlen.rb
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  - utils/enveomics/Scripts/BlastTab.advance.bash
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  - utils/enveomics/Scripts/BlastTab.pairedHits.rb
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  - utils/enveomics/Scripts/Chao1.pl
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  - utils/enveomics/Scripts/CharTable.classify.rb
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  - utils/enveomics/Scripts/EBIseq2tax.rb
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+ - utils/enveomics/Scripts/FastA.N50.pl
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  - utils/enveomics/Scripts/FastA.filter.pl
306
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  - utils/enveomics/Scripts/FastA.filterLen.pl
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  - utils/enveomics/Scripts/FastA.filterN.pl
@@ -309,7 +280,6 @@ files:
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  - utils/enveomics/Scripts/FastA.gc.pl
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  - utils/enveomics/Scripts/FastA.interpose.pl
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  - utils/enveomics/Scripts/FastA.length.pl
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- - utils/enveomics/Scripts/FastA.N50.pl
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  - utils/enveomics/Scripts/FastA.per_file.pl
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  - utils/enveomics/Scripts/FastA.qlen.pl
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  - utils/enveomics/Scripts/FastA.rename.pl
@@ -326,36 +296,21 @@ files:
326
296
  - utils/enveomics/Scripts/FastQ.tag.rb
327
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  - utils/enveomics/Scripts/FastQ.toFastA.awk
328
298
  - utils/enveomics/Scripts/GenBank.add_fields.rb
329
- - utils/enveomics/Scripts/gi2tax.rb
330
299
  - utils/enveomics/Scripts/HMM.essential.rb
331
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  - utils/enveomics/Scripts/HMMsearch.extractIds.rb
332
- - utils/enveomics/Scripts/in_silico_GA_GI.pl
333
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  - utils/enveomics/Scripts/JPlace.distances.rb
334
302
  - utils/enveomics/Scripts/JPlace.to_iToL.rb
335
- - utils/enveomics/Scripts/lib/data/essential.hmm.gz
336
- - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
337
- - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
338
- - utils/enveomics/Scripts/lib/enveomics_rb/og.rb
339
- - utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
340
- - utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
341
- - utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
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- - utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
343
303
  - utils/enveomics/Scripts/M5nr.getSequences.rb
344
304
  - utils/enveomics/Scripts/MeTaxa.distribution.pl
345
305
  - utils/enveomics/Scripts/MyTaxa.fragsByTax.pl
346
306
  - utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb
347
307
  - utils/enveomics/Scripts/NCBIacc2tax.rb
348
308
  - utils/enveomics/Scripts/Newick.autoprune.R
349
- - utils/enveomics/Scripts/ogs.annotate.rb
350
- - utils/enveomics/Scripts/ogs.core-pan.rb
351
- - utils/enveomics/Scripts/ogs.extract.rb
352
- - utils/enveomics/Scripts/ogs.mcl.rb
353
- - utils/enveomics/Scripts/ogs.rb
354
- - utils/enveomics/Scripts/ogs.stats.rb
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309
  - utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
356
- - utils/enveomics/Scripts/rbm.rb
357
310
  - utils/enveomics/Scripts/RefSeq.download.bash
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311
  - utils/enveomics/Scripts/SRA.download.bash
312
+ - utils/enveomics/Scripts/TRIBS.plot-test.R
313
+ - utils/enveomics/Scripts/TRIBS.test.R
359
314
  - utils/enveomics/Scripts/Table.barplot.R
360
315
  - utils/enveomics/Scripts/Table.df2dist.R
361
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  - utils/enveomics/Scripts/Table.filter.pl
@@ -364,10 +319,37 @@ files:
364
319
  - utils/enveomics/Scripts/Table.round.rb
365
320
  - utils/enveomics/Scripts/Table.split.pl
366
321
  - utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb
367
- - utils/enveomics/Scripts/TRIBS.plot-test.R
368
- - utils/enveomics/Scripts/TRIBS.test.R
369
322
  - utils/enveomics/Scripts/VCF.KaKs.rb
370
323
  - utils/enveomics/Scripts/VCF.SNPs.rb
324
+ - utils/enveomics/Scripts/aai.rb
325
+ - utils/enveomics/Scripts/ani.rb
326
+ - utils/enveomics/Scripts/gi2tax.rb
327
+ - utils/enveomics/Scripts/in_silico_GA_GI.pl
328
+ - utils/enveomics/Scripts/lib/data/essential.hmm.gz
329
+ - utils/enveomics/Scripts/lib/enveomics.R
330
+ - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
331
+ - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
332
+ - utils/enveomics/Scripts/lib/enveomics_rb/og.rb
333
+ - utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
334
+ - utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
335
+ - utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
336
+ - utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
337
+ - utils/enveomics/Scripts/ogs.annotate.rb
338
+ - utils/enveomics/Scripts/ogs.core-pan.rb
339
+ - utils/enveomics/Scripts/ogs.extract.rb
340
+ - utils/enveomics/Scripts/ogs.mcl.rb
341
+ - utils/enveomics/Scripts/ogs.rb
342
+ - utils/enveomics/Scripts/ogs.stats.rb
343
+ - utils/enveomics/Scripts/rbm.rb
344
+ - utils/enveomics/Tests/Makefile
345
+ - utils/enveomics/Tests/Mgen_M2288.faa
346
+ - utils/enveomics/Tests/Mgen_M2288.fna
347
+ - utils/enveomics/Tests/Mgen_M2321.fna
348
+ - utils/enveomics/Tests/Nequ_Kin4M.faa
349
+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
350
+ - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
351
+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
352
+ - utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
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353
  - utils/enveomics/Tests/a_mg.cds-go.blast.tsv
372
354
  - utils/enveomics/Tests/a_mg.reads-cds.blast.tsv
373
355
  - utils/enveomics/Tests/a_mg.reads-cds.counts.tsv
@@ -380,11 +362,6 @@ files:
380
362
  - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv
381
363
  - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim
382
364
  - utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec
383
- - utils/enveomics/Tests/Makefile
384
- - utils/enveomics/Tests/Mgen_M2288.faa
385
- - utils/enveomics/Tests/Mgen_M2288.fna
386
- - utils/enveomics/Tests/Mgen_M2321.fna
387
- - utils/enveomics/Tests/Nequ_Kin4M.faa
388
365
  - utils/enveomics/Tests/phyla_counts.tsv
389
366
  - utils/enveomics/Tests/primate_lentivirus.ogs
390
367
  - utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm
@@ -393,10 +370,65 @@ files:
393
370
  - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm
394
371
  - utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm
395
372
  - utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm
396
- - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata
397
- - utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt
398
- - utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv
399
- - utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv
373
+ - utils/enveomics/build_enveomics_r.bash
374
+ - utils/enveomics/enveomics.R/DESCRIPTION
375
+ - utils/enveomics/enveomics.R/NAMESPACE
376
+ - utils/enveomics/enveomics.R/R/autoprune.R
377
+ - utils/enveomics/enveomics.R/R/barplot.R
378
+ - utils/enveomics/enveomics.R/R/cliopts.R
379
+ - utils/enveomics/enveomics.R/R/df2dist.R
380
+ - utils/enveomics/enveomics.R/R/growthcurve.R
381
+ - utils/enveomics/enveomics.R/R/recplot.R
382
+ - utils/enveomics/enveomics.R/R/recplot2.R
383
+ - utils/enveomics/enveomics.R/R/tribs.R
384
+ - utils/enveomics/enveomics.R/R/utils.R
385
+ - utils/enveomics/enveomics.R/README.md
386
+ - utils/enveomics/enveomics.R/data/growth.curves.rda
387
+ - utils/enveomics/enveomics.R/data/phyla.counts.rda
388
+ - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
389
+ - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
390
+ - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
391
+ - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
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+ - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
393
+ - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
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+ - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
395
+ - utils/enveomics/enveomics.R/man/enve.barplot.Rd
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+ - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
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+ - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
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+ - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
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+ - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
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+ - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
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+ - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
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+ - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
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+ - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
404
+ - utils/enveomics/enveomics.R/man/enve.recplot.Rd
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+ - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
406
+ - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
407
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
408
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
409
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
410
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
411
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
412
+ - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
413
+ - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
414
+ - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
415
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
416
+ - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
417
+ - utils/enveomics/enveomics.R/man/enve.tribs.Rd
418
+ - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
419
+ - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
420
+ - utils/enveomics/enveomics.R/man/growth.curves.Rd
421
+ - utils/enveomics/enveomics.R/man/phyla.counts.Rd
422
+ - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
423
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
424
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd
425
+ - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
426
+ - utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd
427
+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd
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+ - utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd
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+ - utils/enveomics/enveomics.R/man/z$-methods.Rd
430
+ - utils/enveomics/globals.mk
431
+ - utils/enveomics/manifest.json
400
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  - utils/index_metadata.rb
401
433
  - utils/mytaxa_scan.R
402
434
  - utils/mytaxa_scan.rb
@@ -406,31 +438,6 @@ files:
406
438
  - utils/subclades-compile.rb
407
439
  - utils/subclades-nj.R
408
440
  - utils/subclades.R
409
- - bin/miga
410
- - actions/about.rb
411
- - actions/add.rb
412
- - actions/add_result.rb
413
- - actions/daemon.rb
414
- - actions/date.rb
415
- - actions/files.rb
416
- - actions/find.rb
417
- - actions/get.rb
418
- - actions/init.rb
419
- - actions/ln.rb
420
- - actions/ls.rb
421
- - actions/new.rb
422
- - actions/plugins.rb
423
- - actions/rm.rb
424
- - actions/run.rb
425
- - actions/stats.rb
426
- - actions/tax_dist.rb
427
- - actions/tax_index.rb
428
- - actions/tax_set.rb
429
- - actions/tax_test.rb
430
- - Gemfile
431
- - Rakefile
432
- - README.md
433
- - LICENSE
434
441
  homepage: http://enve-omics.ce.gatech.edu/miga
435
442
  licenses:
436
443
  - Artistic-2.0
@@ -439,25 +446,25 @@ post_install_message:
439
446
  rdoc_options:
440
447
  - lib
441
448
  - README.md
442
- - --main
449
+ - "--main"
443
450
  - README.md
444
- - --title
451
+ - "--title"
445
452
  - MiGA
446
453
  require_paths:
447
454
  - lib
448
455
  required_ruby_version: !ruby/object:Gem::Requirement
449
456
  requirements:
450
- - - '>='
457
+ - - ">="
451
458
  - !ruby/object:Gem::Version
452
459
  version: '1.9'
453
460
  required_rubygems_version: !ruby/object:Gem::Requirement
454
461
  requirements:
455
- - - '>='
462
+ - - ">="
456
463
  - !ruby/object:Gem::Version
457
464
  version: '0'
458
465
  requirements: []
459
466
  rubyforge_project:
460
- rubygems_version: 2.0.14
467
+ rubygems_version: 2.6.11
461
468
  signing_key:
462
469
  specification_version: 4
463
470
  summary: MiGA
@@ -1,56 +0,0 @@
1
- #!/usr/bin/env perl
2
- #
3
- # @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
4
- # @update: Oct 07 2015
5
- # @license: artistic license 2.0
6
- #
7
- use strict;
8
- use warnings;
9
- use List::Util qw/sum min max/;
10
-
11
- my ($seqs, $minlen, $n__) = @ARGV;
12
- $seqs or die "
13
- Description:
14
- Calculates the N50 value of a set of sequences. Alternatively, it
15
- can calculate other N** values. It also calculates the total number
16
- of sequences and the total added length.
17
-
18
- Usage:
19
- $0 seqs.fa[ minlen[ **]]
20
-
21
- seqs.fa A FastA file containing the sequences.
22
- minlen (optional) The minimum length to take into consideration.
23
- By default: 0.
24
- ** Value N** to calculate. By default: 50 (N50).
25
- ";
26
- $minlen ||= 0;
27
- $n__ ||= 50;
28
-
29
- my @len = ();
30
- open SEQ, "<", $seqs or die "Cannot open file: $seqs: $!\n";
31
- while(<SEQ>){
32
- if(/^>/){
33
- push @len, 0;
34
- }else{
35
- next if /^;/;
36
- chomp;
37
- s/\W//g;
38
- $len[-1]+=length $_;
39
- }
40
- }
41
- close SEQ;
42
- @len = sort { $a <=> $b } map { $_>=$minlen?$_:() } @len;
43
- my $tot = (sum(@len) || 0);
44
-
45
- my $thr = $n__*$tot/100;
46
- my $pos = 0;
47
- for(@len){
48
- $pos+= $_;
49
- if($pos>=$thr){
50
- print "N$n__: $_\n";
51
- last;
52
- }
53
- }
54
- print "Sequences: ".scalar(@len)."\n";
55
- print "Total length: $tot\n";
56
-
@@ -1,60 +0,0 @@
1
- #!/usr/bin/env perl
2
- #
3
- # @author Luis M. Rodriguez-R
4
- # @update Oct-07-2015
5
- # @license artistic license 2.0
6
- #
7
-
8
- use warnings;
9
- use strict;
10
-
11
- my($file, $content, $stretch) = @ARGV;
12
- $file or die <<HELP
13
-
14
- Description:
15
- Filter sequences by N-content and presence of long homopolymers.
16
- Usage:
17
- $0 sequences.fa [content [stretch]] > filtered.fa
18
- Where:
19
- sequences.fa Input file in FastA format
20
- content A number between 0 and 1 indicating the maximum proportion of Ns
21
- (1 to turn off, 0.5 by default)
22
- stretch A number indicating the maximum number of consecutive identical
23
- nucleotides allowed (0 to turn off, 100 by default)
24
- filtered.fa Filtered set of sequences.
25
-
26
- HELP
27
- ;
28
- ($content ||= 0.5)+=0;
29
- ($stretch ||= 100)+=0;
30
-
31
- my $good = 0;
32
- my $N = 0;
33
-
34
- FASTA: {
35
- local $/ = "\n>";
36
- open FILE, "<", $file or die "I can not open the file: $file: $!\n";
37
- SEQ: while(<FILE>){
38
- $N++;
39
- s/^;.*//gm;
40
- s/>//g;
41
- my($n,$s) = split /\n/, $_, 2;
42
- (my $clean = $s) =~ s/[^ACTGN]//g;
43
- if($content < 1){
44
- (my $Ns = $clean) =~ s/[^N]//g;
45
- next SEQ if length($Ns)>length($clean)*$content;
46
- }
47
- if($stretch > 0){
48
- for my $nuc (qw(A C T G N)){
49
- next SEQ if $clean =~ m/[$nuc]{$stretch}/;
50
- }
51
- }
52
- print ">$n\n$s\n";
53
- $good++;
54
- }
55
- close FILE;
56
- print STDERR "Total sequences: $N\nAfter filtering: $good\n";
57
- }
58
-
59
-
60
-
@@ -1,38 +0,0 @@
1
- #!/usr/bin/env perl
2
- #
3
- # @author Luis M Rodriguez-R
4
- # @update Oct-07-2015
5
- # @license artistic license 2.0
6
- #
7
-
8
- use warnings;
9
- use strict;
10
-
11
- $#ARGV>=0 or die "
12
- Usage:
13
- $0 seqs.fa... > length.txt
14
-
15
- seqs.fa One or more FastA files.
16
- length.txt A table with the lengths of the sequences.
17
-
18
- ";
19
-
20
- for my $fa (@ARGV){
21
- open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
22
- my $def = '';
23
- my $len = 0;
24
- while(<FA>){
25
- next if /^;/;
26
- if(m/^>(\S+)\s?/){
27
- print "$def\t$len\n" if $def;
28
- $def = $1;
29
- $len = 0;
30
- }else{
31
- s/[^A-Za-z]//g;
32
- $len+= length $_;
33
- }
34
- }
35
- print "$def\t$len\n" if $def;
36
- close FA;
37
- }
38
-
@@ -1,55 +0,0 @@
1
- #!/usr/bin/env perl
2
- #
3
- # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
4
- # @update Oct-13-2015
5
- # @license artistic license 2.0
6
- #
7
-
8
- use warnings;
9
- use strict;
10
- use Symbol;
11
-
12
- my ($file, $base, $outN) = @ARGV;
13
-
14
- $outN ||= 12;
15
- ($file and $base) or die "
16
- Usage
17
- $0 in_file.fa out_base[ no_files]
18
-
19
- in_file.fa Input file in FastA format.
20
- out_base Prefix for the name of the output files. It will
21
- be appended with .<i>.fa, where <i> is a consecutive
22
- number starting in 1.
23
- no_files Number of files to generate. By default: 12.
24
-
25
- ";
26
-
27
-
28
- my @outSym = ();
29
- for my $i (1 .. $outN){
30
- $outSym[$i-1] = gensym;
31
- open $outSym[$i-1], ">", "$base.$i.fa" or
32
- die "I can not create the file: $base.$i.fa: $!\n";
33
- }
34
-
35
-
36
- my($i, $seq) = (-1, '');
37
- open FILE, "<", $file or die "I can not read the file: $file: $!\n";
38
- while(my $ln=<FILE>){
39
- next if $ln=~/^;/;
40
- if($ln =~ m/^>/){
41
- print { $outSym[$i % $outN] } $seq if $seq;
42
- $i++;
43
- $seq = '';
44
- }
45
- $seq.=$ln;
46
- }
47
- print { $outSym[$i % $outN] } $seq if $seq;
48
- close FILE;
49
-
50
- for(my $j=0; $j<$outN; $j++){
51
- close $outSym[$j];
52
- }
53
-
54
- print STDERR "Sequences: ".($i+1)."\nFiles: $outN\n";
55
-