lsa 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: aeb489df0e1e3be796a50a6ed5f44267da76fcdc
+  data.tar.gz: 03a46fe4c0aee315d155a076026655d42e91f434
+SHA512:
+  metadata.gz: 74f92994363b2f3232f22caf4c951970238ce062b40a0044d4ec946fbe51a5c6190c3904678c3d1f2c4f6866c972fde3afd2debd81a15076840a53cd9ff0ebe3
+  data.tar.gz: 18e4792725af47610fcb0f443ca22389ebea7c6b4414c580b41ca5854094074134ed80efca572e9a65e57caf5465fc8b5d189e6339d021696f41a0f1359ad9b3

data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color

data/.ruby-gemset

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+lsa

data/.ruby-version

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+ruby-2.4.1

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.4.1
+before_install: gem install bundler -v 1.15.1

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at moorer@udel.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

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+source "https://rubygems.org"
+
+# Specify your gem's dependencies in lsa.gemspec
+gemspec

data/Guardfile

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+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+## Uncomment and set this to only include directories you want to watch
+# directories %w(app lib config test spec features) \
+#  .select{|d| Dir.exists?(d) ? d : UI.warning("Directory #{d} does not exist")}
+
+## Note: if you are using the `directories` clause above and you are not
+## watching the project directory ('.'), then you will want to move
+## the Guardfile to a watched dir and symlink it back, e.g.
+#
+#  $ mkdir config
+#  $ mv Guardfile config/
+#  $ ln -s config/Guardfile .
+#
+# and, you'll have to watch "config/Guardfile" instead of "Guardfile"
+
+# Note: The cmd option is now required due to the increasing number of ways
+#       rspec may be run, below are examples of the most common uses.
+#  * bundler: 'bundle exec rspec'
+#  * bundler binstubs: 'bin/rspec'
+#  * spring: 'bin/rspec' (This will use spring if running and you have
+#                          installed the spring binstubs per the docs)
+#  * zeus: 'zeus rspec' (requires the server to be started separately)
+#  * 'just' rspec: 'rspec'
+
+guard :rspec, cmd: "bundle exec rspec" do
+  require "guard/rspec/dsl"
+  dsl = Guard::RSpec::Dsl.new(self)
+
+  # Feel free to open issues for suggestions and improvements
+
+  # RSpec files
+  rspec = dsl.rspec
+  watch(rspec.spec_helper) { rspec.spec_dir }
+  watch(rspec.spec_support) { rspec.spec_dir }
+  watch(rspec.spec_files)
+
+  # Ruby files
+  ruby = dsl.ruby
+  dsl.watch_spec_files_for(ruby.lib_files)
+
+  # Rails files
+  rails = dsl.rails(view_extensions: %w(erb haml slim))
+  dsl.watch_spec_files_for(rails.app_files)
+  dsl.watch_spec_files_for(rails.views)
+
+  watch(rails.controllers) do |m|
+    [
+      rspec.spec.call("routing/#{m[1]}_routing"),
+      rspec.spec.call("controllers/#{m[1]}_controller"),
+      rspec.spec.call("acceptance/#{m[1]}")
+    ]
+  end
+
+  # Rails config changes
+  watch(rails.spec_helper)     { rspec.spec_dir }
+  watch(rails.routes)          { "#{rspec.spec_dir}/routing" }
+  watch(rails.app_controller)  { "#{rspec.spec_dir}/controllers" }
+
+  # Capybara features specs
+  watch(rails.view_dirs)     { |m| rspec.spec.call("features/#{m[1]}") }
+  watch(rails.layouts)       { |m| rspec.spec.call("features/#{m[1]}") }
+
+  # Turnip features and steps
+  watch(%r{^spec/acceptance/(.+)\.feature$})
+  watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$}) do |m|
+    Dir[File.join("**/#{m[1]}.feature")][0] || "spec/acceptance"
+  end
+end

data/LICENSE

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+MIT License
+
+Copyright (c) 2017 Ryan Moore
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Lsa
+
+Library code for [LSA for (Meta)Genomes](https://github.com/mooreryan/lsa_for_genomes)
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'lsa'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install lsa
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/lsa. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## Code of Conduct
+
+Everyone interacting in the Lsa project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/lsa/blob/master/CODE_OF_CONDUCT.md).

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "lsa"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/lsa.rb

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+require "lsa/version"
+
+require "abort_if"
+
+include AbortIf
+
+
+
+
+module Lsa
+
+  def clean_str str
+    str.strip.gsub(/[^\p{Alnum}_]+/, "_").gsub(/_+/, "_")
+  end
+
+
+  def parse_mapping_file mapping_fname, mmseqs_final_outf
+    data_labels = []
+    label2outf = {}
+    doc2new_doc = {}
+    File.open(mapping_fname, "rt").each_line.with_index do |line, idx|
+      if idx.zero?
+        curren_label, *data_labels = line.chomp.split("\t").map do |str|
+          clean_str str
+        end
+
+        abort_unless data_labels.uniq.count == data_labels.count,
+                     "The data labels are not unique in #{mapping_fname}"
+
+        data_labels.each do |label|
+          new_outfname =
+            File.join "#{mmseqs_final_outf}.metadata_#{label}.txt"
+
+          label2outf[label] = File.open new_outfname, "w"
+        end
+      else
+        file_name, *data = line.chomp.split("\t").map do |str|
+          clean_str str
+        end
+
+        abort_unless data_labels.length == data.length,
+                     "Number of columns doesn't match for line " +
+                     "#{idx + 1}"
+
+        abort_if doc2new_doc.has_key?(file_name),
+                 "File #{file_name} is repeated in #{mapping_fname}"
+
+        doc2new_doc[file_name] = {}
+        data_labels.each_with_index do |label, idx|
+          doc2new_doc[file_name][label] = data[idx]
+        end
+      end
+    end
+
+    [label2outf, doc2new_doc]
+  end
+
+  def make_new_cluster_files mmseqs_final_outf, label2outf, doc2new_doc
+    File.open(mmseqs_final_outf).each_line do |line|
+      centroid, member = line.chomp.split "\t"
+
+      centroid_doc, centroid_seq = centroid.split "~"
+      member_doc, member_seq = member.split "~"
+
+      # START HERE write a new line for each label to each label file
+      abort_unless doc2new_doc.has_key?(centroid_doc),
+                   "Missing #{centroid_doc} from #{doc2new_doc}"
+
+      abort_unless doc2new_doc.has_key?(member_doc),
+                   "Missing #{member_doc} from #{doc2new_doc}"
+
+      label2outf.keys.each do |label|
+        new_centroid_doc = doc2new_doc[centroid_doc][label]
+        new_member_doc = doc2new_doc[member_doc][label]
+
+        new_centroid = "#{new_centroid_doc}~#{centroid_seq}"
+        new_member = "#{new_member_doc}~#{member_seq}"
+        new_line = "#{new_centroid}\t#{new_member}"
+
+        label2outf[label].puts new_line
+      end
+    end
+
+    label2outf.each do |label, f|
+      f.close
+    end
+
+    label2outf.map { |labef, f| File.absolute_path f }
+  end
+end

data/lib/lsa/version.rb

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+module Lsa
+  VERSION = "0.1.0"
+end

data/lsa.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "lsa/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "lsa"
+  spec.version       = Lsa::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+
+  spec.summary       = %q{Latent semantic analysis pipeline for genomes and metagenomes}
+  spec.description   = %q{Latent semantic analysis pipeline for genomes and metagenomes}
+  spec.homepage      = "https://github.com/mooreryan/lsa"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency 'abort_if', '~> 0.2.0'
+
+  spec.add_development_dependency "bundler", "~> 1.15"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency 'guard-rspec', '~> 4.7', '>= 4.7.3'
+end

data/test_files/#cluster_file.txt#

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+e_coli_faa_gz~orf_1	e_coli_faa_gz~orf_1
+e_coli_faa_gz~orf_1	m_mazei_faa_gz~orf_1
+e_coli_faa_gz~orf_1	s_flexneri_faa_gz~orf_1

data/test_files/.#cluster_file.txt

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+test_files/moorer@roaming-254-155.host.udel.edu.943

data/test_files/cluster_file_another_group.txt

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+a~orf_1	a~orf_1
+a~orf_1	a~orf_1
+a~orf_1	b~orf_1

data/test_files/cluster_file_group.txt

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+bacteria~orf_1	bacteria~orf_1
+bacteria~orf_1	archaea~orf_1
+bacteria~orf_1	bacteria~orf_1

data/test_files/cluster_file_original.txt

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+e_coli_faa_gz~orf_1	e_coli_faa_gz~orf_1
+e_coli_faa_gz~orf_1	m_mazei_faa_gz~orf_1
+e_coli_faa_gz~orf_1	s_flexneri_faa_gz~orf_1

data/test_files/mapping.txt

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+file name	group	another group
+e_coli.faa.gz	bacteria	a
+m_mazei.faa.gz	archaea	a
+s_flexneri.faa.gz	bacteria	b

data/test_files/test.clu.tsv

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+term_1	doc_1~orf
+term_1	doc_1~orf
+term_1	doc_1~orf
+term_1	doc_2~orf
+term_2	doc_1~orf
+term_2	doc_2~orf
+term_2	doc_2~orf
+term_3	doc_1~orf
+term_3	doc_2~orf
+term_3	doc_3~orf
+term_4	doc_4~orf
+term_5	doc_1~orf
+term_5	doc_2~orf
+term_5	doc_3~orf
+term_5	doc_4~orf

metadata

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+--- !ruby/object:Gem::Specification
+name: lsa
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Ryan Moore
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-07-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: abort_if
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: guard-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 4.7.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 4.7.3
+description: Latent semantic analysis pipeline for genomes and metagenomes
+email:
+- moorer@udel.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-gemset"
+- ".ruby-version"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Guardfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/lsa.rb
+- lib/lsa/version.rb
+- lsa.gemspec
+- test_files/#cluster_file.txt#
+- test_files/.#cluster_file.txt
+- test_files/cluster_file_another_group.txt
+- test_files/cluster_file_group.txt
+- test_files/cluster_file_original.txt
+- test_files/e_coli.faa.gz
+- test_files/m_mazei.faa.gz
+- test_files/mapping.txt
+- test_files/s_flexneri.faa.gz
+- test_files/small/e_coli.faa.gz
+- test_files/small/m_mazei.faa.gz
+- test_files/small/s_flexneri.faa.gz
+- test_files/test.clu.tsv
+homepage: https://github.com/mooreryan/lsa
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.12
+signing_key: 
+specification_version: 4
+summary: Latent semantic analysis pipeline for genomes and metagenomes
+test_files: []