pasv_lib 0.1.0

checksums.yaml

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+---
+SHA1:
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+  data.tar.gz: 832627db920a572f5235f72dc40404af49ee9ec8
+SHA512:
+  metadata.gz: 02e27066e616a082b524da16745e9cc5504e70afb86f10ae0f33709fb3dd09793ea1fc33f4524f3578c889dd8d07003b4aee1ea5d8dc5a57498416f860bf21d4
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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/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.4.1
+before_install: gem install bundler -v 1.15.4

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"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in pasv_lib.gemspec
+gemspec

data/README.md

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+# PasvLib
+
+Library code for [PASV](http://www.github.com/mooreyan/pasv).
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'pasv_lib'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install pasv_lib
+
+## Usage
+
+TODO: Write usage instructions here
+
+## 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/[mooreryan]/pasv_lib. 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 PasvLib project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[mooreryan]/pasv_lib/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 "pasv_lib"
+
+# 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/pasv_lib.rb

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+require "pasv_lib/version"
+
+module PasvLib
+  module CoreExtensions
+    module Time
+      def date_and_time fmt="%F %T.%L"
+        Object::Time.now.strftime fmt
+      end
+
+      def time_it title="", logger=nil, run: true
+        if run
+          t = Object::Time.now
+
+          yield
+
+          time = Object::Time.now - t
+
+          if title == ""
+            msg = "Finished in #{time} seconds"
+          else
+            msg = "#{title} finished in #{time} seconds"
+          end
+
+          if logger
+            logger.info msg
+          else
+            $stderr.puts msg
+          end
+        end
+      end
+    end
+
+    module Process
+      include CoreExtensions::Time
+
+      def run_it *a, &b
+        exit_status, stdout, stderr = systemu *a, &b
+
+
+        puts stdout unless stdout.empty?
+        unless stderr.empty? || stderr.include?("Insecure world writable dir")
+          $stderr.puts stderr
+        end
+
+        exit_status
+      end
+
+      def run_it! *a, &b
+        exit_status = self.run_it *a, &b
+
+        # Sometimes, exited? is not true and there will be no exit
+        # status. Success should catch all failures.
+        AbortIf.abort_unless exit_status.success?,
+                             "Command failed with status " +
+                             "'#{exit_status.to_s}' " +
+                             "when running '#{a.inspect}', " +
+                             "'#{b.inspect}'"
+
+        exit_status
+      end
+
+      # Examples
+      #
+      # Process.extend CoreExtensions::Process
+      # Time.extend CoreExtensions::Time
+      #
+      # Process.run_and_time_it! "Saying hello",
+      #                          %Q{echo "hello world"}
+      #
+      # Process.run_and_time_it! "This will raise SystemExit",
+      #                          "ls arstoeiarntoairnt" do
+      #   puts "i like pie"
+      # end
+      def run_and_time_it! title="",
+                           cmd="",
+                           logger=AbortIf::logger,
+                           &b
+
+        AbortIf.logger.debug { "Running: #{cmd}" }
+
+        time_it title, logger do
+          run_it! cmd, &b
+        end
+      end
+    end
+  end
+
+  module Utils
+    # @note Takes 1-based coordinates.
+    def spans_start query_seq, gapped_start
+      !query_seq[0..gapped_start-1].tr("-", "").empty?
+    end
+
+    # @note Takes 1-based coordinates.
+    def spans_end query_seq, gapped_end
+      !query_seq[gapped_end-1..query_seq.length-1].tr("-", "").empty?
+    end
+
+    # @note Returns a hash that accepts and returns 1-based coordinates.
+    def pos_to_gapped_pos gapped_key_seq
+      pos_to_gapped_pos = {}
+      nongap_idx = 0
+
+      gapped_key_seq.each_char.with_index do |char, gapped_idx|
+        unless char == "-"
+          pos_to_gapped_pos[nongap_idx + 1] = (gapped_idx + 1)
+
+          nongap_idx += 1
+        end
+      end
+
+      pos_to_gapped_pos
+    end
+
+    # @note The key posns are 1-based and non-gapped.  The query seq
+    #   is gapped.
+    def get_oligo gapped_query_seq, key_posns, pos_to_gapped_pos
+      gapped_key_posns = key_posns.map do |pos|
+        pos_to_gapped_pos[pos]
+      end
+
+      gapped_key_posns.map do |pos|
+        idx = pos - 1
+
+        gapped_query_seq[idx]
+      end.join.upcase
+    end
+
+    def get_type oligo, spans
+      if spans == "NA"
+        oligo
+      else
+        "#{oligo}_#{spans}"
+      end
+    end
+  end
+end

data/lib/pasv_lib/version.rb

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+module PasvLib
+  VERSION = "0.1.0"
+end

data/pasv_lib.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "pasv_lib/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "pasv_lib"
+  spec.version       = PasvLib::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+
+  spec.summary       = %q{Library code for PASV}
+  # spec.description   = %q{TODO: Write a longer description or delete this line.}
+  spec.homepage      = "http://www.github.com/mooreryan/pasv_lib"
+
+  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_development_dependency "bundler", "~> 1.15"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+
+  spec.add_runtime_dependency "systemu", "~> 2.6", ">= 2.6.5"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: pasv_lib
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Ryan Moore
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2018-01-31 00:00:00.000000000 Z
+dependencies:
+- !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: systemu
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.6.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.6.5
+description: 
+email:
+- moorer@udel.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/pasv_lib.rb
+- lib/pasv_lib/version.rb
+- pasv_lib.gemspec
+homepage: http://www.github.com/mooreryan/pasv_lib
+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: 2.6.14
+signing_key: 
+specification_version: 4
+summary: Library code for PASV
+test_files: []