aai 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 2bdc68dc8d289e3d9770373f856d9e05d6c1a0b0
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data/.travis.yml

@@ -6,4 +6,12 @@ rvm:
   - 2.2
   - 2.3
   - 2.4
-before_install: gem install bundler -v 1.14.6
+
+addons:
+  apt:
+    packages:
+    - parallel
+    - ncbi-blast+
+
+before_install:
+  - gem install bundler -v 1.14.6

data/README.md

@@ -4,10 +4,25 @@
 [![Coverage Status](https://coveralls.io/repos/github/mooreryan/aai/badge.svg?branch=master)](https://coveralls.io/github/mooreryan/aai?branch=master)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-Calculate Seanie's multi-genome (or genome bin) amino acid similarity.
+Calculate Seanie's multi-genome (or genome bin, or metagenome sample) amino acid similarity.
+
+## Requirements
+
+The following programs must be installed and on your `PATH` for `aai` to work.
+
+- GNU Parallel
+- NCBI Blast suite
 
 ## Installation
 
+### Install with RubyGems
+
+Run
+
+    $ gem install aai
+
+### If bundling aai in another ruby program
+
 Add this line to your application's Gemfile:
 
 ```ruby
@@ -18,18 +33,24 @@ And then execute:
 
     $ bundle
 
-Or install it yourself as:
-
-    $ gem install aai
+## Usage
 
-## Requirements
+### Example
 
-- GNU Parallel
-- NCBI Blast suite
+```
+$ ruby exe/aai.rb --infiles *.fa
+```
 
-## Usage
+### Options
 
-TODO: Write usage instructions here
+```
+Options:
+  -i, --infiles=<s+>    Input files
+  -o, --outdir=<s>      Output directory (default: .)
+  -b, --basename=<s>    Base name for output file (default: aai_scores)
+  -v, --version         Print version and exit
+  -h, --help            Show this message
+```
 
 ## Development
 

data/aai.gemspec

@@ -14,15 +14,6 @@ Gem::Specification.new do |spec|
   spec.homepage      = "https://github.com/mooreryan/aai.git"
   spec.license       = "MIT"
 
-  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
-  # to allow pushing to a single host or delete this section to allow pushing to any host.
-  # if spec.respond_to?(:metadata)
-  #   spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com'"
-  # else
-  #   raise "RubyGems 2.0 or newer is required to protect against " \
-  #     "public gem pushes."
-  # end
-
   spec.files         = `git ls-files -z`.split("\x0").reject do |f|
     f.match(%r{^(test|spec|features)/})
   end

data/exe/{aai.rb → aai}

@@ -38,6 +38,10 @@ end
 abort_if opts[:infiles].nil? || opts[:infiles].empty?,
          "No infiles given"
 
+Aai.check_command "blastp"
+Aai.check_command "makeblastdb"
+Aai.check_command "parallel"
+
 Aai.check_files opts[:infiles]
 
 FileUtils.mkdir_p opts[:outdir]

data/lib/aai/utils.rb

@@ -32,5 +32,28 @@ module Aai
 
       permutations
     end
+
+    # from https://stackoverflow.com/questions/2108727/ \
+    # which-in-ruby-checking-if-program-exists-in-path-from-ruby
+    def command? cmd
+      exts = ENV['PATHEXT'] ? ENV['PATHEXT'].split(';') : ['']
+      ENV['PATH'].split(File::PATH_SEPARATOR).each do |path|
+        exts.each do |ext|
+          exe = File.join(path, "#{cmd}#{ext}")
+          return exe if File.executable?(exe) && !File.directory?(exe)
+        end
+      end
+
+      return nil
+    end
+
+    def check_command cmd
+      path = command? cmd
+
+      AbortIf.abort_unless path,
+                           "MIssing #{cmd} command. Is it on your path?"
+
+      path
+    end
   end
 end

data/lib/aai/version.rb

@@ -1,5 +1,5 @@
 module Aai
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
   COPYRIGHT = "2017 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/aai"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: aai
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Ryan Moore
@@ -152,7 +152,7 @@ description: Calculate Seanie's amino acid similarity score between multiple gen
 email:
 - moorer@udel.edu
 executables:
-- aai.rb
+- aai
 extensions: []
 extra_rdoc_files: []
 files:
@@ -168,7 +168,7 @@ files:
 - aai.gemspec
 - bin/console
 - bin/setup
-- exe/aai.rb
+- exe/aai
 - lib/aai.rb
 - lib/aai/core_extensions.rb
 - lib/aai/utils.rb