fasta_read 1.0.0 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 352cc6460c3d3e90d37bc00ad3270490c7dd2215
+  metadata.gz: 9d46389f8c604841492cdfc937c0ac0c4ac69082
+  data.tar.gz: 79e57cab5fe9d2e5325eb8a8aa9e05ec7393e821
 SHA512:
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-  data.tar.gz: 761c230b6fb31d9ebd2b847026def6e4348a879b99d2d813868e1d475fd9630b8e01f90beec532acb804d75888ef102f02688a4aea43faab09935ddf695cae8b
+  metadata.gz: 06d11757e322c49a9c9607f37212e2dfe4350f9cfbb9498d29aecf89f672b6e7dc6dd6d2c2ef5ea4959800f3745a1a9dc9b0da5f0e5aa63467ecdba08b849795
+  data.tar.gz: a98f489a0d17f7123af3411578c27f716a5c7660f0bdb94adf55f025e337ac0796ebb836dcc44754125327c3f6087a3f75f97a482fe3ff07646b28b9ead4f2eb

data/.rspec

@@ -0,0 +1,2 @@
+--color
+--format documentation

data/.travis.yml

@@ -0,0 +1,4 @@
+language: ruby
+rvm:
+  - 2.1.0
+  - 1.9.3

data/Gemfile.lock

@@ -1,9 +1,9 @@
 PATH
   remote: .
   specs:
-    fasta_read (1.0.0)
-      methadone (~> 1.3.2)
-      rake (~> 0.9)
+    fasta_read (1.1.0)
+      methadone (>= 1.3.2)
+      rake (>= 0.9.2)
 
 GEM
   remote: https://rubygems.org/
@@ -44,7 +44,6 @@ GEM
     guard-rspec (4.2.8)
       guard (~> 2.1)
       rspec (>= 2.14, < 4.0)
-    json (1.8.1)
     listen (2.7.1)
       celluloid (>= 0.15.2)
       celluloid-io (>= 0.15.0)
@@ -61,12 +60,10 @@ GEM
       coderay (~> 1.0)
       method_source (~> 0.8)
       slop (~> 3.4)
-    rake (0.9.6)
+    rake (10.2.2)
     rb-fsevent (0.9.4)
     rb-inotify (0.9.3)
       ffi (>= 0.5.0)
-    rdoc (4.1.1)
-      json (~> 1.4)
     rspec (2.14.1)
       rspec-core (~> 2.14.0)
       rspec-expectations (~> 2.14.0)
@@ -83,10 +80,8 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  aruba
-  bundler (~> 1.5)
+  aruba (>= 0.5.4)
   fasta_read!
-  guard-cucumber
-  guard-rspec
-  rdoc
-  rspec
+  guard-cucumber (>= 1.4.1)
+  guard-rspec (>= 4.2.8)
+  rspec (>= 2.14.1)

data/Guardfile

@@ -1,33 +1,36 @@
 # A sample Guardfile
 # More info at https://github.com/guard/guard#readme
 
-guard 'cucumber', all_on_start: false, change_format: "pretty" do
+group :cucumber do
+  guard 'cucumber', all_on_start: false, change_format: "pretty" do
 
-  watch(%r{^bin/.+$})          { 'features' }
-  watch(%r{^lib/.+$})          { 'features' }
-  watch(%r{^features/.+\.feature$})
-  watch(%r{^features/support/.+$})          { 'features' }
-  watch(%r{^features/step_definitions/(.+)_steps\.rb$}) { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'features' }
+    watch(%r{^bin/.+$})          { 'features' }
+    watch(%r{^lib/.+$})          { 'features' }
+    watch(%r{^features/.+\.feature$})
+    watch(%r{^features/support/.+$})          { 'features' }
+    watch(%r{^features/step_definitions/(.+)_steps\.rb$}) { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'features' }
+  end
 end
 
-guard :rspec do
-  watch(%r{^spec/.+_spec\.rb$})
-  watch(%r{^lib/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
-  watch('spec/spec_helper.rb')  { "spec" }
+group :rspec do
+  guard :rspec do
+    watch(%r{^spec/.+_spec\.rb$})
+    watch(%r{^lib/(.+)\.rb$})     { |m| "spec/#{m[1]}_spec.rb" }
+    watch('spec/spec_helper.rb')  { "spec" }
 
-  # Rails example
-  watch(%r{^app/(.+)\.rb$})                           { |m| "spec/#{m[1]}_spec.rb" }
-  watch(%r{^app/(.*)(\.erb|\.haml|\.slim)$})          { |m| "spec/#{m[1]}#{m[2]}_spec.rb" }
-  watch(%r{^app/controllers/(.+)_(controller)\.rb$})  { |m| ["spec/routing/#{m[1]}_routing_spec.rb", "spec/#{m[2]}s/#{m[1]}_#{m[2]}_spec.rb", "spec/acceptance/#{m[1]}_spec.rb"] }
-  watch(%r{^spec/support/(.+)\.rb$})                  { "spec" }
-  watch('config/routes.rb')                           { "spec/routing" }
-  watch('app/controllers/application_controller.rb')  { "spec/controllers" }
+    # Rails example
+    watch(%r{^app/(.+)\.rb$})                           { |m| "spec/#{m[1]}_spec.rb" }
+    watch(%r{^app/(.*)(\.erb|\.haml|\.slim)$})          { |m| "spec/#{m[1]}#{m[2]}_spec.rb" }
+    watch(%r{^app/controllers/(.+)_(controller)\.rb$})  { |m| ["spec/routing/#{m[1]}_routing_spec.rb", "spec/#{m[2]}s/#{m[1]}_#{m[2]}_spec.rb", "spec/acceptance/#{m[1]}_spec.rb"] }
+    watch(%r{^spec/support/(.+)\.rb$})                  { "spec" }
+    watch('config/routes.rb')                           { "spec/routing" }
+    watch('app/controllers/application_controller.rb')  { "spec/controllers" }
 
-  # Capybara features specs
-  watch(%r{^app/views/(.+)/.*\.(erb|haml|slim)$})     { |m| "spec/features/#{m[1]}_spec.rb" }
+    # Capybara features specs
+    watch(%r{^app/views/(.+)/.*\.(erb|haml|slim)$})     { |m| "spec/features/#{m[1]}_spec.rb" }
 
-  # Turnip features and steps
-  watch(%r{^spec/acceptance/(.+)\.feature$})
-  watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$})   { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'spec/acceptance' }
+    # Turnip features and steps
+    watch(%r{^spec/acceptance/(.+)\.feature$})
+    watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$})   { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'spec/acceptance' }
+  end
 end
-

data/README.md

@@ -1,6 +1,7 @@
+[![Gem Version](https://badge.fury.io/rb/fasta_read.svg)](http://badge.fury.io/rb/fasta_read) [![Build Status](https://travis-ci.org/adamico/ruby-fasta-read.svg?branch=master)](https://travis-ci.org/adamico/ruby-fasta-read) [![Code Climate](https://codeclimate.com/github/adamico/ruby-fasta-read.png)](https://codeclimate.com/github/adamico/ruby-fasta-read)
 # FastaRead
 
-A Ruby command-line program that will take coordinates and return either a unmasked sequence or a snp-masked sequence. The coordinates refer to the start and stop positions, and are "UCSC coordinates" i.e. 0 based and half open (see [UCSC_coordinate_transforms](http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms)) 
+A Ruby command-line program that will take coordinates and return either a unmasked gene sequence or a snp-masked sequence. The coordinates refer to the start and stop positions, and are "UCSC coordinates" i.e. 0 based and half open (see [UCSC_coordinate_transforms](http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms)) 
 
 ## Installation
 

data/Rakefile

@@ -34,15 +34,12 @@ raise
 end
 
 require 'cucumber/rake/task'
-gem 'rdoc' # we need the installed RDoc gem, not the system one
-require 'rdoc/task'
 
 include Rake::DSL
 
 Bundler::GemHelper.install_tasks
 
-
-RSpec::Core::RakeTask.new do |t|
+RSpec::Core::RakeTask.new(:spec) do |t|
   # Put spec opts in a file named .rspec in root
 end
 
@@ -54,13 +51,5 @@ Cucumber::Rake::Task.new(:features) do |t|
   t.fork = false
 end
 
-Rake::RDocTask.new do |rd|
-  
-  rd.main = "README.rdoc"
-  
-  rd.rdoc_files.include("README.rdoc","lib/**/*.rb","bin/**/*")
-end
-
 desc "Run Cucumber features"
-task :default => [:features]
-
+task :default => [:spec, :features]

data/bin/fasta_read

@@ -2,8 +2,7 @@
 
 require 'optparse'
 require 'methadone'
-require 'fasta_read.rb'
-require 'fileutils'
+require 'fasta_read'
 
 class App
   include Methadone::Main
@@ -13,19 +12,18 @@ class App
     snp = masked_unmasked(options)[0]
     subst = masked_unmasked(options)[1]
     path = "fasta/#{assembly}/#{snp}/chr#{chromosome + subst}.fa"
-
+    exit_now_with!(assembly_or_chromosome(assembly, chromosome)) unless File.exist?(path)
+    fasta = IO.read(path)
     debug("About to read #{assembly} #{snp} chr#{chromosome}:#{cstart}-#{cend}")
-    if File.exist?(path)
-      if options[:output]
-        File.open(options[:output], "w") do |file|
-          file.puts IO.read(path, cend.to_i - cstart.to_i, cstart.to_i)
-        end
-      else
-        puts IO.read(path, cend.to_i - cstart.to_i, cstart.to_i)
+    sequence = FastaRead::Sequence.new(fasta, chromosome, cstart, cend).process
+    if options[:output]
+      File.open(options[:output], "w") do |file|
+        file.puts sequence
       end
     else
-      exit_now_with!(assembly_or_chromosome(assembly, chromosome))
+      puts sequence
     end
+    info "#{sequence.length} base pairs"
   end
 
   def self.masked_unmasked(options)
@@ -39,7 +37,6 @@ class App
   def self.exit_now_with!(value_and_argument)
     exit_now!(1, "the '#{value_and_argument[0]}' #{value_and_argument[1]} doesn't exist in directory structure")
   end
-
   # supplemental methods here
 
   # Declare command-line interface here
@@ -49,10 +46,13 @@ class App
   # Accept flags via:
   # on("--flag VAL","Some flag")
   # options[flag] will contain VAL
+  options['multiple-lines'] = true
   #
   # Specify switches via:
   on "-o OUTPUTFILE", "--output", "outputs sequence to a file"
   on "--snp", "return the sequence from the SNP-masked assembly"
+  on "--multiple-lines", "return the sequence from the SNP-masked assembly"
+
   # on("--[no-]switch","Some switch")
   #
   # Or, just call OptionParser methods on opts

data/fasta_read.gemspec

@@ -7,10 +7,10 @@ Gem::Specification.new do |spec|
   spec.name          = "fasta_read"
   spec.version       = FastaRead::VERSION
   spec.authors       = ["Andrea D'Amico"]
-  spec.email         = ["andrea.damico@gmail.com"]
+  spec.email         = ["andrea.damico@gmail.com", "sfcarroll@gmail.com"]
   spec.summary       = %q{Fasta sequence extracter}
   spec.description   = %q{Extract DNA Fasta sequence from assembly files.}
-  spec.homepage      = "https://github.com/adamico/ruby-fasta-read"
+  spec.homepage      = "https://github.com/sfcarroll/ruby-fasta-read"
 
   spec.license       = "MIT"
 
@@ -20,7 +20,7 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_runtime_dependency 'methadone', '>= 1.3.2'
-  spec.add_development_dependency 'rake', '>= 0.9.2'
+  spec.add_runtime_dependency 'rake', '>= 0.9.2'
   spec.add_development_dependency 'aruba', '>= 0.5.4'
   spec.add_development_dependency 'rspec', '>= 2.14.1'
   spec.add_development_dependency "guard-cucumber", '>= 1.4.1'

data/features/fasta_read.feature

@@ -4,16 +4,24 @@ Feature: My bootstrapped app kinda works
   So I don't have to do it myself
 
   Background:
-    Given a file named "fasta/hg19/unmasked/chr12.fa" with:
+    Given a file named "fasta/hg19/unmasked/chr1.fa" with:
       """
-      gatccacctgcctcagcctcccagagtgctgggattataggtgtgagccactgcacccggcc
+      >chr1
+      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
+      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
+      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
+      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
+      C
       """
-    And a file named "fasta/hg19/snp/chr12.subst.fa" with:
+    And a file named "fasta/hg19/snp/chr1.subst.fa" with:
       """
-      GAAAACtttttcttttttttgagataggttctcactctggttgttgcccaggctggagtgca
+      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
+      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
+      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
+      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
+      C
       """
 
-  @announce
   Scenario: Basic UI
     When I get help for "fasta_read"
     Then the exit status should be 0
@@ -32,37 +40,43 @@ Feature: My bootstrapped app kinda works
         |cstart    |which is required|
         |cend      |which is required|
 
-  @announce
-  Scenario Outline: Happy path
-    Given a file named "fasta/hg19/unmasked/chr12.fa" with:
+  Scenario Outline: files with one line stream
+    Given a file named "fasta/hg19/unmasked/chr1.fa" with:
       """
-      gatccacctgcctcagcctcccagagtgctgggattataggtgtgagccactgcacccggcc
+      >chr1
+      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
+      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
+      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
+      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
+      C
       """
-    And a file named "fasta/hg19/snp/chr12.subst.fa" with:
+    And a file named "fasta/hg19/snp/chr1.subst.fa" with:
       """
-      GAAAACtttttcttttttttgagataggttctcactctggttgttgcccaggctggagtgca
+      >chr1
+      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
+      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
+      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
+      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
+      C
       """
     When I successfully run `fasta_read <options>`
     Then the output should contain "<output>"
     Then the output should not contain "<noutput>"
 
     Scenarios: unmasked
-      |options      |output    |noutput|
-      |hg19 12 0 3 --log-level=debug  |gat       |cca    |
-      |hg19 12 10 20|cctcagcctc|ccaga  |
+      |options     |output    |noutput|
+      |hg19 1 0 200|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|ccaga  |
     Scenarios: snp
       |options            |output    |noutput|
-      |hg19 12 10 20 --snp|tctttttttt|ccaga  |
+      |hg19 1 0 200 --snp|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|ccaga  |
 
-  @announce
   Scenario: Export to file
-    When I successfully run `fasta_read hg19 12 10 20 --output=out.txt`
+    When I successfully run `fasta_read hg19 1 0 200 --output=out.txt`
     Then the file "out.txt" should contain:
     """
-    cctcagcctc
+    AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
     """
 
-  @announce
   Scenario Outline: Painful path
     When I run `fasta_read <options>`
     Then the stderr should contain "<output>"

data/lib/fasta_read.rb

@@ -1,5 +1,2 @@
 require "fasta_read/version"
-
-module FastaRead
-  # Your code goes here...
-end
+require "fasta_read/sequence"

data/lib/fasta_read/sequence.rb

@@ -0,0 +1,31 @@
+require 'fileutils'
+
+module FastaRead
+  class Sequence
+    include Methadone::Main
+    include Methadone::CLILogging
+
+    attr_reader :separate_lines
+
+    def initialize(fasta, chromosome, cstart, cend)
+      @fasta =  fasta.gsub("\n", "")
+      @chromosome = ">chr#{chromosome}"
+      @cstart = cstart.to_i
+      @cend =   cend.to_i
+    end
+
+    def process
+      @fasta[real_cstart..real_cend]
+    end
+
+    def real_cstart
+      cstart = @cstart
+      cstart -= 1 unless @cstart == 0
+      cstart + @chromosome.length
+    end
+
+    def real_cend
+      @cend - 1 + @chromosome.length
+    end
+  end
+end

data/lib/fasta_read/version.rb

@@ -1,3 +1,3 @@
 module FastaRead
-  VERSION = "1.0.0"
+  VERSION = "1.1.0"
 end

data/spec/fasta_read/sequence_spec.rb

@@ -0,0 +1,37 @@
+require "spec_helper"
+
+module FastaRead
+  describe Sequence do
+    let(:fasta) {">chr1\nAATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT\nCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC\nACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG\nGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT\nC"}
+    describe "#real_cstart" do
+      context "when @cstart is > 0" do
+        subject {Sequence.new(fasta, "12", "5", "200").real_cstart}
+        it "should add file header string length" do
+          expect(subject).to eq 10
+        end
+      end
+      context "when @cstart is 0" do
+        subject {Sequence.new(fasta, "1", "0", "200").real_cstart}
+        it "should not subtract 1" do
+          expect(subject).to eq 5
+        end
+      end
+    end
+
+    describe "#real_cend" do
+      subject {Sequence.new(fasta, "1", "0", "200").real_cend}
+      it "should subtract 1 and add file header string length" do
+        expect(subject).to eq 204
+      end
+    end
+
+    describe "#process" do
+      subject {Sequence.new(fasta, "1", "0", "200").process}
+      describe "with a continuous character stream" do
+        it "builds a character sequence" do
+          expect(subject).to eq "AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT"
+        end
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,8 @@
+require "methadone"
+require "fasta_read/sequence"
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.filter_run focus: true
+  config.run_all_when_everything_filtered = true
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: fasta_read
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.0
 platform: ruby
 authors:
 - Andrea D'Amico
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-03 00:00:00.000000000 Z
+date: 2014-04-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: methadone
@@ -31,7 +31,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.2
-  type: :development
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
@@ -97,12 +97,15 @@ dependencies:
 description: Extract DNA Fasta sequence from assembly files.
 email:
 - andrea.damico@gmail.com
+- sfcarroll@gmail.com
 executables:
 - fasta_read
 extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- ".rspec"
+- ".travis.yml"
 - Gemfile
 - Gemfile.lock
 - Guardfile
@@ -116,10 +119,12 @@ files:
 - features/step_definitions/fasta_read_steps.rb
 - features/support/env.rb
 - lib/fasta_read.rb
+- lib/fasta_read/sequence.rb
 - lib/fasta_read/version.rb
-- spec/something_spec.rb
+- spec/fasta_read/sequence_spec.rb
+- spec/spec_helper.rb
 - stories.txt
-homepage: https://github.com/adamico/ruby-fasta-read
+homepage: https://github.com/sfcarroll/ruby-fasta-read
 licenses:
 - MIT
 metadata: {}
@@ -147,5 +152,6 @@ test_files:
 - features/fasta_read.feature
 - features/step_definitions/fasta_read_steps.rb
 - features/support/env.rb
-- spec/something_spec.rb
+- spec/fasta_read/sequence_spec.rb
+- spec/spec_helper.rb
 has_rdoc: 

data/spec/something_spec.rb

@@ -1,5 +0,0 @@
-describe "TestSomething" do
-  it "should be true" do
-    true.should be_true
-  end
-end