basil 0.1.1 → 0.1.2

data/Gemfile

@@ -1,5 +1,4 @@
 source :rubygems
-gemspec
 
 gem "dna"
 gem "trollop"

data/basil.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "basil"
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-09-18"
+  s.date = "2012-12-18"
   s.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
   s.email = "harekrishna@gmail.com"
   s.executables = ["basil"]
@@ -22,11 +22,13 @@ Gem::Specification.new do |s|
     "bin/basil",
     "lib/basil.rb",
     "lib/basil/barcodes.rb",
+    "lib/basil/barcodes/triplett.csv",
     "lib/basil/basil.rb",
     "lib/basil/buffer.rb",
     "lib/basil/cli.rb",
     "lib/basil/version.rb",
     "readme.md",
+    "spec/barcodes_spec.rb",
     "spec/basil_spec.rb",
     "spec/buffer_spec.rb",
     "spec/cli_spec.rb",
@@ -42,37 +44,25 @@ Gem::Specification.new do |s|
   s.homepage = "http://audy.github.com/basil"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.24"
+  s.rubygems_version = "1.8.23"
   s.summary = "Weapons-grade HTML demultiplexer"
 
   if s.respond_to? :specification_version then
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<basil>, [">= 0"])
       s.add_runtime_dependency(%q<dna>, [">= 0"])
       s.add_runtime_dependency(%q<trollop>, [">= 0"])
       s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<jeweler>, [">= 0"])
     else
-      s.add_dependency(%q<basil>, [">= 0"])
       s.add_dependency(%q<dna>, [">= 0"])
       s.add_dependency(%q<trollop>, [">= 0"])
       s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
     end
   else
-    s.add_dependency(%q<basil>, [">= 0"])
     s.add_dependency(%q<dna>, [">= 0"])
     s.add_dependency(%q<trollop>, [">= 0"])
     s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
   end
 end
 

data/lib/basil/barcodes.rb

@@ -1,3 +1,30 @@
-class Barcodes
-  # TODO add commonly used barcodes where copyright permits.
-end
+module Basil
+  module Barcodes
+
+    # return a directory with the project libraries
+    def self.gem_libdir
+      File.dirname(__FILE__)
+    end
+
+    # list available barcodes files
+    def self.barcode_files
+      Dir[File.join(self.gem_libdir, 'barcodes', '*.csv')]
+    end
+
+    def self.barcodes
+      self.barcode_files.map { |x| File.basename(x, File.extname(x)) }
+    end
+
+    # returns true if string matches a file in the barcodes directory
+    def self.has_barcode?(string)
+      self.barcodes.include? File.basename(string, File.extname(string))
+    end
+
+    # return path for barcode file given a string
+    def self.barcode_path(string)
+      self.barcode_files.reject { |x| File.basename(x, File.extname(x)) != string }.first rescue nil
+    end
+
+  end
+end
+

data/lib/basil/barcodes/triplett.csv

@@ -0,0 +1,205 @@
+1,AAGGTGG
+2,CTTGTGG
+3,TGAGTGG
+4,CAATTGG
+5,TTCTTGG
+6,GGTATGG
+7,GTGCTGG
+8,GCTGAGG
+9,ATCGAGG
+10,GAGTAGG
+11,TGTTAGG
+12,AGGAAGG
+13,TCGCAGG
+14,AATCAGG
+15,ACAGCGG
+16,TACGCGG
+17,ATGTCGG
+18,GGATCGG
+19,CAGACGG
+20,GTCACGG
+21,CGTCCGG
+22,TTACCGG
+23,CATGGTG
+24,TAGTGTG
+25,AGATGTG
+26,CTCTGTG
+27,ACTAGTG
+28,TGCAGTG
+29,ATGCGTG
+30,GCACGTG
+31,TCGGTTG
+32,GTAGTTG
+33,AGCGTTG
+34,CTGATTG
+35,CGAGATG
+36,ACGTATG
+37,TTATATG
+38,GTTAATG
+39,AACAATG
+40,CAGCATG
+41,TGTGCTG
+42,GCCGCTG
+43,AATTCTG
+44,CCATCTG
+45,CTAGGAG
+46,CCTTGAG
+47,GGAAGAG
+48,CACAGAG
+49,TGGCGAG
+50,GATCGAG
+51,TATGTAG
+52,GCGTTAG
+53,ATATTAG
+54,TCCATAG
+55,AGTCTAG
+56,GTGGAAG
+57,TGCGAAG
+58,CTCCAAG
+59,ATTGCAG
+60,TAATCAG
+61,AGCTCAG
+62,GCTACAG
+63,AAGCCAG
+64,TCTGGCG
+65,GTCGGCG
+66,AAGAGCG
+67,CTTAGCG
+68,CCGCGCG
+69,TAACGCG
+70,CCAGTCG
+71,TGGTTCG
+72,AGAATCG
+73,CATCTCG
+74,ATCCTCG
+75,CTGTACG
+76,GCATACG
+77,GGCAACG
+78,GATGCCG
+79,TCGACCG
+80,ACGTGGT
+81,CTATGGT
+82,CGTAGGT
+83,GACAGGT
+84,AGACGGT
+85,TCTGTGT
+86,ATAGTGT
+87,GCATTGT
+88,TAGTTGT
+89,AGCTTGT
+90,CCGATGT
+91,AATATGT
+92,CTCCTGT
+93,TAAGAGT
+94,CACTAGT
+95,GTGAAGT
+96,TCCAAGT
+97,CGGCAGT
+98,GTTGCGT
+99,CGAGCGT
+100,CCTTCGT
+101,TGGACGT
+102,GAGCCGT
+103,ATTGGTT
+104,TCAGGTT
+105,GTGTGTT
+106,AGGAGTT
+107,CCTCGTT
+108,TACCGTT
+109,CTGGATT
+110,GGCGATT
+111,GCTTATT
+112,TATAATT
+113,AGTCATT
+114,TAGGCTT
+115,CGGTCTT
+116,ATCTCTT
+117,GCGACTT
+118,CTTACTT
+119,GTACCTT
+120,GGTGGAT
+121,AACGGAT
+122,GAATGAT
+123,CGCTGAT
+124,TTGAGAT
+125,ACAAGAT
+126,GCGCGAT
+127,CAAGTAT
+128,GCCGTAT
+129,CTGTTAT
+130,TGATTAT
+131,GAGATAT
+132,GTTCTAT
+133,AGCAGGA
+134,TCGTAAT
+135,GTCTAAT
+136,CATCAAT
+137,GGACAAT
+138,CCGGCAT
+139,AGTACAT
+140,TACACAT
+141,TCTCCAT
+142,AATTGCT
+143,TTCTGCT
+144,GCTAGCT
+145,TGAAGCT
+146,ACGGTCT
+147,CGTGTCT
+148,TCACTCT
+149,GGCCTCT
+150,GAGGACT
+151,AGATACT
+152,CTCAACT
+153,TTGCACT
+154,AACCACT
+155,TTAGCCT
+156,GGTTCCT
+157,ATGACCT
+158,CATTGGA
+159,GCCTGGA
+160,CTGAGGA
+161,TAGCGGA
+162,ACTCGGA
+163,CTCTCGC
+164,GTACGGA
+165,CGCGTGA
+166,TTAATGA
+167,AGGCTGA
+168,GATCTGA
+169,CCACTGA
+170,CTAGAGA
+171,GACGAGA
+172,CCGTAGA
+173,TTCCAGA
+174,AATGCGA
+175,TGCTCGA
+176,TCTACGA
+177,GCTGGTA
+178,TCGAGTA
+179,GTCAGTA
+180,CGGCGTA
+181,ACAGTTA
+182,AGTGACA
+183,TATTACA
+184,CGGAACA
+185,CTTCACA
+186,CTGGCCA
+187,ACCGCCA
+188,TCATCCA
+189,TTCACCA
+190,TTCAGGC
+191,GTCGTGC
+192,CAGCTGC
+193,TGTCTGC
+194,ACGGAGC
+195,CGTGAGC
+196,TTGTAGC
+197,GGCTAGC
+198,GTTCAGC
+199,AGCGCGC
+200,GATTCGC
+201,GCACCGC
+202,GACGGTC
+203,ACCTGTC
+204,GGTAGTC
+205,AATCGTC

data/lib/basil/cli.rb

@@ -31,7 +31,7 @@ module Basil
       end
 
       records.each do |record|
-        
+
         match = basil.recognize record.sequence
         barcode, sequence = match if match
 
@@ -39,7 +39,7 @@ module Basil
           barcode = 'unknown'
           trimmed_sequence = record.sequence
         end
-        
+
         trimmed_sequence = record.sequence[pretrim..afttrim]
 
         new_record = Fasta.new :name => record.name, :sequence => trimmed_sequence
@@ -52,6 +52,14 @@ module Basil
     end
 
     def parse_barcodes barcodes
+      barcodes_file =
+        # barcodes included in barcodes/ directory?
+        if Barcodes.has_barcode? barcodes
+          Barcodes.barcode_path(barcodes)
+        # barcodes specified by filename
+        else
+          barcodes
+        end
       File.open(barcodes) { |h| Basil.parse_barcodes h }
     end
 
@@ -97,6 +105,6 @@ where [options] are:
       Trollop::die :out, "must specify output directory" if !opts[:out]
       opts
     end
-  end 
   end
-end
+  end
+end

data/lib/basil/version.rb

@@ -2,7 +2,7 @@ module Basil
   module Version
     MAJOR = 0
     MINOR = 1
-    PATCH = 1
+    PATCH = 2
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/barcodes_spec.rb

@@ -0,0 +1,23 @@
+require 'spec_helper'
+
+describe Basil::Barcodes do
+  it "#gem_libdir should return full path to lib/ directory" do
+    Basil::Barcodes.gem_libdir.should_not be_nil
+  end
+
+  it "#barcode_files should return an array of barcodes files" do
+    Basil::Barcodes.barcode_files.should_not be_empty
+  end
+
+  it "#barcodes should return an array of barcode names" do
+    Basil::Barcodes.barcodes.should_not be_empty
+  end
+
+  it "#has_barcode? should return true if a barcode files is present in barcodes" do
+    Basil::Barcodes.has_barcode? "triplett"
+  end
+
+  it "#barcode_path returns full path of barcode file given a name" do
+    File.readable?(Basil::Barcodes.barcode_path("triplett")).should_not be_false
+  end
+end

data/spec/cli_spec.rb

@@ -25,4 +25,6 @@ describe Basil::CLI do
     }
     files.should == directory
   end
+
+  it 'should have a method for listing available barcode sets'
 end

metadata

@@ -1,129 +1,71 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: basil
-version: !ruby/object:Gem::Version 
-  hash: 25
+version: !ruby/object:Gem::Version
+  version: 0.1.2
   prerelease: 
-  segments: 
-  - 0
-  - 1
-  - 1
-  version: 0.1.1
 platform: ruby
-authors: 
+authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-09-18 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :runtime
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2012-12-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: dna
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id001
-  name: basil
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id002
-  name: dna
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :runtime
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id003
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: trollop
-  prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id004
-  name: jeweler
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id005
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: jeweler
-  prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id006
-  name: jeweler
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id007
-  name: jeweler
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Split multiplexed Illumina/454/IonTorrent/etc... output by barcode
 email: harekrishna@gmail.com
-executables: 
+executables:
 - basil
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - .rspec
 - .rvmrc
 - Gemfile
@@ -132,11 +74,13 @@ files:
 - bin/basil
 - lib/basil.rb
 - lib/basil/barcodes.rb
+- lib/basil/barcodes/triplett.csv
 - lib/basil/basil.rb
 - lib/basil/buffer.rb
 - lib/basil/cli.rb
 - lib/basil/version.rb
 - readme.md
+- spec/barcodes_spec.rb
 - spec/basil_spec.rb
 - spec/buffer_spec.rb
 - spec/cli_spec.rb
@@ -149,37 +93,31 @@ files:
 - spec/data/test.qseq
 - spec/spec_helper.rb
 homepage: http://audy.github.com/basil
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 356002749428079559
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Weapons-grade HTML demultiplexer
 test_files: []
-