bio-alignment 0.0.3 → 0.0.4

data/README.md

@@ -41,6 +41,19 @@ aligmment (note codon gaps are represented by '---')
   end
 ```
 
+### BioRuby Sequence objects
+
+The BioAlignment supports BioRuby's Bio::Sequence objects:
+
+```ruby
+  require 'bio'  # BioRuby
+  require 'bio-alignment/bioruby' # make Bio::Sequence enumerable
+  
+  aln = Alignment.new
+  aln << Bio::Sequence::NA.new("atgcatgcaaaa")
+  aln << Bio::Sequence::NA.new("atg---tcaaaa")
+```
+
 ### Pal2nal
 
 A protein (amino acid) to nucleotide alignment would first load
@@ -82,16 +95,18 @@ Write a (simple) version of pal2nal would be something like
   end
 ```
 
-With amino acid aln1 and nucleotide aln2 loaded, the library version is the shorter
+With amino acid aln1 and nucleotide aln2 loaded, the library version
+includes validation, and is the shorter command 
 
 ```ruby
-  aln3 = aln1.pal2nal(aln2)
+  aln3 = aln1.pal2nal(aln2, :codon_table => 3)
 ```
 
-aln3 containing the codon alignment.
+resulting in the codon alignment.
 
-The API documentation is online. For more code examples see ./spec/*.rb and
-./features/*
+The API documentation is online. For more code examples see
+[./spec/*.rb](https://github.com/pjotrp/bioruby-alignment/tree/master/spec) and
+[./features/*](https://github.com/pjotrp/bioruby-alignment/tree/master/features).
 
 ## Cite
 

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.4

data/features/bioruby-feature.rb

@@ -0,0 +1,80 @@
+require 'bio'  # yes, we use BioRuby here
+
+$: << 'lib'
+
+require 'bio-alignment/bioruby'
+
+Given /^I have multiple Bio::Sequence objects$/ do
+  @list = []
+  # Read a Fasta file
+  fasta = Bio::FlatFile.open(Bio::FastaFormat, 'test/data/fasta/codon/codon-alignment.fa')
+  fasta.each_entry do |f|
+    naseq = f.naseq
+    # test we can index the sequence
+    ['a','-'].index(naseq[0]).should_not be nil
+    @list << naseq # inject Bio::Sequence object
+  end
+end
+
+When /^I assign BioAlignment$/ do
+  @aln = Alignment.new
+end
+
+Then /^it should accept the objects$/ do
+  @list.each do | bioruby_naseq |
+    @aln.sequences << bioruby_naseq
+  end
+end
+
+Then /^and return a partial sequence$/ do
+  @aln.rows[0][0..8].should == 'atgcccact'
+end
+
+Then /^be indexable$/ do
+  @aln.rows[0][0].should == 'a'
+end
+
+# ---
+
+Given /^I have multiple Bio::Sequence::AA objects$/ do
+  @aalist = []
+  # Read a Fasta file
+  fasta = Bio::FlatFile.open(Bio::FastaFormat, 'test/data/fasta/codon/aa-alignment.fa')
+  fasta.each_entry do |f|
+    aaseq = f.aaseq
+    @aalist << aaseq # inject Bio::Sequence object
+  end
+end
+
+When /^I assign BioAlignment for AA$/ do
+  @aa_aln = Alignment.new
+end
+
+Then /^it should accept the Bio::Sequence::AA objects$/ do
+  @aalist.each do | bioruby_aaseq |
+    @aa_aln.sequences << bioruby_aaseq
+  end
+end
+
+Then /^and return a partial AA sequence$/ do
+  @aa_aln.rows[0][0..8].should == 'MPTRLDIVG'
+end
+
+Then /^be AA indexable$/ do
+  @aa_aln.rows[0][0].should == 'M'
+end
+
+# ----
+
+Given /^I have a BioAlignment$/ do
+  pending # express the regexp above with the code you wish you had
+end
+
+When /^I convert$/ do
+  pending # express the regexp above with the code you wish you had
+end
+
+Then /^I should have a Bio::Alignment$/ do
+  pending # express the regexp above with the code you wish you had
+end
+

data/features/bioruby.feature

@@ -0,0 +1,23 @@
+Feature: BioAlignment should play with BioRuby 
+  In order to use BioRuby functionality
+  I want to convert BioAlignment to Bio::Alignment
+  And I want to support Bio::Sequence objects
+
+  Scenario: Use Bio::Sequence to fill BioAlignment
+    Given I have multiple Bio::Sequence objects
+    When I assign BioAlignment
+    Then it should accept the objects
+    And and return a partial sequence
+    And be indexable
+
+  Scenario: Use Bio::Sequence to fill BioAlignment with AA
+    Given I have multiple Bio::Sequence::AA objects
+    When I assign BioAlignment for AA
+    Then it should accept the Bio::Sequence::AA objects
+    And and return a partial AA sequence
+    And be AA indexable
+
+  Scenario: Convert BioAlignment to Bio::Alignment
+    Given I have a BioAlignment
+    When I convert
+    Then I should have a Bio::Alignment

data/lib/bio-alignment/alignment.rb

@@ -3,6 +3,7 @@
 require 'bio-alignment/pal2nal'
 
 module Bio
+ 
   module BioAlignment
 
     class Alignment
@@ -17,6 +18,10 @@ module Bio
 
       alias rows sequences
 
+      # def [] index  <- need matrix
+      #   rows[index]
+      # end
+
       def each
         rows.each { | seq | yield seq }
       end

data/lib/bio-alignment/bioruby.rb

@@ -0,0 +1,22 @@
+module Bio
+  # Here we override BioRuby Sequence classes, so they are enumerable
+  class Sequence
+    class NA
+      include Enumerable
+      def each
+        to_s.each_byte do | c |
+          yield c
+        end
+      end
+    end
+    class AA
+      include Enumerable
+      def each
+        to_s.each_byte do | c |
+          yield c
+        end
+      end
+    end
+  end
+end
+

data/lib/bio-alignment/pal2nal.rb

@@ -3,14 +3,14 @@
 module Bio
   module BioAlignment
     module Pal2Nal
-      def pal2nal nt_aln
+      def pal2nal nt_aln, options = { :codon_table => 1 }
         aa_aln = self
         codon_aln = Alignment.new
         aa_aln.each_with_index do | aaseq, i |
           ntseq = nt_aln.sequences[i]
           raise "pal2nal sequence IDs do not match (for #{aaseq.id} != #{ntseq.id})" if aaseq.id != ntseq.id
           raise "pal2nal sequence size does not match (for #{aaseq.id}'s #{aaseq.to_s.size}!= #{ntseq.to_s.size * 3})" if aaseq.id != ntseq.id
-          codonseq = CodonSequence.new(ntseq.id, ntseq.seq)
+          codonseq = CodonSequence.new(ntseq.id, ntseq.seq, options)
 
           codon_pos = 0
           result = []
@@ -26,7 +26,7 @@ module Bio
                 codon.to_s
               end
           end
-          codon_seq = CodonSequence.new(aaseq.id, result.join(''))
+          codon_seq = CodonSequence.new(aaseq.id, result.join(''), options)
           codon_aln.sequences << codon_seq
         end
         codon_aln

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-alignment
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-04 00:00:00.000000000Z
+date: 2012-02-06 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &23657180 !ruby/object:Gem::Requirement
+  requirement: &16310560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *23657180
+  version_requirements: *16310560
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &23655840 !ruby/object:Gem::Requirement
+  requirement: &16309720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *23655840
+  version_requirements: *16309720
 - !ruby/object:Gem::Dependency
   name: bio-bigbio
-  requirement: &23654620 !ruby/object:Gem::Requirement
+  requirement: &16309060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -43,10 +43,10 @@ dependencies:
         version: 0.1.3
   type: :development
   prerelease: false
-  version_requirements: *23654620
+  version_requirements: *16309060
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &23653020 !ruby/object:Gem::Requirement
+  requirement: &16308000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *23653020
+  version_requirements: *16308000
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &23651800 !ruby/object:Gem::Requirement
+  requirement: &16306500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *23651800
+  version_requirements: *16306500
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &23650920 !ruby/object:Gem::Requirement
+  requirement: &16305460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *23650920
+  version_requirements: *16305460
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &23650280 !ruby/object:Gem::Requirement
+  requirement: &16304680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,7 +87,7 @@ dependencies:
         version: 1.7.0
   type: :development
   prerelease: false
-  version_requirements: *23650280
+  version_requirements: *16304680
 description: Alignment handler for multiple sequence alignments (MSA)
 email: pjotr.public01@thebird.nl
 executables:
@@ -106,12 +106,15 @@ files:
 - VERSION
 - bin/bio-alignment
 - doc/bio-alignment-design.md
+- features/bioruby-feature.rb
+- features/bioruby.feature
 - features/codon-feature.rb
 - features/codon.feature
 - features/pal2nal-feature.rb
 - features/pal2nal.feature
 - lib/bio-alignment.rb
 - lib/bio-alignment/alignment.rb
+- lib/bio-alignment/bioruby.rb
 - lib/bio-alignment/codonsequence.rb
 - lib/bio-alignment/pal2nal.rb
 - lib/bio-alignment/sequence.rb
@@ -138,7 +141,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3154039158347420524
+      hash: -237499918493109825
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: