genfrag 0.0.0.2 → 0.0.0.3

data/History.txt

@@ -1,9 +0,0 @@
-== 0.0.0.2 / 2009-03-16
-
-* 1 major enhancement
-  - fixes
-
-== 0.0.0.1 / 2009-02-26
-
-* 1 major enhancement
-  - init

data/README.rdoc

@@ -2,6 +2,7 @@ Genfrag version 0.0.0.2
     by Pjotr Prins and Trevor Wennblom
     http://genfrag.rubyforge.org
     http://rubyforge.org/projects/genfrag/
+    http://github.com/trevor/genfrag/
 
 
 == DESCRIPTION:
@@ -24,7 +25,11 @@ This works
 
 == REQUIREMENTS:
 
-* bioruby
+* bio
+
+
+=== Optional
+
 * sqlite3-ruby
 
 

data/Rakefile

@@ -24,12 +24,13 @@ PROJ.authors = 'Pjotr Prins and Trevor Wennblom'
 PROJ.email = 'trevor@corevx.com'
 PROJ.url = 'http://genfrag.rubyforge.org'
 PROJ.version = Genfrag::VERSION
-PROJ.release_name = 'Rough Draught'
+PROJ.release_name = ''
 PROJ.ruby_opts = %w[-W0]
 PROJ.readme_file = 'README.rdoc'
 PROJ.ignore_file = '.gitignore'
 PROJ.exclude << 'genfrag.gemspec'
 PROJ.exclude << '.git'
+PROJ.dependencies = ['bio']
 
 PROJ.rubyforge.name = 'genfrag'
 
@@ -46,7 +47,7 @@ task 'ann:prereqs' do
   PROJ.name = 'Genfrag'
 end
 
-depend_on 'bioruby'
+depend_on 'bio'
 depend_on 'rake'
 
 

data/lib/genfrag.rb

@@ -2,7 +2,7 @@
 module Genfrag
 
   # :stopdoc:
-  VERSION = '0.0.0.2'
+  VERSION = '0.0.0.3'
   LIBPATH = ::File.expand_path(::File.dirname(__FILE__)) + ::File::SEPARATOR
   PATH = ::File.dirname(LIBPATH) + ::File::SEPARATOR
   # :startdoc:

data/lib/genfrag/app.rb

@@ -4,18 +4,14 @@ else
   require 'rubygems'
 end
 
-begin
-  require 'sqlite3'
-rescue LoadError
-  $stderr.print "Warning: no sqlite installed"
-end
-
 require 'fileutils'
 require 'optparse'
 require 'ostruct'
-require 'bio'
 require 'csv'
 
+require 'bio'
+#autoload :SQLite3, 'sqlite3' # => no such file to load -- sqlite3 (LoadError)
+require 'sqlite3'
 
 module Genfrag
 class App

data/lib/genfrag/app/command.rb

@@ -50,15 +50,15 @@ class Command
   def standard_options
     {
       :verbose => ['-v', '--verbose', 'enable verbose output',
-          lambda {
+          lambda { |ruby19bug|
             options[:verbose] = true
           }],
       :tracktime => ['-m', '--tracktime', 'track execution time',
-          lambda {
+          lambda { |ruby19bug|
             options[:tracktime] = true
           }],
       :quiet => ['-q', '--quiet', 'silence output',
-          lambda {
+          lambda { |ruby19bug|
             options[:quiet] = true
           }],
       :indir => ['-i', '--in DIR', String, 'input directory', "(default #{Dir.pwd})",
@@ -77,8 +77,8 @@ class Command
           lambda { |value|
             options[:re3] = value
           }],
-      :sqlite => ['-t', '--sqlite', 'use sqlite', '(default is CSV)',
-          lambda {
+      :sqlite => ['-t', '--sqlite', 'use sqlite', '(default is tab-delimited)',
+          lambda { |ruby19bug|
             options[:sqlite] = true
           }],
       :filelookup => ['-l', '--lookup FILE', String, "name of the frequency lookup file generated by 'index'",

data/lib/genfrag/app/index_command.rb

@@ -128,7 +128,7 @@ END
     end
     
     if @ops.verbose
-      @sizes.each { |@entry| cli_p(cli, @entry.inspect) }
+      @sizes.each { |entry| cli_p(cli, entry.inspect) }
     else
       cli_p(cli, "Cut sites found: #{@sizes.values.flatten.size / 2}")
     end

data/lib/genfrag/app/index_command/db.rb

@@ -64,11 +64,11 @@ class IndexCommand < Command
     end
 
     def write_entry_to_fasta_sqlite(normalized_fasta_id, seq, definitions)
-      @normalized_fasta.execute( "insert into db_normalized_fasta values ( ?, ?, ? )", normalized_fasta_id, CSV.generate_line(definitions), seq )
+      @normalized_fasta.execute( "insert into db_normalized_fasta values ( ?, ?, ? )", normalized_fasta_id, definitions.join('!!-genfrag-!!'), seq )
     end
     
     def write_entry_to_fasta_csv(normalized_fasta_id, seq, definitions)
-      @normalized_fasta.puts [normalized_fasta_id,CSV.generate_line(definitions),seq].join("\t")
+      @normalized_fasta.puts [normalized_fasta_id,definitions.join('!!-genfrag-!!'),seq].join("\t")
     end
     
     

data/lib/genfrag/app/search_command.rb

@@ -3,7 +3,6 @@ module Genfrag
 class App
 
 class SearchCommand < Command
-
   def cli_run( args )
     parse args
 
@@ -23,8 +22,8 @@ class SearchCommand < Command
     end
     
       if options[:fileadapters]
-      processed_adapters = SearchCommand::ProcessFile.process_tdf_adapters( IO.readlines( Genfrag.name_adapters(options[:fileadapters]) + '.tdf' ), options[:named_adapter5], options[:named_adapter3] )
-    end
+        processed_adapters = SearchCommand::ProcessFile.process_tdf_adapters( IO.readlines( Genfrag.name_adapters(options[:fileadapters]) + '.tdf' ), options[:named_adapter5], options[:named_adapter3] )
+      end
     
     run(options, processed_fasta_file, processed_freq_lookup, processed_adapters, true)
   end
@@ -252,7 +251,7 @@ END
           next if !good
         end
         
-        results << {:raw_frag => raw_frag, :primary_frag => primary_frag, :primary_frag_with_adapters => primary_frag_with_adapters, :complement_frag => complement_frag, :complement_frag_with_adapters => complement_frag_with_adapters, :entry => entry, :seq => seq}
+        results << {:raw_frag => raw_frag, :primary_frag => primary_frag, :primary_frag_with_adapters => primary_frag_with_adapters, :complement_frag => complement_frag, :complement_frag_with_adapters => complement_frag_with_adapters, :entry => entry, :seq => seq, :definitions => @sequences[entry[:fasta_id]][:definitions]}
       end
     end
   
@@ -265,6 +264,7 @@ END
       raise "shouldn't happen" if sorted_results[r[:seq]] != nil
       sorted_results[r[:seq]] = {}
       x = sorted_results[r[:seq]]
+      x['fasta definition'] = r[:definitions]
       x['sequence size'] = r[:seq].size
       x['fragment - primary strand'] = r[:primary_frag]
       x['fragment - complement strand'] = r[:complement_frag]
@@ -273,7 +273,7 @@ END
     end
 
     if @ops.verbose
-      ary = ['sequence size', 'fragment - primary strand', 'fragment - complement strand',
+      ary = ['fasta definition', 'sequence size', 'fragment - primary strand', 'fragment - complement strand',
         'fragment with adapters - primary strand', 'fragment with adapters - complement strand']    
     else
       ary = ['fragment with adapters - primary strand', 'fragment with adapters - complement strand']    

data/lib/genfrag/app/search_command/process_file.rb

@@ -13,7 +13,7 @@ class SearchCommand < Command
         f_normalized_fasta[1..-1].each do |line|
           line = line.chomp.split("\t")
           id = line[0].to_i
-          sequences[id] = {:definitions => CSV.parse_line(line[1]), :sequence => line[2]}
+          sequences[id] = {:definitions => line[1].split('!!-genfrag-!!'), :sequence => line[2]}
         end
         return sequences
       end
@@ -23,7 +23,7 @@ class SearchCommand < Command
         sequences = {}
         db_normalized_fasta.execute( "select * from db_normalized_fasta" ) do |row|
           id = row[0].to_i
-          sequences[id] = {:definitions => CSV.parse_line(row[1]), :sequence => row[2]}
+          sequences[id] = {:definitions => row[1].split('!!-genfrag-!!'), :sequence => row[2]}
         end
         return sequences
       end

data/spec/data/index_command/out/a.fasta.tdf

@@ -2,5 +2,5 @@ id	Definitions	Sequence
 1	At1g65300: mRNA 837bp	atgaagagaaagatgaagttatcgttaatagaaaacagtgtatcgaggaaaacaacattcaccaaaaggaagaaagggatgacgaagaaactaaccgagctagtcactctatgtggtgttgaagcatgtgcggtcgtctatagtccgttcaactcgatcccggaggcttggccgtcaagggaaggcgttgaagacgtggtgtcgaaatttatggagttgtcggtgttggaccggaccaagaagatggtggatcaagagacttttataagtcaaaggatcgccaaagaaaaagagcagctgcagaagctacgtgatgagaaccataattctcagattcgggagttaatgtttggttgtctcaaaggggagacgaatgtgtataatcttgatggaagggatcttcaagatttgagtttatatattgataagtatcttaatggtcttactcgcaggattgagatcctTAttgagaacggtgagtcttcttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcggatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctctttatgatttttatgatcagattccaaagaaaattcatggttttaatatgaatatgaataaggattcgaatcaaagtatggttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccaccccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctctag
 2	At1g65300: mRNA 837bp (shortened at end)	atgaagagaaagatgaagttatcgttaatagaaaacagtgtatcgaggaaaacaacattcaccaaaaggaagaaagggatgacgaagaaactaaccgagctagtcactctatgtggtgttgaagcatgtgcggtcgtctatagtccgttcaactcgatcccggaggcttggccgtcaagggaaggcgttgaagacgtggtgtcgaaatttatggagttgtcggtgttggaccggaccaagaagatggtggatcaagagacttttataagtcaaaggatcgccaaagaaaaagagcagctgcagaagctacgtgatgagaaccataattctcagattcgggagttaatgtttggttgtctcaaaggggagacgaatgtgtataatcttgatggaagggatcttcaagatttgagtttatatattgataagtatcttaatggtcttactcgcaggattgagatcctTAttgagaacggtgagtcttcttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcggatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctctttatgatttttatgatcag
 3	At1g65300: mRNA 837bp (shortened from start)	ttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcggatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctctttatgatttttatgatcagattccaaagaaaattcatggttttaatatgaatatgaataaggattcgaatcaaagtatggttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccaccccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctctag
-4	At1g02580 mRNA (2291 bp) UTR's and CDS,At1g02580 mRNA (2291 bp) UTR's and CDS (duplicate)	aggcgagtggttaatggagaaggaaaaccatgaggacgatggtgagggtttgccacccgaactaaatcagataaaagagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactcatgcttcacaccatcaatcgtttgacttaaaccagcccgctgcagaggatgataatggaggagacaacaaatcacttttgtcgagaatgcaaaacccacttcgtcatttcagtgcctcatctgattataattcttacgaagatcaaggttatgttcttgatgaggatcaagattatgctcttgaagaagatgtaccattatttcttgatgaagatgtaccattattaccaagtgtcaagcttccaattgttgagaagctaccacgatccattacatgggtcttcaccaaaagtagccagctgatggctgaaagtgattctgtgattggtaagagacaaatctattatttgaatggtgaggcactagaattgagcagtgaagaagatgaggaagatgaagaagaagatgaggaagaaatcaagaaagaaaaatgcgaattttctgaagatgtagaccgatttatatggacggttgggcaggactatggtttggatgatctggtcgtgcggcgtgctctcgccaagtacctcgaagtggatgtttcggacatattggaaagatacaatgaactcaagcttaagaatgatggaactgctggtgaggcttctgatttgacatccaagacaataactactgctttccaggattttgctgatagacgtcattgccgtcgttgcatgatattcgattgtcatatgcatgagaagtatgagcccgagtctagatccagcgaagacaaatctagtttgtttgaggatgaagatagacaaccatgcagtgagcattgttacctcaaggtgaggagtgtgacagaagctgatcatgtgatggataatgataactctatatcaaacaagattgtggtctcagatccaaacaacactatgtggacgcctgtagagaaggatctttacttgaaaggaattgagatatttgggagaaacagttgtgatgttgcattaaacatacttcgggggcttaagacgtgcctagagatttacaattacatgcgcgaacaagatcaatgtactatgtcattagaccttaacaaaactacacaaagacacaatcaggttaccaaaaaagtatctcgaaaaagtagtaggtcggtccgcaaaaaatcgagactccgaaaatatgctcgttatccgcctgctttaaagaaaacaactagtggagaagctaagttttataagcactacacaccatgcacttgcaagtcaaaatgtggacagcaatgcccttgtttaactcacgaaaattgctgcgagaaatattgcgggtgctcaaaggattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaattcctccttcaaaccaataaaaagattctcattggaaagtctgatgttcatggatggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatcagctcgaaatcgatgctcgccgtaaaggaaacgagttcaaatttctcaatcactcagcaagacctaactgctacgccaagttgatgattgtgagaggagatcagaggattggtctatttgcggagagagcaatcgaagaaggtgaggagcttttcttcgactactgctatggaccagaacatgcggattggtcgcgtggtcgagaacctagaaagactggtgcttctaaaaggtctaaggaagcccgtccagctcgttagtttttgatctgaggagaagcagcaattcaagcagtcctttttttatgttatggtatatcaattaataatgtaatgctattttgtgttactaaaccaaaacttaagtttctgttttatttgttttagggtgttttgtttgtatcatatgtgtcttaactttcaaagttttctttttgtatttcaatttaaaaacaatgtttatgttgtt
+4	At1g02580 mRNA (2291 bp) UTR's and CDS!!-genfrag-!!At1g02580 mRNA (2291 bp) UTR's and CDS (duplicate)	aggcgagtggttaatggagaaggaaaaccatgaggacgatggtgagggtttgccacccgaactaaatcagataaaagagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactcatgcttcacaccatcaatcgtttgacttaaaccagcccgctgcagaggatgataatggaggagacaacaaatcacttttgtcgagaatgcaaaacccacttcgtcatttcagtgcctcatctgattataattcttacgaagatcaaggttatgttcttgatgaggatcaagattatgctcttgaagaagatgtaccattatttcttgatgaagatgtaccattattaccaagtgtcaagcttccaattgttgagaagctaccacgatccattacatgggtcttcaccaaaagtagccagctgatggctgaaagtgattctgtgattggtaagagacaaatctattatttgaatggtgaggcactagaattgagcagtgaagaagatgaggaagatgaagaagaagatgaggaagaaatcaagaaagaaaaatgcgaattttctgaagatgtagaccgatttatatggacggttgggcaggactatggtttggatgatctggtcgtgcggcgtgctctcgccaagtacctcgaagtggatgtttcggacatattggaaagatacaatgaactcaagcttaagaatgatggaactgctggtgaggcttctgatttgacatccaagacaataactactgctttccaggattttgctgatagacgtcattgccgtcgttgcatgatattcgattgtcatatgcatgagaagtatgagcccgagtctagatccagcgaagacaaatctagtttgtttgaggatgaagatagacaaccatgcagtgagcattgttacctcaaggtgaggagtgtgacagaagctgatcatgtgatggataatgataactctatatcaaacaagattgtggtctcagatccaaacaacactatgtggacgcctgtagagaaggatctttacttgaaaggaattgagatatttgggagaaacagttgtgatgttgcattaaacatacttcgggggcttaagacgtgcctagagatttacaattacatgcgcgaacaagatcaatgtactatgtcattagaccttaacaaaactacacaaagacacaatcaggttaccaaaaaagtatctcgaaaaagtagtaggtcggtccgcaaaaaatcgagactccgaaaatatgctcgttatccgcctgctttaaagaaaacaactagtggagaagctaagttttataagcactacacaccatgcacttgcaagtcaaaatgtggacagcaatgcccttgtttaactcacgaaaattgctgcgagaaatattgcgggtgctcaaaggattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaattcctccttcaaaccaataaaaagattctcattggaaagtctgatgttcatggatggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatcagctcgaaatcgatgctcgccgtaaaggaaacgagttcaaatttctcaatcactcagcaagacctaactgctacgccaagttgatgattgtgagaggagatcagaggattggtctatttgcggagagagcaatcgaagaaggtgaggagcttttcttcgactactgctatggaccagaacatgcggattggtcgcgtggtcgagaacctagaaagactggtgcttctaaaaggtctaaggaagcccgtccagctcgttagtttttgatctgaggagaagcagcaattcaagcagtcctttttttatgttatggtatatcaattaataatgtaatgctattttgtgttactaaaccaaaacttaagtttctgttttatttgttttagggtgttttgtttgtatcatatgtgtcttaactttcaaagttttctttttgtatttcaatttaaaaacaatgtttatgttgtt
 5	At1g02580 - shortened for test - inserted cutpoint	gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca

data/spec/genfrag/app/search_command/process_file_spec.rb

@@ -51,7 +51,7 @@ describe Genfrag::App::SearchCommand::ProcessFile do
     describe 'with an array of data' do
       before :all do
         ary = [ %w(id Definitions Sequence),
-                [1,'DescA,DescB','seq-abc'],
+                [1,'DescA!!-genfrag-!!DescB','seq-abc'],
                 [2,'DescC','seq-def'],
                 [3,'DescD,DescE,DescF','seq-ghi'] ]
         d = ary.map {|x| x.join("\t")}

data/spec/genfrag_spec.rb

@@ -1,5 +1,9 @@
 
-require File.join(File.dirname(__FILE__), %w[spec_helper])
+if RUBY_VERSION < '1.9.2'
+  require File.join(File.dirname(__FILE__), %w[spec_helper])
+else
+  require File.join(Dir.pwd, File.dirname(__FILE__), %w[spec_helper])
+end
 
 describe Genfrag do
   

data/tasks/setup.rb

@@ -147,7 +147,7 @@ RCOV = "#{RUBY} -S rcov"
 RDOC = "#{RUBY} -S rdoc"
 GEM  = "#{RUBY} -S gem"
 
-%w(rcov spec/rake/spectask rubyforge bones facets/ansicode).each do |lib|
+%w(rcov spec/rake/spectask rubyforge bones facets/ansicode zentest).each do |lib|
   begin
     require lib
     Object.instance_eval {const_set "HAVE_#{lib.tr('/','_').upcase}", true}

data/tasks/zentest.rake

@@ -0,0 +1,36 @@
+if HAVE_ZENTEST
+
+# --------------------------------------------------------------------------
+if test(?e, PROJ.test.file) or not PROJ.test.files.to_a.empty?
+require 'autotest'
+
+namespace :test do
+  task :autotest do
+    Autotest.run
+  end
+end
+
+desc "Run the autotest loop"
+task :autotest => 'test:autotest'
+
+end  # if test
+
+# --------------------------------------------------------------------------
+if HAVE_SPEC_RAKE_SPECTASK and not PROJ.spec.files.to_a.empty?
+require 'autotest/rspec'
+
+namespace :spec do
+  task :autotest do
+    load '.autotest' if test(?f, '.autotest')
+    Autotest::Rspec.run
+  end
+end
+
+desc "Run the autotest loop"
+task :autotest => 'spec:autotest'
+
+end  # if rspec
+
+end  # if HAVE_ZENTEST
+
+# EOF

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: genfrag
 version: !ruby/object:Gem::Version 
-  version: 0.0.0.2
+  version: 0.0.0.3
 platform: ruby
 authors: 
 - Pjotr Prins and Trevor Wennblom
@@ -9,18 +9,18 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-03-16 00:00:00 -05:00
+date: 2009-08-06 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: bioruby
+  name: bio
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: "0"
+        version: 1.3.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: rake
@@ -30,7 +30,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.8.3
+        version: 0.8.4
     version: 
 - !ruby/object:Gem::Dependency 
   name: bones
@@ -40,7 +40,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 2.4.2
+        version: 2.5.1
     version: 
 description: This is a development release. Some features are functional at this time.  Genfrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers.
 email: trevor@corevx.com
@@ -101,6 +101,7 @@ files:
 - tasks/spec.rake
 - tasks/svn.rake
 - tasks/test.rake
+- tasks/zentest.rake
 has_rdoc: true
 homepage: http://genfrag.rubyforge.org
 post_install_message: |