bio-kmer_counter 0.1.0 → 0.1.1

data/Gemfile

@@ -11,8 +11,8 @@ gem 'bio-logger', '>=1.0.1'
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "shoulda", ">= 0"
-  gem "rdoc", "~> 3.12"
-  gem "jeweler", "~> 1.8.3"
+  gem "rdoc", ">= 3.12"
+  gem "jeweler",">= 1.8.3"
   gem "bundler", ">= 1.0.21"
-  gem "rdoc", "~> 3.12"
+  gem "rdoc", ">= 3.12"
 end

data/README.md

@@ -4,28 +4,47 @@
 
 bio-kmer_counter is a simple [biogem](http://biogem.info) for fingerprinting
 nucleotide sequences by counting the occurences of particular kmers in the
-sequence. The methodology is not new, for references see [Teeling et. al. 2004](http://www.biomedcentral.com/1471-2105/5/163). The default parameters are derived from the methods section of [Dick et. al. 2009](http://genomebiology.com/content/10/8/R85).
+sequence. The methodology is not new, for a reference see 
+[Teeling et. al. 2004](http://www.biomedcentral.com/1471-2105/5/163). 
+The default parameters are derived from the well explained methods section of
+[Dick et. al. 2009](http://genomebiology.com/content/10/8/R85).
 
 This methodology is quite different to that of other software that counts
 kmer content with longer kmers, e.g. [khmer](https://github.com/ged-lab/khmer).
-Here only small kmers are intended (e.g. 1mer or 4mer).
-
-Note: this software is under active development!
+Here only small kmers are intended (e.g. 1-mer or 4-mer).
 
 ## Installation
 
+After installing [Ruby](http://www.ruby-lang.org) itself, install the bio-kmer_counter rubygem:
+
 ```sh
 gem install bio-kmer_counter
 ```
 
-## Usage
+bio-kmer_counter is only tested on Linux, but probably works on OSX too. It might even work on Windows if
+the progress bar is turned off. Maybe.
 
-To analyse a fasta file (that contains one or more sequences in it) for 4-mer (tetranucleotide)
-content, reporting the fingerprint of 5kb windows in each sequence separately,
-plus the leftover part if it is longer than 2kb:
+## Usage
 
+The default parameters analyse a fasta file that contains one or more sequences in it for 4-mer (tetranucleotide)
+content. By default, any sequence 
+in the fasta file 2kb or longer is included at least once. Sequences are split up
+into 5kb windows if they are that long, and each window is reported separately.
+If the leftover bit at the end after any 5kb windows is 2kb or longer then this is also included.
+
+By default, each 4 base window in the input sequence is included exactly once in the output file.
+To account for the fact 
+that the directions of sequences with respect to each other are presumed to be unknown (as is the
+case for de-novo genome assembly), either the forward or reverse complement is included. Which one
+(forward or reverse) depends on which one comes first alphabetically. So for instance if the window is ```CTTT```, then ```AAAG```
+is used. Accounting for palindromic sequences like ```ATAT```, there are 136 of these lowest lexigraphical 4-mers.
+So there are 136 columns in the output, plus one for the name of the window. Using only 1 is
+actually slightly different than the method outlined in Dick et. al. 2009, but we
+don't expect the results to differ.
+
+Example usage, if you wish to fingerprint a fasta file ```my_nucleotide_sequences.fasta```:
 ```sh
-kmer_counter.rb <fasta_file> >tetranucleotide_content.csv
+kmer_counter.rb my_nucleotide_sequences.fasta >tetranucleotide_content.csv
 ```
 
 The fingerprints are reported in percentages. Well, between 0 and 1, that is.

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bin/kmer_counter.rb

@@ -64,8 +64,8 @@ o = OptionParser.new do |opts|
   opts.on("-l", "--window-length", "print the length of the window in the output [default #{options[:sequence_length]}]") do |v|
     options[:sequence_length] = true
   end
-  
-  
+
+
   # logger options
   opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") do |q|
     Bio::Log::CLI.trace('error')
@@ -90,7 +90,7 @@ Bio::Log::CLI.configure(LOG_NAME)
 
 # Print headers
 print "ID\t"
-print Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form(Bio::Sequence::Kmer.empty_full_kmer_hash(options[:kmer])).keys.join("\t")
+print Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form(Bio::Sequence::Kmer.empty_full_kmer_hash(options[:kmer])).keys.sort.join("\t")
 print "\tWindowLength" if options[:sequence_length]
 print "\tcontig" if options[:contig_name]
 puts
@@ -99,7 +99,7 @@ orig = Bio::Sequence::Kmer.empty_full_kmer_hash(options[:kmer])
 process_window = lambda do |window,kmer,sequence_name,contig_name|
   counts = orig.dup
   num_kmers_counted = 0
-  
+
   window.window_search(options[:kmer],1) do |tetranucleotide|
     str = tetranucleotide.to_s
     next unless str.gsub(/[ATGC]+/,'') == ''
@@ -107,10 +107,10 @@ process_window = lambda do |window,kmer,sequence_name,contig_name|
     counts[str]+=1
     #counts[Bio::Sequence::NA.new(tetranucleotide).lowest_lexigraphical_form.to_s.upcase] += 1
   end
-  
+
   # Merge everything into lowest lexigraphical form
   new_counts = Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form counts
-  
+
   if num_kmers_counted == 0
     log.warn "Skipping window #{sequence_name} because few/none ATGC's were detected (was it all N's?)"
   else
@@ -127,7 +127,7 @@ end
 fasta_filename = ARGV[0]
 progress = nil
 progress = ProgressBar.new('kmer_counter', `grep -c '>' '#{fasta_filename}'`.to_i) if options[:progressbar]
-ff = Bio::FlatFile.open(fasta_filename) 
+ff = Bio::FlatFile.open(fasta_filename)
 
 ff.each do |sequence|
   window_counter = 0

data/test/data/100random.fa

@@ -0,0 +1,2 @@
+>random
+GCAGAGCACCTCCGCGTGACATTCTATTATGGAATTGAAGTCCAGTCAGACCAGTACCCTTGCACAGGCAATACATTGGAACTGGATCAGAACTTCCTAC

data/test/helper.rb

@@ -14,5 +14,7 @@ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'bio-kmer_counter'
 
+TEST_DATA_DIR = File.join(File.dirname(__FILE__), 'data')
+
 class Test::Unit::TestCase
 end

data/test/test_bio-kmer_counter.rb

@@ -8,12 +8,12 @@ class TestBioKmerCounter < Test::Unit::TestCase
     assert_equal Bio::Sequence::NA.new('AA'), Bio::Sequence::NA.new('TT').lowest_lexigraphical_form
     assert_equal Bio::Sequence::NA.new('AG'), Bio::Sequence::NA.new('CT').lowest_lexigraphical_form
   end
-  
+
   should 'test_empty_full_kmer_hash' do
     answer = {}; %w(A C G T).each{|k| answer[k] = 0}
     assert_equal answer, Bio::Sequence::Kmer.empty_full_kmer_hash(1)
   end
-  
+
   should 'test merge down' do
     answer = {}; %w(A C).each{|k| answer[k] = 0}
     full = Bio::Sequence::Kmer.empty_full_kmer_hash(1)
@@ -21,11 +21,11 @@ class TestBioKmerCounter < Test::Unit::TestCase
     full = Bio::Sequence::Kmer.empty_full_kmer_hash #defaults to kmer hash length 4
     assert_equal 136, Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form(full).length
   end
-  
+
   def script_path
     File.join(File.dirname(__FILE__),'..','bin','kmer_counter.rb')
   end
-  
+
   should 'test_running1' do
     Tempfile.open('one') do |tempfile|
       tempfile.puts '>one'
@@ -35,7 +35,7 @@ class TestBioKmerCounter < Test::Unit::TestCase
       assert_equal "ID\tA\tC\none_0\t0.6\t0.4\n", `#{script_path} -w 5 -k 1 #{tempfile.path}`
     end
   end
-  
+
   should 'not whack out when there isnt any sequence to count' do
     Tempfile.open('one') do |tempfile|
       tempfile.puts '>one'
@@ -45,13 +45,13 @@ class TestBioKmerCounter < Test::Unit::TestCase
       assert_equal "ID\tA\tC\n", `#{script_path} -w 5 -k 1 #{tempfile.path}`
     end
   end
-  
+
   should 'give correct increments in window numbering' do
     Tempfile.open('one') do |tempfile|
       tempfile.puts '>one'
       tempfile.puts 'ATGCATGCAT' #10 letters long
       tempfile.close
-      
+
       expected = "ID\tA\tC\n"+
       "one_0\t0.5\t0.5\n"+
       "one_1\t0.5\t0.5\n"+
@@ -60,14 +60,14 @@ class TestBioKmerCounter < Test::Unit::TestCase
       assert_equal expected, `#{script_path} -w 4 -k 1 -m 2 #{tempfile.path}`
     end
   end
-  
+
   should "print help when no arguments are given" do
     command = "#{script_path}"
     Open3.popen3(command) do |stdin, stdout, stderr|
       assert stderr.readlines[0].match(/^Usage: kmer_counter/)
     end
   end
-  
+
   should 'work with lowercase' do
     Tempfile.open('one') do |tempfile|
       tempfile.puts '>one'
@@ -77,4 +77,31 @@ class TestBioKmerCounter < Test::Unit::TestCase
       assert_equal "ID\tA\tC\none_0\t0.6\t0.4\n", `#{script_path} -w 5 -k 1 #{tempfile.path}`
     end
   end
+
+  should 'by default count contigs greater than 2kb but less than 5kb' do
+    Tempfile.open('one') do |tempfile|
+      tempfile.puts '>one'
+      tempfile.puts 'A'*2500
+      tempfile.close
+
+      assert_equal "ID\tA\tC\none_leftover_0\t1.0\t0.0\n", `#{script_path} -k 1 #{tempfile.path}`
+    end
+  end
+
+  should 'by default count contigs greater than 2kb but less than 5kb' do
+    Tempfile.open('one') do |tempfile|
+      tempfile.puts '>one'
+      tempfile.puts 'A'*7500
+      tempfile.close
+
+      assert_equal "ID\tA\tC\none_0\t1.0\t0.0\none_leftover_1\t1.0\t0.0\n", `#{script_path} -k 1 #{tempfile.path}`
+    end
+  end
+
+  should 'work simulated example with kmer length = 2' do
+    expected = %w(ID	AA	AC	AG	AT	CA	CC	CG	GA	GC	TA).join("\t")+"\n"+
+    %w(random_leftover_0	0.1111111111111111	0.13131313131313133	0.1414141414141414	0.0707070707070707	0.1717171717171717	0.1111111111111111	0.020202020202020204	0.1414141414141414	0.050505050505050504	0.050505050505050504).join("\t")+"\n"
+
+    assert_equal expected, `#{script_path} -k 2 -m 1 #{File.join(TEST_DATA_DIR,'100random.fa')}`
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-kmer_counter
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-29 00:00:00.000000000 Z
+date: 2013-03-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &85076110 !ruby/object:Gem::Requirement
+  requirement: &73018740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *85076110
+  version_requirements: *73018740
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &85075540 !ruby/object:Gem::Requirement
+  requirement: &73018270 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.11.0
   type: :runtime
   prerelease: false
-  version_requirements: *85075540
+  version_requirements: *73018270
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &85075130 !ruby/object:Gem::Requirement
+  requirement: &73017680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 0.5.17
   type: :runtime
   prerelease: false
-  version_requirements: *85075130
+  version_requirements: *73017680
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &85074690 !ruby/object:Gem::Requirement
+  requirement: &73016840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: 1.0.1
   type: :runtime
   prerelease: false
-  version_requirements: *85074690
+  version_requirements: *73016840
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &85074250 !ruby/object:Gem::Requirement
+  requirement: &73016590 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,32 +65,32 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *85074250
+  version_requirements: *73016590
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &85073740 !ruby/object:Gem::Requirement
+  requirement: &73016160 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *85073740
+  version_requirements: *73016160
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &85093940 !ruby/object:Gem::Requirement
+  requirement: &73015700 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *85093940
+  version_requirements: *73015700
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &85093260 !ruby/object:Gem::Requirement
+  requirement: &73015320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,18 +98,18 @@ dependencies:
         version: 1.0.21
   type: :development
   prerelease: false
-  version_requirements: *85093260
+  version_requirements: *73015320
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &85092790 !ruby/object:Gem::Requirement
+  requirement: &73015000 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *85092790
+  version_requirements: *73015000
 description: A biogem for counting small kmers for fingerprinting nucleotide sequences.
   See README for details.
 email: gmail.com after donttrustben
@@ -130,6 +130,7 @@ files:
 - bin/kmer_counter.rb
 - lib/bio-kmer_counter.rb
 - lib/bio-kmer_counter/kmer_counter.rb
+- test/data/100random.fa
 - test/helper.rb
 - test/test_bio-kmer_counter.rb
 homepage: http://github.com/wwood/bioruby-kmer_counter
@@ -147,7 +148,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 285575987
+      hash: -117512543
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: