bio-kmer_counter 0.0.2 → 0.0.3

data/README.md

@@ -15,7 +15,7 @@ Note: this software is under active development!
 ## Installation
 
 ```sh
-    gem install bio-kmer_counter
+gem install bio-kmer_counter
 ```
 
 ## Usage
@@ -25,11 +25,16 @@ content, reporting the fingerprint of 5kb windows in each sequence separately,
 plus the leftover part if it is longer than 2kb:
 
 ```sh
-    kmer_counter.rb <fasta_file> >tetranucleotide_content.csv
+kmer_counter.rb <fasta_file> >tetranucleotide_content.csv
 ```
 
 The fingerprints are reported in percentages. Well, between 0 and 1, that is.
-From there it is up to you how to use the fingerprints, sorry.
+From there it is up to you how to use the fingerprints, sorry. For the full
+gamut of options, see
+
+```sh
+kmer_counter.rb -h
+```
 
 ## Project home page
 

data/VERSION

@@ -1 +1 @@
-0.0.2
+0.0.3

data/bin/kmer_counter.rb

@@ -23,7 +23,7 @@ options = {
   :progressbar => true,
 }
 
-OptionParser.new do |opts|
+o = OptionParser.new do |opts|
   opts.banner = USAGE
 
   opts.on("-w", "--window-size SIZE", "Length of the window to be used [default #{options[:window_size]}]") do |v|
@@ -92,7 +92,7 @@ OptionParser.new do |opts|
   opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG") do | s |
     Bio::Log::CLI.trace(s)
   end
-end.parse!
+end; o.parse!
 if ARGV.length != 1
   $stderr.puts o
   exit 1

data/lib/bio-kmer_counter/kmer_counter.rb

@@ -1,4 +1,4 @@
-# Initialise the hash of the different
+
 module Bio
   class Sequence
     class NA
@@ -12,6 +12,8 @@ module Bio
     end
 
     class Kmer
+      # Return a hash of Strings to 0, for each kmer of length k. For instance
+      # empty_full_kmer_hash(1) => {'A'=>0, 'T'=>0, 'C'=>0, 'G'=>0}
       def self.empty_full_kmer_hash(k=4)
         return @empty_full_hash.dup unless @empty_full_hash.nil?
         
@@ -29,6 +31,13 @@ module Bio
         counts
       end
       
+      # Take a kmer hash, and merge those keys to the lowest lexigraphical form
+      # (See Bio::Sequence::NA#lowest_lexigraphical_form for what this means)
+      # When 2 keys are reverse complements they get merged into one hash entry, 
+      # where the key is the lowest_lexigraphical_form of the two and the
+      # value is the sum of the original 2 values
+      # 
+      # For instance {'A'=>2,'T'=>5} #=> {'A'=>7}  
       def self.merge_down_to_lowest_lexigraphical_form(hash)
         keys = empty_full_kmer_hash.keys
         

data/test/test_bio-kmer_counter.rb

@@ -95,4 +95,11 @@ class TestBioKmerCounter < Test::Unit::TestCase
       end
     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
 end

metadata

@@ -1,179 +1,175 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-kmer_counter
-version: !ruby/object:Gem::Version 
-  hash: 27
+version: !ruby/object:Gem::Version
+  version: 0.0.3
   prerelease: 
-  segments: 
-  - 0
-  - 0
-  - 2
-  version: 0.0.2
 platform: ruby
-authors: 
+authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-06-08 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 1
-        - 4
-        - 2
-        version: 1.4.2
-  version_requirements: *id001
+date: 2012-07-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: bio
-  prerelease: false
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 51
-        segments: 
-        - 0
-        - 11
-        - 0
-        version: 0.11.0
-  version_requirements: *id002
-  name: progressbar
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: progressbar
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.11.0
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 41
-        segments: 
-        - 0
-        - 5
-        - 17
-        version: 0.5.17
-  version_requirements: *id003
-  name: parallel
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.11.0
+- !ruby/object:Gem::Dependency
+  name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.17
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 21
-        segments: 
-        - 1
-        - 0
-        - 1
-        version: 1.0.1
-  version_requirements: *id004
-  name: bio-logger
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.17
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.1
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id005
-  name: shoulda
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-- !ruby/object:Gem::Dependency 
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
-  version_requirements: *id006
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: rdoc
-  prerelease: false
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-- !ruby/object:Gem::Dependency 
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 49
-        segments: 
-        - 1
-        - 8
-        - 3
-        version: 1.8.3
-  version_requirements: *id007
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
   name: jeweler
-  prerelease: false
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
   type: :development
-- !ruby/object:Gem::Dependency 
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 61
-        segments: 
-        - 1
-        - 0
-        - 21
-        version: 1.0.21
-  version_requirements: *id008
-  name: bundler
   prerelease: false
-  type: :development
-- !ruby/object:Gem::Dependency 
-  requirement: &id009 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
-  version_requirements: *id009
-  name: rdoc
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-description: A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: A biogem for counting small kmers for fingerprinting nucleotide sequences.
+  See README for details.
 email: gmail.com after donttrustben
-executables: 
+executables:
 - kmer_counter.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.md
-- README.rdoc
-files: 
+files:
 - .document
 - .travis.yml
 - Gemfile
 - LICENSE.txt
 - README.md
-- README.rdoc
 - Rakefile
 - VERSION
 - bin/kmer_counter.rb
@@ -182,37 +178,31 @@ files:
 - test/helper.rb
 - test/test_bio-kmer_counter.rb
 homepage: http://github.com/wwood/bioruby-kmer_counter
-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: -309263761
+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
 signing_key: 
 specification_version: 3
 summary: A biogem for counting small kmers for fingerprinting nucleotide sequences
 test_files: []
-

data/README.rdoc

@@ -1,48 +0,0 @@
-= bio-kmer_counter
-
-{<img
-src="https://secure.travis-ci.org/wwood/bioruby-kmer_counter.png"
-/>}[http://travis-ci.org/#!/wwood/bioruby-kmer_counter]
-
-Full description goes here
-
-Note: this software is under active development!
-
-== Installation
-
-        gem install bio-kmer_counter
-
-== Usage
-
-== Developers
-
-To use the library 
-
-        require 'bio-kmer_counter'
-
-The API doc is online. For more code examples see also the test files in
-the source tree.
-        
-== Project home page
-
-Information on the source tree, documentation, issues and how to contribute, see
-
-  http://github.com/wwood/bioruby-kmer_counter
-
-The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
-
-== Cite
-
-  If you use this software, please cite one of
- 
-* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
-* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
-
-== Biogems.info
-
-This Biogem is published at http://biogems.info/index.html#bio-kmer_counter
-
-== Copyright
-
-Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
-