bix 0.0.1

data/lib/bix.rb

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+require "#{File.dirname(__FILE__)}/bix/fastq"

data/lib/bix/fastq.rb

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+class Fastq
+  attr_accessor :header, :seq, :qual, :invalid
+
+  def initialize(header="", seq="", qual="")
+    @header = header
+    @seq = seq
+    @qual = qual
+  end
+
+  def from_io(io)
+    @header = io.gets
+    @seq = io.gets
+    io.gets #plus line
+    @qual = io.gets
+
+    return false if @header == nil || @seq == nil || @qual == nil
+    return true
+  end
+
+  def qual_val(i)
+    return @qual[i].ord
+  end
+
+  def to_lines
+    return "#{@header}\n#{@seq}\n+\n#{@qual}"
+  end
+
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: bix
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.1
+platform: ruby
+authors: 
+- Jesse Rodriguez
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-08-09 00:00:00 Z
+dependencies: []
+
+description: Lightweight bioinformatics tools for Ruby, with a focus on next-gen sequencing
+email: jesserod@cs.stanford.edu
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- lib/bix.rb
+- lib/bix/fastq.rb
+homepage: http://rubygems.org/gems/bix
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.5
+signing_key: 
+specification_version: 3
+summary: Lightweight bioinformatics tools for Ruby
+test_files: []
+