vcf 0.0.1

data/lib/vcf.rb

@@ -0,0 +1,60 @@
+class Vcf
+public
+  attr_accessor :chrom, :pos, :id, :ref, :alt, :qual, :filter, :info, :format, :samples
+
+  def initialize(line=nil)
+    samples = {}
+  end
+
+  def parse_line(line, sample_names=nil)
+    f = line.split("\t", -1)
+    raise "VCF lines must have at least 8 fields" if f.size < 8
+    chrom = f[0]
+    pos = f[1].to_i
+    id = f[2]
+    ref = f[3]
+    alt = f[4]
+    qual = f[5].to_i
+    filter = f[6]
+
+    info = {}
+    info_vec = f[7].split(";")
+    info_vec.each do |x|
+      keyval = x.split("=", -1)
+      if keyval.size == 2 # If it's key=value
+        info[keyval[0]] = keyval[1]
+      else # Otherwise, it's just a flag
+        info[x] = ""
+      end
+    end
+
+    samples = {}
+    return true if f.size == 8  # Has just upto info
+    raise "Can't have format with no samples" if f.size == 9
+    
+    format = f[8]
+
+    sample_keys = format.split(":")
+
+    num_samples = f.size - 9 # How many fields are past the format
+
+    if sample_names == nil # Make the sample names just ["1", "2", ... , "num_samples}"
+      sample_names = (1..num_samples).to_a.map{|i| i.to_s} 
+    elsif f.size != num_samples
+      raise "Expected #{sample_names.size} but got #{num_samples}"
+    end
+
+    sample_names.each_with_index do |sample_name, sample_index|
+      i = sample_index + 9 # index into columns (f)
+      sample_values = f[i].split(":")
+      raise "Expected number of sample values to match number of sample keys in FORMAT column" if sample_values.size != sample_keys.size
+      samples[sample_name] = {}
+      sample_keys.each_with_index {|key, value_index| samples[sample_name][k] = sample_values[value_index]}
+    end
+    
+    return true;
+  end
+
+private
+  attr_accessor :
+end

metadata

@@ -0,0 +1,54 @@
+--- !ruby/object:Gem::Specification 
+name: vcf
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.1
+platform: ruby
+authors: 
+- Jesse Rodriguez
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-07-01 00:00:00 Z
+dependencies: []
+
+description: Lightweight VCF interface for ruby
+email: jesserod@cs.stanford.edu
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- lib/vcf.rb
+homepage: http://rubygems.org/gems/vcf
+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: VCF (Variant Call Format) interface for ruby
+test_files: []
+