bix 0.0.3 → 0.0.5

data/lib/bix.rb

@@ -5,4 +5,5 @@ end
 require "#{File.dirname(__FILE__)}/bix/fastq"
 require "#{File.dirname(__FILE__)}/bix/fasta"
 require "#{File.dirname(__FILE__)}/bix/blast"
+require "#{File.dirname(__FILE__)}/bix/gtf"
 

data/lib/bix/fastq.rb

@@ -11,10 +11,15 @@ module Bix
     def from_io(io)
       @header = io.gets
       @seq = io.gets
-      io.gets #plus line
+      io.gets # Throw away + line
       @qual = io.gets
 
       return false if @header == nil || @seq == nil || @qual == nil
+
+      @header.chomp!
+      @seq.chomp!
+      @qual.chomp!
+
       return true
     end
 

data/lib/bix/gtf.rb

@@ -0,0 +1,73 @@
+require 'csv'
+
+module Bix
+  class Gtf
+    attr_accessor :chr, :prog, :feature, :start, :stop, :score, :strand, :frame, :props
+
+    def from_line(line)
+      f = line.chomp.split("\t", -1)
+      @chr = f[0]
+      @prog = f[1]
+      @feature = f[2]
+      @start = f[3].to_i
+      raise if @start < 1
+      @stop = f[4].to_i
+      raise if @stop < 1
+      @score = f[5].to_f
+      @strand = f[6]
+      raise if @strand.size > 1
+      @frame = f[7].to_i
+
+      group = f[8]
+
+      group.gsub!(/; /, " ") # Remove semicolons
+      group.gsub!(/;$/, "") # Remove semicolons
+      f = CSV::parse_line(group, :col_sep => ' ')
+      raise "Unexpected number of fields in group: '#{f[7]}'" unless f.size % 2 == 0
+
+      @props = {}
+      while f.size > 0
+        key = f.shift
+        value = f.shift
+
+        @props[key] = value
+      end
+    end
+
+    # E.g. to get all exons
+    def self.get_all(io, feature_regex=//)
+      gtfs = []
+      for line in io
+        g = Gtf.new
+        g.from_line(line)
+        if g.feature =~ feature_regex
+          gtfs << g
+        end
+      end
+      return gtfs
+    end
+
+    def self.get_all_by_prop(io, prop_key, feature_regex=//)
+      gtfs = get_all(io, feature_regex)
+      gtfs_by_key = {}
+      for g in gtfs
+        gtfs_by_key[g.props[prop_key]] ||= []
+        gtfs_by_key[g.props[prop_key]] << g
+      end
+      return gtfs_by_key
+    end
+
+    def to_s
+      propstr = ""
+      i = 0
+      for key, value in @props
+        if i > 0
+          propstr << " "
+        end
+        propstr << "#{key} \"#{value}\";"
+        i += 1
+      end
+      return [@chr, @prog, @feature, @start, @stop, @score, @strand, @frame, propstr].join("\t")
+    end
+  end
+end

metadata

@@ -2,7 +2,7 @@
 name: bix
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.3
+  version: 0.0.5
 platform: ruby
 authors: 
 - Jesse Rodriguez
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-02 00:00:00 Z
+date: 2012-02-29 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: swak
@@ -58,6 +58,7 @@ files:
 - lib/bix/fasta.rb
 - lib/bix/fastq.rb
 - lib/bix/blast.rb
+- lib/bix/gtf.rb
 homepage: https://github.com/jesserod/bixruby
 licenses: []