forage 0.0.2 → 0.0.3

data/bin/forage

@@ -7,10 +7,13 @@ if ARGV.length != 2
   exit
 end
 
-forage = Forage.new File.open(ARGV[0]), ARGV[1]
+filename, query = ARGV[0], ARGV[1]
+
+
+forage = Forage.new File.open(filename), query
 
 forage.each do |matches|
   matches[1].each_with_index do |match, i|
-    puts ">#{matches[0]}:#{i}\n#{match}"
+    puts ">#{matches[0]}:#{i}\n#{match.join}"
   end
 end

data/lib/forage.rb

@@ -4,10 +4,19 @@ class Forage
   def initialize(handle, query)
     @handle = handle
     
-    @iupac = Hash.new { |h, k| h[k] = k }.merge(
-      { 'R' => 'AG', 'Y' => 'CTUY', 'S' => 'GCS', 'W' => 'ATUW', 'K' =>
-      'GTUK', 'M' => 'ACM', 'B' => 'CGTUB', 'D' => 'AGTUD', 'H' => 'ACTUH',
-      'V' => 'ACGV', 'N' => '.', '-' => '.'}
+    @iupac = Hash.new{ |h, k| h[k] = k }.merge({
+      'R' => '[AG]',
+      'Y' => '[CTUY]',
+      'S' => '[GCS]',
+      'W' => '[ATUW]',
+      'K' => '[GTUK]',
+      'M' => '[ACM]',
+      'B' => '[CGTUB]',
+      'D' => '[AGTUD]', 
+      'H' => '[ACTUH]',
+      'V' => '[ACGV]',
+      'N' => '.',
+      '-' => '.'}
     )
     
     @regex = self.convert query
@@ -26,7 +35,7 @@ class Forage
 
   # convert string to regex
   def convert(s)
-    @regex = s.each_char.collect { |n| "[#{@iupac[n]}]" }.join
+    @regex = s.each_char.collect { |n| "#{@iupac[n]}" }.join
     Regexp.new @regex
   end
   
@@ -39,7 +48,7 @@ class Forage
         sequence = ''
         header = line[1..-1].strip
       else
-        sequence << line.strip.tr(' ','')
+        sequence << line.strip.tr(' ','').upcase
       end
     end
     yield [ header, sequence ]

metadata

@@ -1,48 +1,65 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: forage
-version: !ruby/object:Gem::Version
-  version: 0.0.2
-  prerelease: 
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 3
+  version: 0.0.3
 platform: ruby
-authors:
+authors: 
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-07-06 00:00:00.000000000Z
+
+date: 2011-07-06 00:00:00 -04:00
+default_executable: forage
 dependencies: []
-description: Forage is grep for nucleotide data. With Forage, you can grep nucleotide
-  sequences in FASTA using the IUPAC ambiguous nucleotides code.
+
+description: Forage is grep for nucleotide data. With Forage, you can grep nucleotide sequences in FASTA using the IUPAC ambiguous nucleotides code. Useful for predicting PCR products.
 email: harekrishna@gmail.com
-executables:
+executables: 
 - forage
 extensions: []
+
 extra_rdoc_files: []
-files:
+
+files: 
 - bin/forage
 - lib/forage.rb
+has_rdoc: true
 homepage: http://www.github.com/audy/forage
 licenses: []
+
 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
-      version: '0'
-required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
 requirements: []
+
 rubyforge_project: forage
-rubygems_version: 1.8.5
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: Grep for nucleotide data.
 test_files: []
+