fasta_util 0.2.2 → 0.2.3

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.3

data/bin/fasta_util

@@ -56,12 +56,16 @@ class FastaUtility < Thor
   method_option :length_cutoff, :aliases => '-l', :type => :numeric, :default => 0,  :desc => 'Only entries with length >= cutoff will be returned.'
   method_option :inverse_match,  :aliases => '-v', :type => :boolean, :desc => "Return the inverse of the match after all the other filters have been applied."
   method_option :defline_grep,  :aliases => '-d', :type => :string,  :default => '', :desc => "A regular expression, used to search the entry's definition line."
+  method_option :definitions_file, :aliases => '-f', :type => :string, :default => '', :desc => "A file with definitions to match, one per line."
   def filter(filename)
     invoke :filecheck
+    invoke :filecheck, [options.definitions_file]
+    requested_definitions = File.open(options.definitions_file).map{|definition| definition.strip}
     Bio::FlatFile.open(filename).each do |entry|
       passed = true
       passed &&= (entry.length >= options.length_cutoff)
       passed &&= (entry.definition.match(Regexp.new(options.defline_grep)))
+      passed &&= (requested_definitions.include? entry.definition)
       passed = !passed if options.inverse_match
       puts entry if passed
     end

data/fasta_util.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{fasta_util}
-  s.version = "0.2.2"
+  s.version = "0.2.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["robsyme"]
-  s.date = %q{2011-02-18}
+  s.date = %q{2011-03-09}
   s.default_executable = %q{fasta_util}
   s.description = %q{Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.}
   s.email = %q{rob.syme@gmail.com}

metadata

@@ -2,7 +2,7 @@
 name: fasta_util
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors: 
 - robsyme
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-18 00:00:00 +08:00
+date: 2011-03-09 00:00:00 +08:00
 default_executable: fasta_util
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -125,7 +125,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -443172315906729972
+      hash: 1980362110866900024
       segments: 
       - 0
       version: "0"