bio-tm_hmm 0.1.0 → 0.2.0

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/bin/biotm_hmm

@@ -23,11 +23,11 @@ if $0 == __FILE__
       "\tfasta file can also be piped in on STDIN.",
       "\twithout arguments, a description of the transmembranes is printed out for each input sequence"
     ]
-    opts.on('-f','--filter-in','Print those sequences that have a transmembrane domain') do
-      options[:filter_in] = true
+    opts.on('-f','--filter-in [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are printed out') do |m|
+      options[:filter_in] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
     end
-    opts.on('-g','--filter-out','Print those sequences that do NOT have a transmembrane domain') do
-      options[:filter_out] = true
+    opts.on('-g','--filter-out [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that do NOT have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are filtered out') do |m|
+      options[:filter_out] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
     end
   end
   o.parse!
@@ -58,12 +58,12 @@ if $0 == __FILE__
       ].join("\t")
       end
 
-    elsif options[:filter_in]
-    	if result.has_domain?
+    elsif options[:filter_in] != false
+    	if result.transmembrane_domains.length >= options[:filter_in]
     		puts seq
     	end
-    elsif options[:filter_out]
-    	unless result.has_domain?
+    elsif options[:filter_out] != false
+    	unless result.transmembrane_domains.length >= options[:filter_out]
     		puts seq
     	end
     end

data/bio-tm_hmm.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-tm_hmm}
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ben J. Woodcroft"]
-  s.date = %q{2011-04-03}
+  s.date = %q{2011-04-06}
   s.default_executable = %q{biotm_hmm}
   s.description = %q{A bioruby plugin for interaction with the transmembrane predictor TMHMM}
   s.email = %q{donttrustben@gmail.com}

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: bio-tm_hmm
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 23
   prerelease: 
   segments: 
   - 0
-  - 1
+  - 2
   - 0
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
 - Ben J. Woodcroft
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-03 00:00:00 +11:00
+date: 2011-04-06 00:00:00 +10:00
 default_executable: biotm_hmm
 dependencies: 
 - !ruby/object:Gem::Dependency