bio-octopus 0.1.0 → 0.1.1

data/README.rdoc

@@ -2,6 +2,15 @@
 
 A bioruby plugin for running and parsing octopus, available from http://octopus.cbr.su.se/ Currently, the plugin is not Ruby 1.9 (only 1.8) compatible, because of the dependency on the rio gem.
 
+To run it as a script, a fasta file of sequences to predict, and a database formatted in legacy blast database format needs to be specified:
+
+    $ /usr/local/rvm/gems/ruby-1.8.7-p334/gems/bio-octopus-0.1.0/bin/biooctopus my.fasta /blastdb/UniProt2011_04/uniprot_sprot.fasta
+
+Output are topology predictions, including signal peptide and transmembrane domain predictions. If that is not the best format for you, look at the script file and modify it - it is just a front-end. Also required are:
+* a working install of SPOCTOPUS
+* NCBI legacy blast
+Binaries for these must be accessible in the PATH.
+
 == Contributing to bio-octopus
  
 * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bin/biooctopus

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 #
 # BioRuby bio-octopus Plugin
-# Version 0.0.1
+# Version 0.1.1
 # Author:: Ben J Woodcroft
 # Copyright:: 2011
 # License:: The Ruby License
@@ -21,12 +21,12 @@ if $0 == __FILE__
     ].flatten
   end
   o.parse!
-  
+
   unless ARGV.length == 2
-  	puts o.help
-  	exit
+    puts o.help
+    exit
   end
-  
+
   fasta_path = ARGV[0]
   blastdb_path = ARGV[1]
 
@@ -36,6 +36,21 @@ if $0 == __FILE__
     result = runner.calculate(seq.seq, blastdb_path)
     name = seq.definition
 
+    # Output singal peptide if it has one
+    if result.signal?
+      puts [
+    		name,
+    		'Signal peptide',
+    		result.signal_peptide.start,
+    		result.signal_peptide.stop
+    	].join("\t")
+    else
+      puts [
+    		name,
+    		'No signal peptide found'
+    	].join("\t")
+    end
+
     if result.has_domain?
       # At least one TMD found. Output each on a separate line
       result.transmembrane_domains.each do |tmd|
@@ -50,7 +65,7 @@ if $0 == __FILE__
     else
       puts [
         name,
-        'No Transmembrane Domain Found'
+        'No transmembrane domain found'
       ].join("\t")
     end
   end

data/bin/biooctopus.rb

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 #
 # BioRuby bio-octopus Plugin
-# Version 0.0.1
+# Version 0.1.1
 # Author:: Ben J Woodcroft
 # Copyright:: 2011
 # License:: The Ruby License
@@ -21,12 +21,12 @@ if $0 == __FILE__
     ].flatten
   end
   o.parse!
-  
+
   unless ARGV.length == 2
-  	puts o.help
-  	exit
+    puts o.help
+    exit
   end
-  
+
   fasta_path = ARGV[0]
   blastdb_path = ARGV[1]
 
@@ -36,6 +36,21 @@ if $0 == __FILE__
     result = runner.calculate(seq.seq, blastdb_path)
     name = seq.definition
 
+    # Output singal peptide if it has one
+    if result.signal?
+      puts [
+    		name,
+    		'Signal peptide',
+    		result.signal_peptide.start,
+    		result.signal_peptide.stop
+    	].join("\t")
+    else
+      puts [
+    		name,
+    		'No signal peptide found'
+    	].join("\t")
+    end
+
     if result.has_domain?
       # At least one TMD found. Output each on a separate line
       result.transmembrane_domains.each do |tmd|
@@ -50,7 +65,7 @@ if $0 == __FILE__
     else
       puts [
         name,
-        'No Transmembrane Domain Found'
+        'No transmembrane domain found'
       ].join("\t")
     end
   end

data/bio-octopus.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-octopus}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ben J Woodcroft"]
-  s.date = %q{2011-04-17}
+  s.date = %q{2011-05-02}
   s.description = %q{Running and parsing of the protein transmembrane domain predictor octopus}
   s.email = %q{gmail.com after donttrustben}
   s.executables = ["biooctopus.rb", "biooctopus"]

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: bio-octopus
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 25
   prerelease: 
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Ben J Woodcroft
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-17 00:00:00 +10:00
+date: 2011-05-02 00:00:00 +10:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency