bio-signalp 0.2.2 → 0.2.3

data/VERSION

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

data/bin/signalp.rb

@@ -2,118 +2,114 @@
 
 require 'rubygems'
 require 'bio'
+require 'optparse'
+
 
 # always load from the directory relative to the current script's directory
 $LOAD_PATH.unshift File.join(File.dirname(__FILE__), *%w[.. lib])
 require 'bio-signalp'
 
-# if this was not called as a module, run as a script.
-if $0 == __FILE__
-  require 'bio'
-  require 'optparse'
-  
-  runner = Bio::SignalP::Wrapper.new
-  
-  options = ARGV.getopts("sShvfF") #s for summary, no args required
-  if options['h']
-    $stderr.puts "Usage: signalp.rb [-svf] <my.fasta>"
-    $stderr.puts "Where my.fasta is the name of the fasta file you want to analyse. Default output is all the sequences with their signal sequences cleaved."
-    $stderr.puts "-s: summary: print a tab separated table indicating if the sequence had a signal peptide according to the HMM and NN results, respectively."
-    $stderr.puts "-S: bigger_summary: like -s, except also includes where the cleavage site is predicted"
-    $stderr.puts "-v: verbose summary: much like -s except more details of the prediction are predicted."
-    $stderr.puts "-f: filter in: print those sequences that have a signal peptide"
-    $stderr.puts "-F: filter out: print those sequences that don't have a signal peptide"
-    exit
-  end
-  
-  # Print headers if required
-  if options['s']
+runner = Bio::SignalP::Wrapper.new
+
+options = ARGV.getopts("sShvfF") #s for summary, no args required
+if options['h']
+  $stderr.puts "Usage: signalp.rb [-svf] <my.fasta>"
+  $stderr.puts "Where my.fasta is the name of the fasta file you want to analyse. Default output is all the sequences with their signal sequences cleaved."
+  $stderr.puts "-s: summary: print a tab separated table indicating if the sequence had a signal peptide according to the HMM and NN results, respectively."
+  $stderr.puts "-S: bigger_summary: like -s, except also includes where the cleavage site is predicted"
+  $stderr.puts "-v: verbose summary: much like -s except more details of the prediction are predicted."
+  $stderr.puts "-f: filter in: print those sequences that have a signal peptide"
+  $stderr.puts "-F: filter out: print those sequences that don't have a signal peptide"
+  exit
+end
+
+# Print headers if required
+if options['s']
+  puts [
+    'Name',
+    'NN Prediction',
+    'HMM Prediction'
+  ].join("\t")
+elsif options['S']
+  puts [
+    'Name',
+    'NN Prediction',
+    'HMM Prediction',
+    'Predicted?',
+    'Cleavege site (if predicted)'
+  ].join("\t")
+
+elsif options['v']
+  #       [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction, 
+  #      :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction, 
+  #      :nn_Smax, :nn_Smax_position, :nn_Smax_prediction, 
+  #      :nn_Smean, :nn_Smean_prediction,
+  #      :nn_D, :nn_D_prediction]
+  #    @@hmm_results = [
+  #      :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, :hmm_Sprob, :hmm_Sprob_prediction]
+  puts [
+    'Name',
+    'NN Cmax',
+    'NN Cmax position',
+    'NN Cmax prediction',
+    'NN Ymax',
+    'NN Ymax position',
+    'NN Ymax prediction',
+    'NN Smax',
+    'NN Smax position',
+    'NN Smax prediction',
+    'NN Smean',
+    'NN Smean prediction',
+    'NN D',
+    'NN D prediction',
+    'HMM result',
+    'HMM Cmax',
+    'HMM Cmax position',
+    'HMM Cmax prediction',
+    'HMM Sprob',
+    'HMM Sprob prediction',
+  ].join("\t")
+end
+
+Bio::FlatFile.open(ARGF).each do |seq|
+  result = runner.calculate(seq.seq)
+  if result.nil?
+    $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
+  elsif options['s']
     puts [
-      'Name',
-      'NN Prediction',
-      'HMM Prediction'
+    seq.entry_id,
+    result.nn_D_prediction ? 'T' : 'F',
+    result.hmm_Sprob_prediction ? 'T' : 'F'
     ].join("\t")
   elsif options['S']
     puts [
-      'Name',
-      'NN Prediction',
-      'HMM Prediction',
-      'Predicted?',
-      'Cleavege site (if predicted)'
+    seq.entry_id,
+    result.nn_D_prediction ? 'T' : 'F',
+    result.hmm_Sprob_prediction ? 'T' : 'F',
+    result.signal? ? 'T' : 'F',
+    result.signal? ? result.cleavage_site : 0,
     ].join("\t")
-
   elsif options['v']
-    #       [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction, 
-    #      :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction, 
-    #      :nn_Smax, :nn_Smax_position, :nn_Smax_prediction, 
-    #      :nn_Smean, :nn_Smean_prediction,
-    #      :nn_D, :nn_D_prediction]
-    #    @@hmm_results = [
-    #      :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, :hmm_Sprob, :hmm_Sprob_prediction]
-    puts [
-      'Name',
-      'NN Cmax',
-      'NN Cmax position',
-      'NN Cmax prediction',
-      'NN Ymax',
-      'NN Ymax position',
-      'NN Ymax prediction',
-      'NN Smax',
-      'NN Smax position',
-      'NN Smax prediction',
-      'NN Smean',
-      'NN Smean prediction',
-      'NN D',
-      'NN D prediction',
-      'HMM result',
-      'HMM Cmax',
-      'HMM Cmax position',
-      'HMM Cmax prediction',
-      'HMM Sprob',
-      'HMM Sprob prediction',
-    ].join("\t")
-  end
-  
-  Bio::FlatFile.open(ARGF).each do |seq|
-    result = runner.calculate(seq.seq)
-    if result.nil?
-      $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
-    elsif options['s']
-      puts [
-      seq.entry_id,
-      result.nn_D_prediction ? 'T' : 'F',
-      result.hmm_Sprob_prediction ? 'T' : 'F'
-      ].join("\t")
-    elsif options['S']
-      puts [
-      seq.entry_id,
-      result.nn_D_prediction ? 'T' : 'F',
-      result.hmm_Sprob_prediction ? 'T' : 'F',
-      result.signal? ? 'T' : 'F',
-      result.signal? ? result.cleavage_site : 0,
-      ].join("\t")
-    elsif options['v']
-      taputs = [seq.definition]
-      [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction, 
-      :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction, 
-      :nn_Smax, :nn_Smax_position, :nn_Smax_prediction, 
-      :nn_Smean, :nn_Smean_prediction,
-      :nn_D, :nn_D_prediction,
-      :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, 
-      :hmm_Sprob, :hmm_Sprob_prediction].each do |meth|
-        taputs.push result.send(meth)
-      end
-      puts taputs.join("\t")
-    elsif options['f']
-      if result.signal?
-        puts seq
-      end
-    elsif options['F']
-      if !result.signal?
-        puts seq
-      end
-    else
-      puts ">#{seq.entry_id}\n#{result.cleave(seq.seq)}"
+    taputs = [seq.definition]
+    [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction, 
+    :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction, 
+    :nn_Smax, :nn_Smax_position, :nn_Smax_prediction, 
+    :nn_Smean, :nn_Smean_prediction,
+    :nn_D, :nn_D_prediction,
+    :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, 
+    :hmm_Sprob, :hmm_Sprob_prediction].each do |meth|
+      taputs.push result.send(meth)
+    end
+    puts taputs.join("\t")
+  elsif options['f']
+    if result.signal?
+      puts seq
+    end
+  elsif options['F']
+    if !result.signal?
+      puts seq
     end
+  else
+    puts ">#{seq.entry_id}\n#{result.cleave(seq.seq)}"
   end
 end

data/bio-signalp.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-signalp"
-  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 = ["Ben J Woodcroft"]
-  s.date = "2012-03-29"
+  s.date = "2012-04-04"
   s.description = "A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least."
   s.email = "donttrustben near gmail.com"
   s.executables = ["signalp.rb"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-signalp
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-29 00:00:00.000000000 Z
+date: 2012-04-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &68905280 !ruby/object:Gem::Requirement
+  requirement: &75320500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *68905280
+  version_requirements: *75320500
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &68904090 !ruby/object:Gem::Requirement
+  requirement: &75320020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *68904090
+  version_requirements: *75320020
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &68962450 !ruby/object:Gem::Requirement
+  requirement: &75318990 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *68962450
+  version_requirements: *75318990
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &68960950 !ruby/object:Gem::Requirement
+  requirement: &75318160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.6.0
   type: :development
   prerelease: false
-  version_requirements: *68960950
+  version_requirements: *75318160
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &68958790 !ruby/object:Gem::Requirement
+  requirement: &75317190 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *68958790
+  version_requirements: *75317190
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &68994130 !ruby/object:Gem::Requirement
+  requirement: &75316460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,7 +76,7 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *68994130
+  version_requirements: *75316460
 description: A wrapper for the signal peptide prediction algorith SignalP. Not very
   well supported, but seems to work for the author, at least.
 email: donttrustben near gmail.com
@@ -114,7 +114,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -84068147
+      hash: 903911101
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: