bio-signalp 0.2.2 → 0.2.3

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Files changed (4) hide show
  1. data/VERSION +1 -1
  2. data/bin/signalp.rb +97 -101
  3. data/bio-signalp.gemspec +2 -2
  4. metadata +15 -15
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.2
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+ 0.2.3
@@ -2,118 +2,114 @@
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  require 'rubygems'
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  require 'bio'
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+ require 'optparse'
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+
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  # always load from the directory relative to the current script's directory
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  $LOAD_PATH.unshift File.join(File.dirname(__FILE__), *%w[.. lib])
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  require 'bio-signalp'
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- # if this was not called as a module, run as a script.
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- if $0 == __FILE__
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- require 'bio'
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- require 'optparse'
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-
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- runner = Bio::SignalP::Wrapper.new
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-
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- options = ARGV.getopts("sShvfF") #s for summary, no args required
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- if options['h']
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- $stderr.puts "Usage: signalp.rb [-svf] <my.fasta>"
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- $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."
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- $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."
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- $stderr.puts "-S: bigger_summary: like -s, except also includes where the cleavage site is predicted"
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- $stderr.puts "-v: verbose summary: much like -s except more details of the prediction are predicted."
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- $stderr.puts "-f: filter in: print those sequences that have a signal peptide"
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- $stderr.puts "-F: filter out: print those sequences that don't have a signal peptide"
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- exit
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- end
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-
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- # Print headers if required
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- if options['s']
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+ runner = Bio::SignalP::Wrapper.new
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+
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+ options = ARGV.getopts("sShvfF") #s for summary, no args required
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+ if options['h']
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+ $stderr.puts "Usage: signalp.rb [-svf] <my.fasta>"
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+ $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."
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+ $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."
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+ $stderr.puts "-S: bigger_summary: like -s, except also includes where the cleavage site is predicted"
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+ $stderr.puts "-v: verbose summary: much like -s except more details of the prediction are predicted."
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+ $stderr.puts "-f: filter in: print those sequences that have a signal peptide"
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+ $stderr.puts "-F: filter out: print those sequences that don't have a signal peptide"
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+ exit
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+ end
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+
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+ # Print headers if required
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+ if options['s']
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+ puts [
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+ 'Name',
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+ 'NN Prediction',
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+ 'HMM Prediction'
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+ ].join("\t")
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+ elsif options['S']
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+ puts [
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+ 'Name',
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+ 'NN Prediction',
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+ 'HMM Prediction',
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+ 'Predicted?',
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+ 'Cleavege site (if predicted)'
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+ ].join("\t")
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+
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+ elsif options['v']
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+ # [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction,
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+ # :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction,
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+ # :nn_Smax, :nn_Smax_position, :nn_Smax_prediction,
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+ # :nn_Smean, :nn_Smean_prediction,
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+ # :nn_D, :nn_D_prediction]
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+ # @@hmm_results = [
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+ # :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, :hmm_Sprob, :hmm_Sprob_prediction]
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+ puts [
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+ 'Name',
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+ 'NN Cmax',
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+ 'NN Cmax position',
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+ 'NN Cmax prediction',
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+ 'NN Ymax',
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+ 'NN Ymax position',
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+ 'NN Ymax prediction',
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+ 'NN Smax',
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+ 'NN Smax position',
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+ 'NN Smax prediction',
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+ 'NN Smean',
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+ 'NN Smean prediction',
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+ 'NN D',
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+ 'NN D prediction',
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+ 'HMM result',
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+ 'HMM Cmax',
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+ 'HMM Cmax position',
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+ 'HMM Cmax prediction',
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+ 'HMM Sprob',
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+ 'HMM Sprob prediction',
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+ ].join("\t")
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+ end
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+
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+ Bio::FlatFile.open(ARGF).each do |seq|
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+ result = runner.calculate(seq.seq)
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+ if result.nil?
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+ $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
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+ elsif options['s']
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  puts [
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- 'Name',
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- 'NN Prediction',
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- 'HMM Prediction'
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+ seq.entry_id,
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+ result.nn_D_prediction ? 'T' : 'F',
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+ result.hmm_Sprob_prediction ? 'T' : 'F'
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  ].join("\t")
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  elsif options['S']
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  puts [
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- 'Name',
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- 'NN Prediction',
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- 'HMM Prediction',
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- 'Predicted?',
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- 'Cleavege site (if predicted)'
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+ seq.entry_id,
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+ result.nn_D_prediction ? 'T' : 'F',
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+ result.hmm_Sprob_prediction ? 'T' : 'F',
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+ result.signal? ? 'T' : 'F',
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+ result.signal? ? result.cleavage_site : 0,
43
91
  ].join("\t")
44
-
45
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  elsif options['v']
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- # [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction,
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- # :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction,
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- # :nn_Smax, :nn_Smax_position, :nn_Smax_prediction,
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- # :nn_Smean, :nn_Smean_prediction,
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- # :nn_D, :nn_D_prediction]
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- # @@hmm_results = [
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- # :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, :hmm_Sprob, :hmm_Sprob_prediction]
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- puts [
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- 'Name',
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- 'NN Cmax',
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- 'NN Cmax position',
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- 'NN Cmax prediction',
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- 'NN Ymax',
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- 'NN Ymax position',
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- 'NN Ymax prediction',
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- 'NN Smax',
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- 'NN Smax position',
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- 'NN Smax prediction',
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- 'NN Smean',
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- 'NN Smean prediction',
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- 'NN D',
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- 'NN D prediction',
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- 'HMM result',
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- 'HMM Cmax',
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- 'HMM Cmax position',
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- 'HMM Cmax prediction',
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- 'HMM Sprob',
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- 'HMM Sprob prediction',
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- ].join("\t")
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- end
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-
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- Bio::FlatFile.open(ARGF).each do |seq|
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- result = runner.calculate(seq.seq)
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- if result.nil?
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- $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
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- elsif options['s']
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- puts [
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- seq.entry_id,
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- result.nn_D_prediction ? 'T' : 'F',
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- result.hmm_Sprob_prediction ? 'T' : 'F'
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- ].join("\t")
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- elsif options['S']
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- puts [
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- seq.entry_id,
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- result.nn_D_prediction ? 'T' : 'F',
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- result.hmm_Sprob_prediction ? 'T' : 'F',
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- result.signal? ? 'T' : 'F',
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- result.signal? ? result.cleavage_site : 0,
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- ].join("\t")
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- elsif options['v']
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- taputs = [seq.definition]
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- [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction,
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- :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction,
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- :nn_Smax, :nn_Smax_position, :nn_Smax_prediction,
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- :nn_Smean, :nn_Smean_prediction,
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- :nn_D, :nn_D_prediction,
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- :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction,
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- :hmm_Sprob, :hmm_Sprob_prediction].each do |meth|
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- taputs.push result.send(meth)
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- end
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- puts taputs.join("\t")
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- elsif options['f']
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- if result.signal?
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- puts seq
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- end
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- elsif options['F']
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- if !result.signal?
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- puts seq
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- end
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- else
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- puts ">#{seq.entry_id}\n#{result.cleave(seq.seq)}"
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+ taputs = [seq.definition]
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+ [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction,
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+ :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction,
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+ :nn_Smax, :nn_Smax_position, :nn_Smax_prediction,
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+ :nn_Smean, :nn_Smean_prediction,
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+ :nn_D, :nn_D_prediction,
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+ :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction,
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+ :hmm_Sprob, :hmm_Sprob_prediction].each do |meth|
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+ taputs.push result.send(meth)
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+ end
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+ puts taputs.join("\t")
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+ elsif options['f']
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+ if result.signal?
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+ puts seq
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+ end
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+ elsif options['F']
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+ if !result.signal?
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+ puts seq
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  end
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+ else
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+ puts ">#{seq.entry_id}\n#{result.cleave(seq.seq)}"
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  end
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  end
@@ -5,11 +5,11 @@
5
5
 
6
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  Gem::Specification.new do |s|
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  s.name = "bio-signalp"
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- s.version = "0.2.2"
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+ s.version = "0.2.3"
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9
 
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Ben J Woodcroft"]
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- s.date = "2012-03-29"
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+ s.date = "2012-04-04"
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  s.description = "A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least."
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  s.email = "donttrustben near gmail.com"
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  s.executables = ["signalp.rb"]
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: bio-signalp
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  version: !ruby/object:Gem::Version
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- version: 0.2.2
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+ version: 0.2.3
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,11 +9,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-03-29 00:00:00.000000000 Z
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+ date: 2012-04-04 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &68905280 !ruby/object:Gem::Requirement
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+ requirement: &75320500 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
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  version: 1.4.1
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  type: :runtime
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  prerelease: false
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- version_requirements: *68905280
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+ version_requirements: *75320500
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25
  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &68904090 !ruby/object:Gem::Requirement
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+ requirement: &75320020 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *68904090
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+ version_requirements: *75320020
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &68962450 !ruby/object:Gem::Requirement
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+ requirement: &75318990 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -43,10 +43,10 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *68962450
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+ version_requirements: *75318990
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47
  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &68960950 !ruby/object:Gem::Requirement
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+ requirement: &75318160 !ruby/object:Gem::Requirement
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50
  none: false
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51
  requirements:
52
52
  - - ~>
@@ -54,10 +54,10 @@ dependencies:
54
54
  version: 1.6.0
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  type: :development
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  prerelease: false
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- version_requirements: *68960950
57
+ version_requirements: *75318160
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58
  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &68958790 !ruby/object:Gem::Requirement
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+ requirement: &75317190 !ruby/object:Gem::Requirement
61
61
  none: false
62
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  requirements:
63
63
  - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
65
65
  version: 1.4.1
66
66
  type: :development
67
67
  prerelease: false
68
- version_requirements: *68958790
68
+ version_requirements: *75317190
69
69
  - !ruby/object:Gem::Dependency
70
70
  name: rdoc
71
- requirement: &68994130 !ruby/object:Gem::Requirement
71
+ requirement: &75316460 !ruby/object:Gem::Requirement
72
72
  none: false
73
73
  requirements:
74
74
  - - ~>
@@ -76,7 +76,7 @@ dependencies:
76
76
  version: '3.12'
77
77
  type: :development
78
78
  prerelease: false
79
- version_requirements: *68994130
79
+ version_requirements: *75316460
80
80
  description: A wrapper for the signal peptide prediction algorith SignalP. Not very
81
81
  well supported, but seems to work for the author, at least.
82
82
  email: donttrustben near gmail.com
@@ -114,7 +114,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
114
114
  version: '0'
115
115
  segments:
116
116
  - 0
117
- hash: -84068147
117
+ hash: 903911101
118
118
  required_rubygems_version: !ruby/object:Gem::Requirement
119
119
  none: false
120
120
  requirements: