npsearch 0.0.1 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 4225c7b066e5fc0e0bcc44b931f0259b4dcf2f2a
+  metadata.gz: 97d1818dc3219f272bd1acb116dbed684e6b0dbe
+  data.tar.gz: dc03e0976e737f28ab93f6899d21278601dd6c4f
 SHA512:
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-  data.tar.gz: f7941f0b612650181b95969caba43218dfdba53b1d8d655567388c4bc4d39c22615802b1550cd93a7489567fbb5fb86fda8ab650fb51ed83afcc3b917ca3a7fb
+  metadata.gz: 6a95520149d8ced28c465cfafa55eaefd3cec1c3cd0cc94796931b8017f940ee8df681ea254bbc063464e9ed67d713bca34da85ff8ffed84e0c5c576cd93ec85
+  data.tar.gz: 88da9e2e6a2bcbba268ecfbf3f7bc1ce4351d33430826bd6571b8ecdb74f087308cb4ed86f69ff8f80f3899420a252cb822a4d656b3c025b736a3ca0f9ff39c0

data/bin/npsearch

@@ -9,58 +9,48 @@ opt = {}
 optparse = OptionParser.new do |opts|
   opts.banner = <<Banner
 
-* Usage: npsearch [Options] -i [Input File] -o [Output Folder Name]
+* Usage: npsearch [Options] -i [Input File]
 
 * Mandatory Options:
 
 Banner
 
   opt[:input_file] = nil
-  opts.on('-i', '--input [file]', 'Path to the input fasta file') do |f|
+  opts.on('-i', '--input [file]',
+          'Path to the input fasta file') do |f|
     opt[:input_file] = f
   end
 
   opts.separator ''
   opts.separator '* Optional Options:'
 
-  opt[:motif] = 'KR|RR|KK'
-  opts.on('-m', '--motif [Query Motif]', 'By default NpSearch only searches',
-          ' for dibasic cleavage site ("KR", "RR" or "KK"). This option allows',
-          ' one to change the set of cleavage sites to be searched.',
-          ' The period "." can be used to denote any character. Multiple',
-          ' motifs query can be used by using a pipeline character ("|")',
-          ' between each query and putting the motif query in speech marks',
-          ' e.g. "KR|RR|R..R"',
-          ' Advanced Users: Regular expressions are supported.') do |motif|
-    opt[:motif] = motif
+  opt[:signalp_path] = File.join(ENV['HOME'], 'signalp/signalp')
+  opts.on('-s', '--signalp_path', String,
+          'The full path to the signalp script. This can be downloaded from',
+          ' CBS. See https://www.github.com/wurmlab/NpSearch for more',
+          ' information') do |p|
+    opt[:signalp_path] = p
   end
 
-  opt[:cut_off] = 10
-  opts.on('-c', '--cut_off N', Integer, 'Changes the minimum Open Reading',
-          ' Frame from the default 10 amino acid residues to N amino acid',
-          ' residues.') do |n|
-    opt[:cut_off] = n
+  opt[:usearch_path] = File.join(ENV['HOME'], 'bin/uclust')
+  opts.on('-u', '--usearch_path', String,
+          'The full path to the usearch binary. This script can be downloaded',
+          ' from .... See https://www.github.com/wurmlab/NpSearch for more',
+          ' information') do |p|
+    opt[:usearch_path] = p
   end
 
-  opt[:signalp_file] = nil
-  opts.on('-s', '--signalp_file [file]',
-          'Is used to supply the signal peptide results to the program. These',
-          ' signal peptide results must be created using the SignalP program',
-          " (Version 4.x), downloadable from CBS. If this argument isn't ",
-          ' suplied, then NpSearch will try to run a local version of the',
-          ' Signal P script.') do |signalp_file|
-    opt[:signalp_file] = signalp_file
+  opt[:num_threads] = 1
+  opts.on('-n', '--num_threads', Integer,
+          'The number of threads to use when analysing the input file') do |n|
+    opt[:num_threads] = n
   end
 
-  opt[:extract_orf] = false
-  opts.on('-e', '--extract_orf', 'Only extracts the Open Reading Frames.') do
-    opt[:extract_orf] = true
-  end
-
-  opt[:verbose] = false
-  opts.on('-v', '--verbose', 'Provides more information on each step taken',
-          ' in this program.') do
-    opt[:verbose] = true
+  opt[:orf_min_length] = 10
+  opts.on('-m', '--orf_min_length N', Integer,
+          'The minimum length of a potential neuropeptide precursor.',
+          ' Default: 30') do |n|
+    opt[:orf_min_length] = n
   end
 
   opts.on('-h', '--help', 'Display this screen') do
@@ -68,98 +58,17 @@ Banner
     exit
   end
 
-  opts.on('--version', 'Shows version') do
+  opts.on('-v', '--version', 'Shows version') do
     puts NpSearch::VERSION
     exit
   end
 end
 optparse.parse!
 
+# Temporary hard coding my defaults...
+opt[:num_threads] = 8
+opt[:signalp_path] = '/Volumes/Data/data/programs/signalp-4.1/signalp'
+opt[:usearch_path] = '/Volumes/Data/data/programs/bin/usearch'
+
 NpSearch.init(opt)
 NpSearch.run
-
-
-
-
-# ############# Argument Validation...##############
-# arg_vldr = NpSearch::ArgValidators.new(opt[:verbose])
-# input_type = arg_vldr.arg(opt[:motif], opt[:input], opt[:output_dir],
-#                           opt[:cut_off], opt[:extract_orf], opt[:signalp_file],
-#                           optparse.help)
-
-# ############# General Validation...##############
-# vldr = NpSearch::Validators.new
-# vldr.output_dir(opt[:output_dir])
-# if opt[:signalp_file].nil? && opt[:extract_orf] == false
-#   sp_dir = vldr.signalp_dir
-# end
-
-# ############# Converting input file to Bio::FastaFormat. #############
-# input_read = NpSearch::Input.read(opt[:input], input_type)
-
-# ############# Extract_ORF #############
-# if input_type == 'genetic'
-#   # Translate Sequences in all 6 frames
-#   translated = NpSearch::Translation.translate(input_read)
-#   translated.to_fasta('translated seq.', "#{opt[:output_dir]}/1_protein.fa")
-#   # Extract all possible ORF that are longer than the ORF_min_length
-#   orf = NpSearch::Translation.extract_orf(translated, opt[:cut_off])
-#   orf.to_fasta('Open Reading Frames', "#{opt[:output_dir]}/2_orf.fa")
-
-#   if opt[:extract_orf]
-#     puts "\nSuccess: All output files created in the directory:" \
-#          "#{opt[:output_dir]}'.\n "
-#     exit
-#   end
-# end
-
-# ############# Setting up more variables...##############
-# if opt[:motif] == 'neuro_clv'
-#   motif = 'KK|KR|RR|' \
-#           'R..R|R....R|R......R|H..R|H....R|H......R|K..R|K....R|K......R'
-# else
-#   motif = opt[:motif]
-# end
-# vldr.motif_type(motif)
-
-# if input_type == 'genetic'
-#   sp_input_file = "#{opt[:output_dir]}/2_orf.fa"
-#   sp_hash = orf
-#   file_number = 3
-# else # i.e. if the input is protein
-#   sp_input_file = opt[:input]
-#   sp_hash = input_read
-#   file_number = 1
-# end
-
-# if opt[:signalp_file].nil?
-#   sp_out_file = "#{opt[:output_dir]}/#{file_number}_signalp_out.txt"
-#   file_number += 1
-#   NpSearch::Signalp.signalp(sp_dir, sp_input_file, sp_out_file)
-# else
-#   sp_out_file = opt[:signalp_file]
-#   file_number = 1
-# end
-
-# ############# Signal P Results file Validation #############
-# vldr.sp_results(sp_out_file)
-
-# ############# Extract sequences with a signal peptide #############
-# secretome = NpSearch::Analysis.parse(sp_out_file, sp_hash, motif)
-# secretome.to_fasta('secretome file',
-#                    "#{opt[:output_dir]}/#{file_number}_secretome.fa")
-# file_number += 1
-
-# ############# Remove any duplicate data #############
-# flattened_seq = NpSearch::Analysis.flattener(secretome)
-
-# ############# Creating Output Files #############
-# flattened_seq.to_fasta('fasta output file',
-#                        "#{opt[:output_dir]}/#{file_number}_output.fa")
-# flattened_seq.to_html(motif,
-#                       "#{opt[:output_dir]}/#{file_number}_output.html")
-
-# ############# Success #############
-# puts # a blank line.
-# puts "Success: All output files created in the directory:'#{opt[:output_dir]}'."
-# puts # a blank line

data/lib/npsearch.rb

@@ -2,38 +2,35 @@ require 'bio'
 require 'fileutils'
 
 # require 'npsearch/arg_validator'
-require 'npsearch/logger'
+require 'npsearch/output'
+require 'npsearch/pool'
+require 'npsearch/scoresequence'
 require 'npsearch/sequence'
 require 'npsearch/signalp'
-require 'npsearch/pool'
 
 # Top level module / namespace.
 module NpSearch
   class <<self
-    MIN_ORF_SIZE = 40 # amino acids (including potential signal peptide)
+    MIN_ORF_SIZE = 30 # amino acids (including potential signal peptide)
 
     attr_accessor :opt
     attr_accessor :sequences
-
-    def logger
-      @logger ||= Logger.new(STDERR, @opt[:verbose])
-    end
+    attr_reader :sorted_sequences
 
     def init(opt)
       # @opt = args_validation(opt)
       @opt        = opt
       @sequences  = []
-      @opt[:num_threads] = 8
+      @sorted_sequences = nil
       @opt[:type] = guess_sequence_type
-      @opt[:signalp_path] = '/Volumes/Data/programs/signalp-4.1/signalp'
       @pool       = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1
     end
 
     def run
       iterate_input_file
-      # score_sequence
-      # scan(?<=(KR|RR|KK))(\w+?)(?=(KR|RR|KK|$))
-      @sequences.each { |s| puts ">#{s.id}\n#{s.seq}" }
+      @sorted_sequences = @sequences.sort_by(&:score).reverse
+      Output.to_fasta(@opt[:input_file], @sorted_sequences, @opt[:type])
+      Output.to_html(@opt[:input_file])
     end
 
     private
@@ -60,7 +57,10 @@ module NpSearch
 
     def initialise_protein_seq(id, seq)
       sp = Signalp.analyse_sequence(seq)
-      @sequences << Sequence.new(id, seq, sp) if sp[:sp] == 'Y'
+      return unless sp[:sp] == 'Y'
+      seq = Sequence.new(id, seq, sp)
+      ScoreSequence.run(seq)
+      @sequences << seq
     end
 
     def initialise_transcriptomic_seq(id, naseq)
@@ -72,15 +72,15 @@ module NpSearch
     end
 
     def initialise_orfs(id, orfs, frame)
-      idx = 0
       orfs.each do |orf|
         sp = Signalp.analyse_sequence(orf)
         next if sp[:sp] == 'N'
-        seq                  = Sequence.new(id, orf, sp)
-        seq.translated_frame = frame
-        seq.orf_index        = idx
+        seq = Sequence.new(id, orf, sp, frame)
+        ScoreSequence.run(seq)
         @sequences << seq
-        idx += 1
+        # The remaining ORF in this frame are simply shorter versions of the
+        # same orf so break loop once signal peptide is found.
+        break if sp[:sp] == 'Y'
       end
     end
 

data/lib/npsearch/output.rb

@@ -0,0 +1,29 @@
+require 'slim'
+
+module NpSearch
+  # Class that generates the output
+  class Output
+    class << self
+      def to_html(input_file)
+        templates_path = File.expand_path(File.join(__FILE__, '../../../',
+                                                    'templates/contents.slim'))
+        contents_temp = File.read(templates_path)
+        html_content = Slim::Template.new { contents_temp }.render(NpSearch)
+        File.open("#{input_file}.out.html", 'w') { |f| f.puts html_content }
+      end
+
+      def to_fasta(input_file, sorted_sequences, input_type)
+        File.open("#{input_file}.out.fa", 'w') do |f|
+          sorted_sequences.each do |s|
+            if input_type == :protein
+              f.puts ">#{s.id}\n#{s.signalp}#{s.seq}"
+            elsif input_type == :nucleotide
+              f.puts ">#{s.id}-(frame:#{s.translated_frame})"
+              f.puts "#{s.signalp}#{s.seq}"
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/npsearch/scoresequence.rb

@@ -0,0 +1,109 @@
+require 'csv'
+require 'tempfile'
+
+module NpSearch
+  # A class to score the Sequences
+  class ScoreSequence
+    class << self
+      DI_CLV = 'KR|RR|KK'
+      MONO_NP_CLV_2 = '[KR]..R'
+      MONO_NP_CLV_4 = '[KR]....R'
+      MONO_NP_CLV_6 = '[KR]......R'
+      NP_CLV = "(#{DI_CLV})|(#{MONO_NP_CLV_2})|(#{MONO_NP_CLV_4})|" \
+               "(#{MONO_NP_CLV_6})"
+
+      def run(sequence)
+        @sequence = sequence
+        split_into_neuropeptides
+        count_np_cleavage_sites
+        count_c_terminal_glycines
+        np_similarity
+        acidic_spacers
+      end
+
+      private
+
+      def split_into_neuropeptides
+        potential_nps = []
+        results = @sequence.seq.scan(/(?<=^|#{NP_CLV})(\w+?)(?=#{NP_CLV}|$)/i)
+        headers = %w(di_clv_st mono_2_clv_st mono_4_clv_st mono_6_clv_st np
+                     di_clv_end mono_2_clv_end mono_4_clv_end mono_6_clv_end)
+        results.each { |e| potential_nps << Hash[headers.map(&:to_sym).zip(e)] }
+        @sequence.potential_cleaved_nps = potential_nps
+      end
+
+      def count_np_cleavage_sites
+        @sequence.potential_cleaved_nps.each do |e|
+          count_dibasic_np_clv(e[:di_clv_end])
+          count_mono_basic_np_clv(e[:mono_2_clv_end], e[:mono_4_clv_end],
+                                  e[:mono_6_clv_end])
+        end
+      end
+
+      def count_dibasic_np_clv(dibasic_clv)
+        case dibasic_clv
+        when 'KR'
+          @sequence.score += 0.09
+        when 'RR', 'KK'
+          @sequence.score += 0.05
+        end
+      end
+
+      def count_mono_basic_np_clv(mono_2_clv, mono_4_clv, mono_6_clv)
+        return if mono_2_clv.nil? && mono_4_clv.nil? && mono_6_clv.nil?
+        @sequence.score += 0.02
+      end
+
+      # Counts the number of C-terminal glycines
+      def count_c_terminal_glycines
+        @sequence.potential_cleaved_nps.each do |e|
+          if e[:np] =~ /G$/ && e[:di_clv_end] == 'KR'
+            @sequence.score += 0.25
+          elsif e[:np] =~ /G$|GK$|GR$/
+            @sequence.score += 0.10
+          end
+        end
+      end
+
+      def acidic_spacers
+        @sequence.potential_cleaved_nps.each do |e|
+          acidic_residue = e[:np].count('DE')
+          percentage_acidic = acidic_residue / e[:np].length
+          @sequence.score += 0.10 if percentage_acidic > 0.5
+        end
+      end
+
+      def np_similarity
+        results = run_uclust
+        results.gsub!(/^[^C].*\n/, '')
+        results.each_line do |c|
+          cluster = c.split(/\t/)
+          no_of_seq_in_cluster = cluster[3].to_i
+          if no_of_seq_in_cluster > 1
+            @sequence.score += (0.15 * no_of_seq_in_cluster)
+          end
+        end
+      end
+
+      def run_uclust
+        f = Tempfile.new('uclust')
+        fo = Tempfile.new('uclust_out')
+        write_sequence_content_to_tempfile(f)
+        `usearch -cluster_fast #{f.path} -id 0.5 -uc #{fo.path} >/dev/null 2>&1`
+        IO.read(fo.path)
+      ensure
+        f.unlink
+        fo.unlink
+      end
+
+      def write_sequence_content_to_tempfile(tempfile)
+        content = ''
+        @sequence.potential_cleaved_nps.each_with_index do |e, i|
+          content += ">seq#{i}\n#{e[:np]}\n"
+        end
+        tempfile.write(content)
+        tempfile.close
+      end
+    end
+  end
+end

data/lib/npsearch/sequence.rb

@@ -1,25 +1,37 @@
-require 'forwardable'
-
 module NpSearch
   # A class to hold sequence data
   class Sequence
-    extend Forwardable
-    def_delegators NpSearch, :opt
+    DI_NP_CLV = 'KR|KK|RR'
+    MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R'
 
-    attr_accessor :id
-    attr_accessor :seq
-    attr_accessor :signalp
-    attr_accessor :translated_frame
-    attr_accessor :orf_index
+    attr_reader :id
+    attr_reader :signalp
+    attr_reader :seq
+    attr_reader :html_seq
+    attr_reader :signalp_output
+    attr_reader :translated_frame
     attr_accessor :score
+    attr_accessor :potential_cleaved_nps
+
+    def initialize(id, seq, signalp_output, frame = nil)
+      @id                    = id
+      sp_cleavage_site_idx   = signalp_output[:ymax_pos].to_i - 1
+      @signalp               = seq[0..(sp_cleavage_site_idx - 1)]
+      @seq                   = seq[sp_cleavage_site_idx..-1]
+      @html_seq              = format_seq_for_html
+      @translated_frame      = frame
+      @score                 = 0
+      @potential_cleaved_nps = nil
+    end
 
-    def initialize(id, seq, signalp_output)
-      @id               = id
-      @seq              = seq
-      @signalp          = signalp_output
-      @translated_frame = 0 # 0 means opt[:type] == :protein
-      @orf_index        = 0
-      @score            = 0
+    def format_seq_for_html
+      seq = @seq.gsub(/C/, '<span class=cysteine>C</span>')
+      seq.gsub!(/#{DI_NP_CLV}/i, '<span class=np_clv>\0</span>')
+      seq.gsub!(/#{MONO_NP_CLV}/i, '\0::NP_CLV::') # so that we can target R >>
+      seq.gsub!('R::NP_CLV::', '<span class=mono_np_clv>R</span>')
+      seq.gsub!('G<span class=np_clv>',
+                '<span class=glycine>G</span><span class=np_clv>')
+      "<span class=signalp>#{@signalp}</span><span class=seq>#{seq}</span>"
     end
   end
 end

data/lib/npsearch/signalp.rb

@@ -1,4 +1,3 @@
-require 'csv'
 require 'forwardable'
 require 'tempfile'
 
@@ -7,28 +6,10 @@ module NpSearch
   class Signalp
     class << self
       extend Forwardable
-      def_delegators NpSearch, :opt, :sequences, :signalp_path
-
-      def run
-      end
-
-      def analyse_file(file)
-        sp_out = []
-        sp_headers = %w(name cmax cmax-pos ymax ymax-pos smax smax-pos smean d
-                        sp dmaxcut networks)
-        output = `#{opt[:signalp_path]} -t euk -f short -U 0.34 -u 0.34 \
-                  #{file}`
-        lines = CSV.parse(output.gsub(/ +/, ','), col_sep: ',',
-                                                  skip_lines: /^#/,
-                                                  header_converters: :symbol,
-                                                  converters: :all,
-                                                  headers: sp_headers)
-        lines.each { |line| sp_out << line.to_hash }
-        sp_out
-      end
+      def_delegators NpSearch, :opt
 
       def analyse_sequence(seq)
-        sp_headers = %w(name cmax cmax-pos ymax ymax-pos smax smax-pos smean d
+        sp_headers = %w(name cmax cmax_pos ymax ymax_pos smax smax_pos smean d
                         sp dmaxcut networks)
         f = Tempfile.new('signalp')
         f.write(">seq\n#{seq}")

data/lib/npsearch/version.rb

@@ -1,4 +1,4 @@
 # Top level module / namespace.
 module NpSearch
-  VERSION = '0.0.1'
+  VERSION = '2.0.0'
 end

data/npsearch.gemspec

@@ -29,5 +29,5 @@ Gem::Specification.new do |s|
   s.add_development_dependency 'coveralls'
 
   s.add_dependency 'bio', '~> 1.4'
-  s.add_dependency 'haml', '~> 4'
+  s.add_dependency 'slim', '~> 3.0'
 end

data/templates/contents.slim

@@ -0,0 +1,54 @@
+doctype html
+html lang="en"
+  head
+    meta charset="utf-8"
+    meta content="IE=edge" http-equiv="X-UA-Compatible"
+    meta content="width=device-width, initial-scale=1" name="viewport"
+    meta content="NpSearch | Identify Novel Neuropeptides" name="description"
+    meta content="Wurmlab" name="author"
+    title NpSearch | Identify Novel Neuropeptides
+    css:
+      html { position: relative; min-height: 100%; }
+      body {margin:0 0 100px; background-color:#F5F5F5; font-family:"Helvetica Neue", Helvetica, Arial, sans-serif; font-size:15px; line-height:1.42857143; color:#2c3e50;}
+      .container {margin-right:auto; margin-left:auto; padding-left:15px; padding-right:15px; max-width:1170px; width:95%;}
+      footer {bottom:0; width:100%; margin:0 auto; position:absolute; height:100px; overflow:hidden; border-top:2px solid #DBDBDB; color:#b4bcc2;text-align:center;}
+      a{color:#18bc9c; text-decoration:none}a:hover,a:focus{color:#18bc9c; text-decoration:underline}
+      p {margin:0 0 10.5px}
+      .id {font-weight:bold;}
+      .sequence {word-break:break-all; font-family:Courier New, Courier, Mono;}
+      .signalp {color:#007AC0; font-weight:bold;}
+      .np_clv {color:#00B050; font-weight:bold;}
+      .mono_np_clv {color:#00B050;}
+      .glycine {color:#FF0000; font-weight:bold;}
+      .cysteine {text-decoration: underline; font-weight:bold;}
+  body
+    .container
+      h1 NpSearch Results
+      .results
+        - @sorted_sequences.each do |seq|
+          p.sequence
+            span.id
+              - if @opt[:type] == :protein
+                | >#{seq.id}
+              - elsif @opt[:type] == :nucleotide
+                | >#{seq.id}-(frame:#{seq.translated_frame})
+            br
+            span.seq== seq.html_seq
+      br
+      br
+      br
+    footer
+      p
+        | Please cite "Moghul I, Rowe M, Priyam A, Elphick M & Wurm Y 
+        em
+          | (in prep) 
+        | NpSearch: A tool to identify novel neuropeptides"
+        br
+        |  Developed at 
+        a href="https://wurmlab.github.io" target="_blank" Wurm Lab
+        | , 
+        a href="http://www.sbcs.qmul.ac.uk" target="_blank" QMUL
+        br
+        | This page was created by 
+        a href="https://github.com/wurmlab/NpSearch" target="_blank"  NpSearch 
+        | v#{NpSearch::VERSION}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: npsearch
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 2.0.0
 platform: ruby
 authors:
 - Ismail Moghul
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-13 00:00:00.000000000 Z
+date: 2015-09-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -71,19 +71,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '1.4'
 - !ruby/object:Gem::Dependency
-  name: haml
+  name: slim
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '3.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '3.0'
 description: Search for Neuropeptides based solely on the common neuropeptide markers
   (e.g. signal peptide, dibasic cleavage sites etc.) i.e. not based on homology to
   known neuropeptides.
@@ -104,12 +104,14 @@ files:
 - bin/npsearch
 - lib/npsearch.rb
 - lib/npsearch/arg_validator.rb
-- lib/npsearch/logger.rb
+- lib/npsearch/output.rb
 - lib/npsearch/pool.rb
+- lib/npsearch/scoresequence.rb
 - lib/npsearch/sequence.rb
 - lib/npsearch/signalp.rb
 - lib/npsearch/version.rb
 - npsearch.gemspec
+- templates/contents.slim
 - test/files/1_protein.fa
 - test/files/2_orf.fa
 - test/files/3_signalp_out.txt

data/lib/npsearch/logger.rb

@@ -1,12 +0,0 @@
-require 'logger'
-
-module NpSearch
-  # Extend stdlib's Logger class for custom initialization and log format.
-  class Logger < Logger
-    def initialize(dev, verbose = false)
-      super dev
-      self.level     = verbose ? DEBUG : INFO
-      self.formatter = proc { |_, datetime, _, msg| "#{datetime}: #{msg}\n" }
-    end
-  end
-end