npsearch 2.1.2 → 2.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 036557512365e70a5fcc7cb9ca30134db25bfc70
-  data.tar.gz: af59a6031d843d7244820d1a7be721db542e6617
+  metadata.gz: 6357adc8080129fa2b76256669596bd7c0b956ba
+  data.tar.gz: a78e79d1462978dcb599d62d848a604aa86d883f
 SHA512:
-  metadata.gz: 372005332db090e60d2012a7ffda5c0fea85143185a0fcdc47a1f7a52bc7dafdde7dc3555fc309a48dbdb7e969d3af95f99ba3c9506f565ad760c08418c40b16
-  data.tar.gz: 13b0ff78295b3b12400883f84e9119ce867474b76dabd8b7d57820a2d594e5ece81c6555c23c568aebb418021bcd1e1317f9ef449af3e8b5e74193d53ad89857
+  metadata.gz: 6557749bff5b29c99dc26edcf577df767f64382f6eb6cf8ab3f62c73b9ef5916fba201788efcb38914c9412971d42399825fb1b35c2be54e0b5e5e54c6891b3d
+  data.tar.gz: 96129c33bb5f7c21628d2578959283c72b4201d157992c0f2bf54f4881af6b8c6b85b309f86cab4a4307c249db4b3653973039c8273264540787e60740ec5a80

data/bin/npsearch

@@ -23,7 +23,7 @@ Banner
 
   opt[:temp_dir] = File.join(Dir.pwd, '.temp',
                              Dir::Tmpname.make_tmpname('', nil))
-  opts.on('-d', '--temp_dir path_to_temp_dir',
+  opts.on('-t', '--temp_dir path_to_temp_dir',
           'The full path to the temp dir. NpSearch will create the folder and',
           ' then delete the folder once it has finished using them.',
           ' Default: Hidden folder in the current working directory') do |p|
@@ -36,6 +36,11 @@ Banner
     opt[:num_threads] = n
   end
 
+  opt[:debug] = false
+  opts.on('-d', '--debug', 'Run in debug mode') do
+    opt[:debug] = true
+  end
+
   opt[:min_orf_length] = 30
   opts.on('-l', '--min_orf_length N', Integer,
           'The minimum length of a potential neuropeptide precursor.',

data/exemplar_data/protein.fa

@@ -0,0 +1,112 @@
+>1108382 length 1440 cvg_15.4_tip_1
+CTGGCGTAATTCACGAGCCTCGATGTGAGACGTCAGATGTTCAGGCTATGACAGGATGTGCATGTTATCATGCGGCCCAAATCTTACCTTTTCCTCTTCT
+TCTTAGGCCTTTTTGCTGTGCTGGATTGATCGGTGCATTCTTTTCTCTTGTGAGTGAGTGAGCCACAGATGTGGCACCCCATAGACTGCCTATTGCATTG
+ATGATCTGGTAACTCACATCGCTGGCAAACTGTACAGTGAACGTAACCTGGTTTGACGCATCTCTGACAATCCTTGCAATGCTTATACGTGCTGCCATCT
+TTGGACGTGCAGCTGTTGCATTGAGTACAGTGTATATTCTCTTCCGCAACGTAGCGTTTACACGCTTTACAAAACCTGTAGCCTTCATCGAGAGGAAGAT
+GGATTTCGGAGGGTTGAAGATTGGTGAAGACTCTGACAGGGGAGCCTTTCTTACGAGCCTTCTTCTGATTGCTCTGGAACAACGGGTGATTATCATAGTC
+AACCTTATAGTCAAGCATTGTAAAAGAAGGAAAACTATCCAGAATTCTTTGTTCTAAGAAGTATGGGAAGATCCAAAGTAGTGGAAGCTTAGCTGTTGAG
+CCAAGGTCTTGTAACCCCATTGTCCATCTTCCCATCATCCTCTGGATGACCTCAGCCAGGATCTCCACCCTGCCTCCAAAAGGAGGGTCAGTAACCATAA
+CGATACCATCGCCATGGTTACGATGCAAAAAGTCCTCGCAGATAGTCCTGCTCTTCTCGCCGTCTAAAAAGTGATCGTTGAACATGTTGTAACGACAGAA
+GAGGCTCGGAGGGTAGAAATGACCATAACTATGGTCTATATCCAACAACAGACTGCTGAGGTCTGATGATGCCTCAGACTGTATCATCTCATGTAATCTG
+GGAGACCCAACACACAGCACTCTGTCATAACCGAGCCTCTTAATGGTGGTGATCAGAAACTCAGTGGCTGTTTTAGAGAACAGATATTGAGCGTTTGTTT
+TGTTGTCCTCTAGCGGGAGGAGGAGATAGGATGGTTGACTCAGGATAGCGTCGGTGAGGTCAGCCTTTATCTTATGCTTCGAGTGAGTCTGGACTTCTTG
+TGGACGCAGTAACAGGCTGCAGGATTGACAAAATTTCCTCTCAGATGGACTCAAATCCTTAGTGTCCTGCATTCTTTGGAAAAAATGTTCATGGCTGGTC
+CACGGCTGCTGTGATCTGTTGAGTTCCTCTCTGCTCATCTTCTTAGCCTCAGAGACTTTCTCATCAGCGAGCTGGTAAAAGCTGCAATCTTTACGATCTC
+TGCATGCCGAGCAGGCATAGTAGCGCTGTTTCTTGCGCTTCCCATTGAACCGCTCAAACAGTAACGTCGGACCATGTGGACAACAAGGTGAATTCTGCAC
+CAGAGACACCTCTACGCCTAGAGTATTTGCCACACTAGCA
+>1108384 length 1440 cvg_51.3_tip_1
+AAAAAAAAGACAATTTGTGTTCTTAGTAATTTTTATGTTTTTTTTCTTCGGGTAATCATGGAATCAAACAAACTTTTATACCTCACCGTTGGAGGCTTCA
+TGATGGTAGGGGGCACCACACATACCAGGTTATTTTCCAATCTTTAAAGAGTATCCACACTTTCCATCTTACATAAACTTTCCAATGGAACGTACCGGCA
+GTCCAACAGAACAGCCCTTGTGCACGCGCTGGATACTTTAAAATCCAATCAGAACATTCCTACCTTTCTTACTTTTGAGTCGCCTCACTGGTAATAGCTA
+CACAAAATTCAAATTTTACACAAGTGAATATTATGCGCATCAGTATTTGAAACTTTCCAGTGGAACGATTTGGCACTCCAACGAAATAGCTTGTGTGCAC
+GAACTGGGATTCTTATCCAATCAAATGAGAACAATCCTACTATTCCTTCTTTTGAGGCGCTCCCCAATGTTAATAGTTACTAAAAATTCCACAAATGAAT
+CGATCCATCGTGTCATCATTTCTGCCTCTCCTGACTGATGTCACTCTCGAGTTTTTCCACCTCTCGTTCGATCCCAGTCCGTATATTCTCTGGCAGTTTC
+CACTGCTGTAGGAGGTCCATGCGTTTGTAGTCTGGTAGCCACCATGTTTTACCTTGTTCTACGAGTTCTTCTTTGACGTTGGAGAAATCTACACCCTGTA
+GCTCCGCCCTCTCCCAGCGTTTGTACCACGGCCTCGGCTTCAGTTTGACCTTGATATCATTGATGGGTACTGGTTTGCCAGGGGGGTGTTTGATAGGCAC
+CATGTTAGGATCGATGGTGCTGTATTCCGGCAGAGCATCCTGTAGATATTTCAAGTCGCTGTCTAACCTCTTCTCTAACTTCAACATCTCAACCTTCTGG
+ATGAGTGGGTTGTACAACTCAAAACAAATTTCAACTCCTAAATCGTTAATGACGTTGCGAAGGATGAATGTAGCTCCCAGCCCATAGCCACCTCTTCTTG
+TACAAATACCAACAAATCGGTTGGATTTACCCTTTGCATATATGTCCGCTGTTGTCACTGCCATTATGCTGCCAACATAGAATTCAGGGATATCGATGAC
+TTTCCTTCTCTTGTAGCAATCCTGTCTCTCTAAGTAATCAAGGAGTTTTGACCGTGTTCCCATCGGTGGCAATAACTCTGGACTTGTAAAGCGCTCTCTT
+ATCTCACCGTACCCACTGCCATCGTCGTCATGTGTAAACTCGTGCTTCTTATCGGCTGTAGTTTCTGCAATGGTGATGTCATCTACCGATGTGGCGAAAT
+TGCATTTACCAGCACCTGCAACCGAGACATGTTTATGTAGAGAACCAGCTCTACCGGCCAATCTTAAACTCGATCCAGCCCGCAATAAACACGAAGTTCG
+CACCAGAACACATGCAGACGTCGTGGCCGCCATGATGAAT
+>1108386 length 1440 cvg_65.7_tip_0
+TTTTTTGTTGCACTTTTGAATCAAGCCCCTTGCTTTCTTTGTCTCTTACTGCTGTTTTTATGTCCTCATCAAAAAATTAGCATTTTAAAATAAACCCACC
+ACCAGTAAATACTCTACCTGCTGAAAATTACACTCATAACAACAAACACAAACACAAGTTTTGGTCAGTTAAAGATGAGATTTAAGTATCATGCAGTAAA
+GGATATGTTGTCCAGTCTGTTCAATCTTGTTTCCTCAGCTTTTTTTTTTAAAGAAGAAATTTAGAACTTTCACCGATACTTGATTCTTAAAGATATATAA
+ACACACTCATGATCATCATGTGCGATTACTATAGAGTGACACAAGTAGGATACCACTACACACTTTACTTTATCAAGTAATAAACCACAAGGCCGGCTGG
+GTAACTTTTGATTCATTTTGAGTTGAACGTTTCATTTTAAGCTGACATTAGATAAACGTGTTGTTGCATTTAACTTCTCGGCTAAAATGAACTTGTTCCC
+TTTATTCCCTCAAATTCTTTTCAAACCGTAAATTTTAATTATATTCATTGTAAATATCTTGAGTATTTATTTCTATGGTTTATATCTTACTCTTCTATTA
+ATAAGCGCTTTTAGTTGTGAGTATTAGAGTTATTAATAAAATGTTTTGCTCGTTATGATCCCCCAAAGGGGCTGTTCCACACATAACTGTTTTTGAATCT
+TCAACAAATCTCATCAAATATGCTGGGATGAAACTAAAATAGACAATGAGAAGAGGGTGTGGAACAGTTTTAACTTGCGAGGGCCACGCTGATCTATTGC
+TCATATGGTGGTGGCTTGCTATCAGGAGACTGGATAGCATCACTGTAGGTTGGCAGCTTGGGGAGCAGAGCCTCAGCATCCATGGCATAATTGCCAGATT
+GGGCATTGTCTCCCATCTCACGGGCTGCGATGTACTTGTAGCATGACCACACACAGGCAATGCAGTAGGCCTTGACTACCATGATCATCATGAAGATGAC
+CAGGGCAACGATGACAAACCACTGGTTGTCCAGATCCATCTTGTTGATGGGCAGCTTCTCCTTCCAGTGCATGAACTCCTGGTTGTACGGGAACTTGCCA
+CTGTCTTCGTAGTCAAATTCTGGGTAGTATGACATTAGGCCGATAGCTGTCAGGCATGTGATGAAGAAATCAAACAGCTGCAGGCAGAAGAACGGCAGCA
+GGTAACTTGACTGGTGCTGTGCAACTCCCTTAATCATCATGCTTGTGATCAGAAAGTAGCAACAGATGATGACCAGTCCAACACAGTAATCAGATGCATC
+ATGCTGGTCCTCAATTGACAAACTGGTGGACGTGCTGTCCTCAGTCTTGACAGTGCCCTTGATGATCATAGATGCAATAAGCAGCATAGCACATACTTGC
+CCAACCATGTGCCATAACCCGATCAAAACCGAGCCAGTTC
+>1108388 length 1440 cvg_25.5_tip_1
+CAGCTTATGTAGTTATCCATTGTATCCCACTGGCAGCATTGGAAACACAAAGACCATTAGAGCAGAAAGCAATGGTAATGTGTTCTCATTGGGTACTTTC
+GCTCAGTAACTGGTGATTAGTGGTCAACCATAGCATGATCAAGGCCAACATTGTCATTTTGTGGATTGCTGTTTCGTTTACTGAATACTTCTAGGGTCTT
+ATTAACTGAAGATACACCGCACGCCAGGTCAGCAGCCTGAGAGCTTAGACCGAAAGCAAGAGTGCTGGCTTCGCACACGCTCGTTTCTTTGATAGCTAAG
+GAGTAAACACTGTCATCATCTGAGACCATGGAAGTTGCAGCACTGGGTCCTTTGGAATACTACATCATGGGATTGATACTCACTGTGGAAGCTATACTTG
+GAACAATATGCTGTGTTCGTCTTCTCCTGGTGTATTTGAAAAATCCAACCCTCCACCAACCGCAGAGTCTTCTAGGCATCACACTGTGCATTGGAGACTT
+GGGAATAGCTCTGATGTGCCCATTTGCCGCCTTTGCAAGCTTCAGTGAAACCTGGCCATTTGGAGATGAGTACTGCCAGCTGTATGCCTTTGCTGGGATG
+CTGTTTGGTACACTCAGCATATCAGCTATGGCATGCTTGGCTTTGGACAAATATTACTCAAGCTCAAACGATGCTAAAGGGGGTTCTAGTCAGCCTTACA
+TCTTGATTACATCAATCATCTGGCTAAACGCCCTCTTCTGGTCACTAACCCCACTGAGTCCCATCGGTTGGGGGCGCTATGCCATCGAACCGCCTAAATC
+GACGTGCATGTTGGACTTTGCAAACCGTGAGCCATCATACATGATGTACTTGTTCTTAATGACAAGCACGGTCTATGCGTTGCCAGTAGGCGCCATCTTA
+TGGTGCTTAGTGAAGCTCAGAAAGGGAAAAGATCCAAACAACGGAAAGAGCAAGGTATGTCTTTTGGTGTTGTTCTCATTGATTGTGTACTGGGGAGCCT
+ATGGAATCGTAGCACTATGGGCAGCACTAGATGACATACATAATGTCCCGCTCCGATTGGTTGCTGCTGCTCCAATCCTGGCCAAGATCTGTCCAATCGG
+AAACACTGTAATGCAGGTGCTGACCAATAGGAACATCCGTTGTCTGATGTACAGAAAGGAAACAGTTGCATCCAACAAGAGGGAATGAGGAGCATAATGC
+AGAAAATAATTTCGTGTTATGATAGGTCTAATAATGCCGGTGTTCTCCTTTTCTTTGCACACGCTAAAGGCCATATTTTGTTACACAGCATTGTTTTTAT
+TTCATATCGTTATTGTAGACTTGTATTGCCATTTAAGTTGCAATGTCAGATTTCCTTAGATTTTTTTTTTATCTGAACTAAGTTTGACAGATGGTGCTTT
+TTTAAAACGAAAAAAAACCACAAATTTCCTTAAACCATGG
+>1108390 length 1440 cvg_34.1_tip_1
+GCAACCTTTTGGGTACAGAATGCGAGAAAATCTGGGCAGATCGGTCACAGTATTTTAAGGATTTCTAGGTTAACTTTGAATCAAATAAATTCAAACTCTA
+GGAGGAAGATTATCACATCATGCTGCTGTCGTGGGATTCATCACAAACCGGTATTTGTTTCATTACTGAAAGACAAACTTAAAGGAAGTCTTAATAGGAG
+CCTGGGTCCATGTTACTCCACAAATTCACATTTGTTTCCTAAAGAAGTGACTAGTCCGGAGAAACTCACGCAAGATGAAATAACGGCCCTGCACCAAAAT
+ATTTGTAAGGAATTAATTACAGATGAGAGATCTTTACAAGAGGTTGCACAGTACTATTTTGATGGAAAAGGCAAAGCGTTTAGACCCATGTTGGTTTTAC
+TCACGGCTGGTGCATGCAATACTCATACTCAGGGTTCTAATAGTAAACTGGTGGATACTCAGAGACGGATTGCAATGATAGCAGAGATGATCCACACAGC
+GAGTCTCATGCATGATGATGTCATCGATAATGCAGATACAAGGAGGAACAAAACAGCAATCAATGAAATGTGGGGACAGAGAAAGGCAATTTTAGCTGGA
+GACTTTGTTCTATCAGTTTCATCTCAGGTTTTAGCAAGAATAGGAAACGAGGAAGTTGTTTTAATTCTTTCCCAAGTCATAGAAGATCTTGTTAGAGGGG
+AATTTATGCAACTTGGTTCTAAGGAGGATGAAAATGAGCGCTTTGCCCACTACCTCAAGAAGACGTTCAAGAAAACAGCAAGTCTCATGGCTTACAGCTG
+TCAAGCAGTAGCAATTCTGGGTGGTTGCAGTGCTGAGGTGTGTCAGATAGCCTACGAGTACGGCCGGAATACAGGCATGGCATTCCAGCTGATAGATGAT
+GTATTAGACTTTGTATCCAGTGACGCCGCTATGGGGAAACCGACGGCTGCTGACTTGAAGCTGGGCCTTGCAACCGGGCCAGTGCTGTTTGCTGCCGAGA
+AGTTTCCAGAGTTGGATGCCATGATCATGAGACGGTTTAGCGAGACTGGTGATGTAATGGCTGCAAGGGAAGCTGTTGCCAAGACTGAAGGCATCGAGCA
+GACAAGACACATCGCTAACCAGCACAGCTTAGAAGCTCAGAAACAGATCAGTAAACTACATCCCAGTCCAGAGAGGCAAGCACTTATAGAACTTGCACAG
+CGAGTTGTTACAAGAATAAAGTAAATCCGTAGTTAAAATCCTTGTGTCAGTGCAAGAATGTTGGATCTCTAAAAACAGCCTTTATGCAATACAGGTTGTG
+AAAAATGCACAATGTTGTCTTTCACCATAACTACCCCTGATGTGCACTAGTGTACACAGAAACCCGGTTGCGTCAAAATGAAATGGTGTGAGACAAGACG
+TCCTAATGAAATAGAGGAAACACGTTTTGCATAGATTTCT
+>1108392 length 1440 cvg_27.6_tip_1
+ATTTGATTTGATTTGAAATGGTTAATTAAAGTAAAAAACTGTTTCACAGCCAGTAGGCTGAATTACATGATTTGTATTAGTTAAAAAATATTCAAATGTA
+TTATAGAAATTACAATAAAAACAAACAAATAATGCATAGGCAGTGGAACAGAAAAATGAACGTGGGGATCCCCAAGGAAAACAAGATTTTTACAAGAGCA
+CTTAAAATAAAACAAGGTAAAATAAGGGCACACCGCTGTGAACGACCCAAAACAATGCAATTAAGTAGATTTAATAATAATAAAAAAAAAACAATAAAAA
+TTTTAATAATACGCGTGAGATAAGGAACTTGACTGTTTTAAACCATTCAGCTCTACAGCGATGTATAGTATGCTTTGTTGAACTCCGAGTTTGGTGAATT
+CTTACGTTTCTTCGGTGTAGCAAATGACGGAGGCTTGTTAGTGAATTTTGCATGGATTATGCAAAAGAAAGGCACGATTGAAAGCACCTGCTCTCCCAGG
+TAGGGAGCTGACAAGACAGTGCTTGAGCGCTTGTTCATATTGACTATAGTTGGTATCAAGTATAATCCTGCCTGCTCGCTTCTGTGTCCACTCATGGCTT
+ATACACTGCTCCTTTGTTAGACCTCAAGATCAGACAACAGTCAGCATACTCCAGGACTAGCCTGACAATCGTCATGTAGTAAGTCAGACGGTCGCCTCGT
+GGAAAAGTTGTCTAAATTGAGAGAATGAAGACATATTGATGACTTTTGGAAGGTTTAATGATGGACGCAATATGCGCATTCAGTTCCTAGCAATTTAACG
+GTGTTATGTTGAATGATGACCTCTTTTTTCCCAAAGGAAACGTTCATTGTTGCGCACTTGTTCAGGTTTAGTTGTATTTGTTCCTGTCTGACCAATCATA
+GGGTAACCAGATAGTATCAGGCAACATTGAATGAGCTGATGCATGGCGAGTCTCTACCACTGTTGGGTTGTTCACGTGTCTGAGAACGTGAAGAGCATTA
+GCTGCATCACCAGTGGGCAGCATCATGTTGGTGTCTTTACCACATAGAGCATCTTTGATGAGCAACAGAAAAAGTATAGGTCCCAATTTAGTTCCTTGGG
+GAACACCGGCTGTTGTTGACTGCCACACAGACTTCACACTTTTTGTACTTCACCCATTGTCTGCAATCTGTTAAAAAGTTTGCGAATTATGTTACCAGAC
+TGACGTCAAGTTTGACCAACTTGGATATTGCGATTTCGTGGTCAATGCCATTAAATGCTTTGATGAAGTCAGTAAGGAGGACCGTCGACTCGTATGACAT
+GAAAGAAACTCGAGGGGTCTCGCGAAACATTTACAATTTAAAACAGGATCATTAAGAATTAATTAAAGGAAGATCAGCGTATCGACTCTGACAAATACCA
+GCAGGTTCAGGTTAAGGTTCAGGTTTATTTTCCATACCAT
+>1108394 length 1440 cvg_66.6_tip_0
+AGATAACGACGGGAAAAAGTCAAGATAATTTCACGTACACAACTCTTCAGAAGAAGAACGGAAGCAAGAAAGGATAAGATGATGGTGCGATTCGTAGCCT
+TACTCGGGGCAGTCAGCCTACTGGTATGTCAATCTGCAGGACTTGATGCCGCAGACGTCGAGGAACAAGACGAGTTCAACAAACCCTATGCTCCTGACAG
+TTCGTATGCGGATTTAAATGCACTTTTGGGCAACAATGTGCCAAGTCTACACAGCGCCTCCAAGCGTCAACAAAGTGACAGGGAGCGTGAGGTTGAAGCA
+GCCCAGACGCAATTTTACCCGTATGGAAGAAGAACTGATCCCAGGAAAGCGTCTGGTGGATTCACCTTTGGCAAGAGAGGGCAGTATTTTATCCCCATTC
+CGTACGAGAAACGAGAGATGGATGAGGTGAACCCGTACAGCGTAGCTAAGCGCGACGACGAGCTGACCGGACTAGAGGAGTACCAAGCTAGCAAGAGGTC
+AGGTCCTTATTCCTTTAACAGCGGGCTGACCTTTGGCAAGAGGGAACCCGAGAAGAGGAACATATTCGGATCTTATGACTTCGGGAAGCGGGCTTACGGC
+AACAATTTCAGCTTCGGCAAGCGAGGCATGGGAGTGTCCAGTTTTAGCTTTGGCAAACGATCCGGACTTGAGGGTGAACAAATGATGCCGGAAGACAAAC
+GGGCGTTCGGAGACTTTTCCTTCGGCAAGCGCAATAATGGTCTGTCCAGCTTCACATTCGGCAAGCGAGAGGGTGAACGATAGAACACGAGAGGGCGCCA
+TACTGTCTACAATGTGATAATTATAGTATCTTAATTATTTCAAAACCATACTTGATAAGAAATAACTGCTTGCGTTTTGAGTTAAAACATCAGTTCCAAG
+TATACAAACAAATTTTAAATAACATTGTTTAAAGCACGGATTTTGAATTAAAATGAAACGATAACGCAAAAGTGTGTAAATATAAGCATAGTAAGCTATC
+AACATCTAGAATTATGGAAGATATTTCAAGATACTAAAACTTGGAAGCTTTAGTTAATTTTAGATCTGGTTGAGATTCAAGTCTTCTTTTCTAGATTTTG
+TTTCCAGCCAGGGCTTTTACTATCCTTAACGTTTGGGGAAATTGCCAGGGTTGTGGTCACCTTGTTAAGGTCCTAAACAACACATTTTTTGTTAGTAAAA
+AATTACCCAATTAAGACAATTCATGAGTAAGCGACAAAAACTTAATAATTTAGCATATTTGCTTACGTTAGTTACTACAACAATAATTGAAACTTTCTTA
+AACACGGTTTTTCTAGTATGCTTTCCTGGTCAGCAATTAACTTGTAGATGTTTTTCAAATACTATGAATTCATATCTACGTAGAAATCTTAAAGATGTTT
+TCTGTGATTAAGTTTAGAACAACCTTAGCCAACAATCTCC

data/lib/npsearch.rb

@@ -1,7 +1,9 @@
 require 'bio'
+require 'english'
 require 'fileutils'
 
 require 'npsearch/arg_validator'
+require 'npsearch/logger'
 require 'npsearch/output'
 require 'npsearch/pool'
 require 'npsearch/scoresequence'
@@ -11,21 +13,23 @@ require 'npsearch/signalp'
 # Top level module / namespace.
 module NpSearch
   class <<self
+    attr_accessor :logger
     attr_accessor :opt
     attr_accessor :sequences
     attr_reader :sorted_sequences
 
     def init(opt)
-      @opt              = ArgumentsValidators.run(opt)
+      @opt = opt
+      ArgumentsValidators.run(opt)
       @sequences        = []
       @sorted_sequences = nil
-      @pool             = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1
-      FileUtils.mkdir_p(@opt[:temp_dir])
-      extract_orf if @opt[:type] == :genetic
+      @pool             = initialise_thread_pool
+      create_temp_directory
+      extract_orf
     end
 
     def run
-      input_file = @opt[:type] == :protein ? @opt[:input_file] : @opt[:orf]
+      input_file = @opt[:type] == :genetic ? @opt[:orf] : @opt[:input_file]
       iterate_input_file(input_file)
       @sorted_sequences = @sequences.sort_by(&:score).reverse
       Output.to_fasta(@opt[:input_file], @sorted_sequences, @opt[:type])
@@ -33,16 +37,37 @@ module NpSearch
       remove_temp_dir
     end
 
+    def logger
+      @logger ||= Logger.new(STDOUT, @opt[:debug])
+    end
+
     private
 
+    def initialise_thread_pool
+      return if @opt[:num_threads] == 1
+      logger.debug "Creating a thread pool of size #{@opt[:num_threads]}"
+      Pool.new(@opt[:num_threads])
+    end
+
+    def create_temp_directory
+      FileUtils.mkdir_p(@opt[:temp_dir])
+      logger.debug "Successfully creating temp directory at: #{@opt[:temp_dir]}"
+    end
+
     # Uses getorf from EMBOSS package to extract all ORF
     def extract_orf(input = @opt[:input_file], minsize = 90)
+      return if @opt[:type] == :protein
+      logger.debug 'Attempting to extract ORF.'
       @opt[:orf] = File.join(@opt[:temp_dir], 'input.orf.fa')
-      system "getorf -sequence #{input} -outseq #{@opt[:orf]}" \
-             " -minsize #{minsize} >/dev/null 2>&1"
+      cmd = "getorf -sequence #{input} -outseq #{@opt[:orf]}" \
+            " -minsize #{minsize} >/dev/null 2>&1"
+      logger.debug "Running: #{cmd}"
+      system(cmd)
+      logger.debug("EGexit Code: #{$CHILD_STATUS.exitstatus}")
     end
 
     def iterate_input_file(input_file)
+      logger.debug "Iterating the Input File: #{input_file}"
       Bio::FlatFile.open(Bio::FastaFormat, input_file).each_entry do |entry|
         if @opt[:num_threads] > 1
           @pool.schedule(entry) { |e| initialise_seqs(e) }
@@ -54,10 +79,10 @@ module NpSearch
     end
 
     def initialise_seqs(entry)
+      logger.debug "-- Analysing: '#{entry.definition}' (#{entry.aaseq.length})"
       return if entry.aaseq.length > @opt[:max_orf_length]
       sp = Signalp.analyse_sequence(entry.aaseq.to_s)
       return if sp[:sp] == 'N'
-      # seq = Sequence.new(entry.entry_id, entry.definition, entry.aaseq, sp)
       seq = Sequence.new(entry, sp)
       ScoreSequence.run(seq, @opt)
       @sequences << seq
@@ -65,6 +90,7 @@ module NpSearch
 
     def remove_temp_dir
       return unless File.directory?(@opt[:temp_dir])
+      logger.debug "Deleting Temporary directory: #{@opt[:temp_dir]}"
       FileUtils.rm_rf(@opt[:temp_dir])
     end
   end

data/lib/npsearch/arg_validator.rb

@@ -1,69 +1,86 @@
 require 'bio'
+require 'forwardable'
 
 # Top level module / namespace.
 module NpSearch
   # A class that validates the command line opts
   class ArgumentsValidators
     class << self
+      extend Forwardable
+      def_delegators NpSearch, :logger
+
       def run(opt)
         assert_file_present('input fasta file', opt[:input_file])
         opt[:input_file] = File.expand_path(opt[:input_file])
         assert_input_file_not_empty(opt[:input_file])
         assert_input_file_probably_fasta(opt[:input_file])
-        opt[:type] = assert_input_sequence(opt[:input_file])
+        opt[:type]        = assert_input_sequence(opt[:input_file])
         opt[:num_threads] = check_num_threads(opt[:num_threads])
         assert_binaries('SignalP 4.1 Script', opt[:signalp_path])
+        logger.debug "The validated OPT hash contains: #{opt}"
         opt
       end
 
       private
 
       def assert_file_present(desc, file, exit_code = 1)
+        logger.debug "Testing if the #{desc} exists: '#{file}'."
         return if file && File.exist?(File.expand_path(file))
-        $stderr.puts "*** Error: Couldn't find the #{desc}: #{file}."
+        error_msg = "*** Error: Couldn't find the #{desc}: '#{file}'."
+        logger.fatal error_msg
+        $stderr.puts error_msg
         exit exit_code
       end
 
       def assert_input_file_not_empty(file)
+        logger.debug "Testing if the input file ('#{file}') is empty."
         return unless File.zero?(File.expand_path(file))
-        $stderr.puts "*** Error: The input_file (#{file})" \
-                     ' seems to be empty.'
+        error_msg = "*** Error: The input_file ('#{file}') seems to be empty."
+        logger.fatal error_msg
+        $stderr.puts error_msg
         exit 1
       end
 
       def assert_input_file_probably_fasta(file)
+        logger.debug("Testing whether the input, ('#{file}') is a fasta file.")
         File.open(file, 'r') do |f|
-          fasta = (f.readline[0] == '>') ? true : false
+          fasta = f.readline[0] == '>' ? true : false
           return fasta if fasta
         end
-        $stderr.puts "*** Error: The input_file (#{file})" \
-                     ' does not seems to be a fasta file.'
+        error_msg = "*** Error: The input file (#{file}) does not seems to be" \
+                     ' to be a fasta file.'
+        logger.fatal error_msg
+        $stderr.puts error_msg
         exit 1
       end
 
       def assert_input_sequence(file)
         type = type_of_sequences(file)
         return type unless type.nil?
-        $stderr.puts '*** Error: The input files seems to contain a mixture of'
-        $stderr.puts '    both protein and nucleotide data.'
-        $stderr.puts '    Please correct this and try again.'
+        error_msg = '*** Error: The input files seems to contain a mixture of' \
+                    ' both protein and nucleotide data.' \
+                    ' Please correct this and try again.'
+        logger.fatal error_msg
+        $stderr.puts error_msg
         exit 1
       end
 
       # determine file sequence type based on first 500 lines
       def type_of_sequences(file)
+        logger.debug 'Checking the type of sequence in the input file based' \
+                     ' on the first 500 lines.'
         fasta_content = File.foreach(file).first(500).join("\n")
         # the first sequence does not need to have a fasta definition line
         sequences = fasta_content.split(/^>.*$/).delete_if(&:empty?)
         # get all sequence types
         sequence_types = sequences.collect { |seq| guess_sequence_type(seq) }
                                   .uniq.compact
+        logger.debug " The guessed typed of Sequences are: #{sequence_types}"
         return nil if sequence_types.empty?
         sequence_types.first if sequence_types.length == 1
       end
 
       def guess_sequence_type(seq)
-        # removing non-letter and ambiguous characters
         cleaned_sequence = seq.gsub(/[^A-Z]|[NX]/i, '')
         return nil if cleaned_sequence.length < 10 # conservative
         type = Bio::Sequence.new(cleaned_sequence).guess(0.9)
@@ -71,20 +88,27 @@ module NpSearch
       end
 
       def check_num_threads(num_threads)
+        logger.debug "Checking the number of threads: #{num_threads}"
         num_threads = Integer(num_threads)
         unless num_threads > 0
-          $stderr.puts 'Number of threads can not be lower than 0'
-          $stderr.puts 'Changing number of threads to 1'
+          warn_msg = 'Number of threads can not be lower than 0. Changing' \
+                     ' number of threads to 1'
+          logger.warn warn_msg
+          $stderr.puts warn_msg
           num_threads = 1
         end
         return num_threads unless num_threads > 256
-        $stderr.puts "Number of threads set at #{num_threads} is" \
-                     ' unusually high.'
+        warn_msg = "Number of threads set at #{num_threads} is unusually high."
+        logger.warn warn_msg
+        $stderr.puts warn_msg
       end
 
       def assert_binaries(desc, bin)
+        logger.debug "Checking #{desc} binary at: #{bin}."
         return if command?(bin.to_s)
-        $stderr.puts "NpSearch is unable to use the #{desc} at #{bin}"
+        warn_msg = "NpSearch is unable to use the #{desc} at #{bin}"
+        logger.warn warn_msg
+        $stderr.puts warn_msg
       end
 
       # Return `true` if the given command exists and is executable.

data/lib/npsearch/logger.rb

@@ -0,0 +1,11 @@
+require 'logger'
+
+module NpSearch
+  # Extend stdlib's Logger class for custom initialization
+  class Logger < Logger
+    def initialize(dev, verbose = false)
+      super dev
+      self.level = verbose ? DEBUG : INFO
+    end
+  end
+end

data/lib/npsearch/signalp.rb

@@ -8,15 +8,15 @@ module NpSearch
   class Signalp
     class << self
       extend Forwardable
-      def_delegators NpSearch, :opt
+      def_delegators NpSearch, :opt, :logger
 
       def analyse_sequence(seq)
         sp_headers = %w(name cmax cmax_pos ymax ymax_pos smax smax_pos smean d
                         sp dmaxcut networks orf)
         seqs       = setup_analysis(seq)
         sp_results = []
-        seqs.each do |seq|
-          sp_results << run_signalp(seq, sp_headers)
+        seqs.each do |sequence|
+          sp_results << run_signalp(sequence, sp_headers)
         end
         sp_results.sort_by { |h| h[:d] }.reverse[0]
       end
@@ -24,10 +24,10 @@ module NpSearch
       private
 
       def run_signalp(seq, sp_headers)
-        Timeout::timeout(300) do
+        timeout(300) do
           cmd = "echo '>seq\n#{seq}\n' | #{opt[:signalp_path]} -t euk" \
-                " -f short -U 0.34 -u 0.34"
-          stdin, stdout, stderr, wait_thr = Open3.popen3(cmd)
+                ' -f short -U 0.34 -u 0.34'
+          stdin, stdout, stderr = Open3.popen3(cmd)
           out = stdout.gets(nil).split("\n").delete_if { |l| l[0] == '#' }
           if out.nil? || out.empty?
             print stdout
@@ -40,13 +40,13 @@ module NpSearch
           stdin.close; stdout.close; stderr.close
         end
       rescue Timeout::Error
-        no_results = [0,0,1,1,1,1,1,1,1,'N',1,1, seq]
+        no_results = [0, 0, 1, 1, 1, 1, 1, 1, 1, 'N', 1, 1, seq]
         return Hash[sp_headers.map(&:to_sym).zip(no_results)]
       end
 
       def setup_analysis(seq)
         orfs = seq.scan(/(?=(M\w{#{opt[:min_orf_length]},}))./).flatten
-        (opt[:type] == :protein || orfs.empty? || orfs.nil?) ? [seq] : orfs
+        opt[:type] == :protein || orfs.empty? || orfs.nil? ? [seq] : orfs
       end
     end
   end

data/lib/npsearch/version.rb

@@ -1,4 +1,4 @@
 # Top level module / namespace.
 module NpSearch
-  VERSION = '2.1.2'.freeze
+  VERSION = '2.1.3'.freeze
 end

data/test/test_argument_validator.rb

@@ -1,12 +1,13 @@
 require_relative 'test_helper'
-
+require 'npsearch'
 require 'npsearch/arg_validator'
 
 # Class to test the how well the CLI arguments are validated.
 class TestInputArgumentValidator < Minitest::Test
   def setup
+    NpSearch.logger = Logger.new(STDOUT, true)
     @c = NpSearch::ArgumentsValidators
-    @opt = { num_threads: 1, min_orf_length: 30 }
+    @opt = { num_threads: 1, min_orf_length: 30, debug: true }
   end
 
   def test_assert_file_present

data/test/test_sequence.rb

@@ -17,7 +17,7 @@ class TestSequences < Minitest::Test
     sp = { name: 'test_sequences', cmax: '0.492', cmax_pos: '31', ymax: '0.612',
            ymax_pos: '31', smax: '0.950', smax_pos: '17', smean: '0.786',
            d: '0.706', sp: 'Y', dmaxcut: '0.300', networks: 'SignalP-noTM',
-           orf: sequence.seq}
+           orf: sequence.seq }
     @seq = NpSearch::Sequence.new(sequence, sp, 2)
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: npsearch
 version: !ruby/object:Gem::Version
-  version: 2.1.2
+  version: 2.1.3
 platform: ruby
 authors:
 - Moghul et al.
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-11-13 00:00:00.000000000 Z
+date: 2016-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -115,8 +115,10 @@ files:
 - bin/npsearch
 - exemplar_data/README.md
 - exemplar_data/genetic_data.fa
+- exemplar_data/protein.fa
 - lib/npsearch.rb
 - lib/npsearch/arg_validator.rb
+- lib/npsearch/logger.rb
 - lib/npsearch/output.rb
 - lib/npsearch/pool.rb
 - lib/npsearch/scoresequence.rb