npsearch 2.0.1 → 2.1.0

data/lib/npsearch/scoresequence.rb

@@ -1,108 +1,110 @@
-require 'csv'
-require 'tempfile'
-
+# Top level module / namespace.
 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'
+      DI_CLV        = 'KR|RR|KK'.freeze
+      MONO_NP_CLV_2 = '[KR]..R'.freeze
+      MONO_NP_CLV_4 = '[KR]....R'.freeze
+      MONO_NP_CLV_6 = '[KR]......R'.freeze
       NP_CLV = "(#{DI_CLV})|(#{MONO_NP_CLV_2})|(#{MONO_NP_CLV_4})|" \
-               "(#{MONO_NP_CLV_6})"
+               "(#{MONO_NP_CLV_6})".freeze
 
-      def run(sequence)
-        @sequence = sequence
-        split_into_neuropeptides
-        count_np_cleavage_sites
-        count_c_terminal_glycines
-        np_similarity
-        acidic_spacers
+      def run(sequence, opt)
+        split_into_potential_neuropeptides(sequence)
+        count_np_cleavage_sites(sequence)
+        count_c_terminal_glycines(sequence)
+        np_similarity(sequence, opt[:temp_dir])
+        acidic_spacers(sequence)
       end
 
       private
 
-      def split_into_neuropeptides
+      def split_into_potential_neuropeptides(sequence)
         potential_nps = []
-        results = @sequence.seq.scan(/(?<=^|#{NP_CLV})(\w+?)(?=#{NP_CLV}|$)/i)
+        results = sequence.seq.scan(/(?<=^|#{NP_CLV})(\w+?)(?=#{NP_CLV}|$)/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
+        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])
+      def count_np_cleavage_sites(sequence)
+        return if sequence.potential_cleaved_nps.empty?
+        sequence.potential_cleaved_nps.each do |e|
+          count_dibasic_np_clv(sequence, e[:di_clv_end])
+          count_mono_basic_np_clv(sequence, e[:mono_2_clv_end],
+                                  e[:mono_4_clv_end], e[:mono_6_clv_end])
         end
       end
 
-      def count_dibasic_np_clv(dibasic_clv)
+      def count_dibasic_np_clv(sequence, dibasic_clv)
         case dibasic_clv
         when 'KR'
-          @sequence.score += 0.09
+          sequence.score += 0.09
         when 'RR', 'KK'
-          @sequence.score += 0.05
+          sequence.score += 0.05
         end
       end
 
-      def count_mono_basic_np_clv(mono_2_clv, mono_4_clv, mono_6_clv)
+      def count_mono_basic_np_clv(sequence, 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
+        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$/ && e[:di_clv_end] == 'KR'
-            @sequence.score += 0.25
+      def count_c_terminal_glycines(sequence)
+        return if sequence.potential_cleaved_nps.empty?
+        sequence.potential_cleaved_nps.each do |e|
+          if e[:np] =~ /FG$/ && e[:di_clv_end] == 'KR'
+            sequence.score += 0.40
+          elsif e[:np] =~ /G$/ && e[:di_clv_end] == 'KR'
+            sequence.score += 0.25
           elsif e[:np] =~ /G$|GK$|GR$/
-            @sequence.score += 0.10
+            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
+      # Adds 0.10 if the acidic spacer is detected.
+      # Acidic Spacer is defined as being less than 25% of the precursor length
+      # (not including the Signalp) && having more than 50% D and E amino acids.
+      def acidic_spacers(sequence)
+        sequence.potential_cleaved_nps.each do |e|
+          next if e[:np].length / sequence.seq.length > 0.25
+          sequence.score += 0.10 if e[:np].count('DE') / e[:np].length > 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)
+      def np_similarity(sequence, temp_dir, results = nil)
+        results  = run_cdhit(sequence, temp_dir) if results.nil?
+        clusters = results.split(/^>Cluster \d+\n/)
+        clusters.each do |c|
+          next if c.nil?
+          no_of_seqs_in_cluster = c.split("\n").length
+          if no_of_seqs_in_cluster > 1
+            sequence.score += (0.15 * no_of_seqs_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
+      def run_cdhit(sequence, temp_dir)
+        f = Tempfile.new('clust', temp_dir)
+        fo = Tempfile.new('clust_out', temp_dir)
+        return unless write_potential_peptides_to_tempfile(sequence, f)
+        `cd-hit -c 0.5 -n 3 -l 4 -i #{f.path} -o #{fo.path}`
+        IO.read("#{fo.path}.clstr")
       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"
+      def write_potential_peptides_to_tempfile(sequence, tempfile)
+        return false if sequence.potential_cleaved_nps.empty?
+        sequences = ''
+        sequence.potential_cleaved_nps.each_with_index do |e, i|
+          sequences += ">seq#{i}\n#{e[:np]}\n"
         end
-        tempfile.write(content)
+        tempfile.write(sequences)
         tempfile.close
+        true
       end
     end
   end

data/lib/npsearch/sequence.rb

@@ -1,23 +1,26 @@
+# Top level module / namespace.
 module NpSearch
+  # Adapted from GeneValidator's Query Class..
   # A class to hold sequence data
   class Sequence
-    DI_NP_CLV = 'KR|KK|RR'
-    MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R'
+    DI_NP_CLV   = 'KR|KK|RR'.freeze
+    MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R'.freeze
 
     attr_reader :id
+    attr_reader :defline
     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]
+    def initialize(entry, sp, frame = nil)
+      @id                    = entry.entry_id
+      @defline               = entry.definition
+      sp_cleavage_site_idx   = sp[:ymax_pos].to_i - 1
+      @signalp               = sp[:orf][0..(sp_cleavage_site_idx - 1)]
+      @seq                   = sp[:orf][sp_cleavage_site_idx..-1]
       @html_seq              = format_seq_for_html
       @translated_frame      = frame
       @score                 = 0
@@ -27,7 +30,7 @@ module NpSearch
     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!(/#{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>')

data/lib/npsearch/signalp.rb

@@ -1,6 +1,6 @@
 require 'forwardable'
-require 'tempfile'
 
+# Top level module / namespace.
 module NpSearch
   # A class to hold sequence data
   class Signalp
@@ -10,15 +10,34 @@ module NpSearch
 
       def analyse_sequence(seq)
         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}")
-        f.close
-        s = `#{opt[:signalp_path]} -t euk -f short -U 0.3 -u 0.3 '#{f.path}' | \
-             sed -n '3 p'`
-        Hash[sp_headers.map(&:to_sym).zip(s.split)]
-      ensure
-        f.unlink
+                        sp dmaxcut networks orf)
+        data       = setup_analysis(seq)
+        orf_results = []
+        s = `echo "#{data[:fasta]}\n" | #{opt[:signalp_path]} -t euk \
+             -f short -U 0.34 -u 0.34`
+        sp_results = s.split("\n").delete_if { |l| l[0] == '#' }
+        sp_results.each_with_index do |line, idx|
+          line = line + ' ' + data[:seq][idx].to_s
+          orf_results << Hash[sp_headers.map(&:to_sym).zip(line.split)]
+        end
+        orf_results.sort_by { |h| h[:d] }.reverse[0]
+      end
+
+      def setup_analysis(seq)
+        if opt[:type] == :protein
+          data = { seq: [seq], fasta: ">seq\n#{seq}" }
+        else
+          orfs = seq.scan(/(?=(M\w+))./).flatten
+          orfs.unshift(seq)
+          data = { seq: orfs, fasta: create_orf_fasta(orfs) }
+        end
+        data
+      end
+
+      def create_orf_fasta(m_orf)
+        fasta = ''
+        m_orf.each_with_index { |seq, idx| fasta << ">#{idx}\n#{seq}\n" }
+        fasta
       end
     end
   end

data/lib/npsearch/version.rb

@@ -1,4 +1,4 @@
 # Top level module / namespace.
 module NpSearch
-  VERSION = '2.0.1'
+  VERSION = '2.1.0'.freeze
 end

data/lib/npsearch.rb

@@ -1,7 +1,7 @@
 require 'bio'
 require 'fileutils'
 
-# require 'npsearch/arg_validator'
+require 'npsearch/arg_validator'
 require 'npsearch/output'
 require 'npsearch/pool'
 require 'npsearch/scoresequence'
@@ -11,33 +11,39 @@ require 'npsearch/signalp'
 # Top level module / namespace.
 module NpSearch
   class <<self
-    MIN_ORF_SIZE = 30 # amino acids (including potential signal peptide)
-
     attr_accessor :opt
     attr_accessor :sequences
     attr_reader :sorted_sequences
 
     def init(opt)
-      # @opt = args_validation(opt)
-      @opt        = opt
-      @sequences  = []
+      @opt              = ArgumentsValidators.run(opt)
+      @sequences        = []
       @sorted_sequences = nil
-      @opt[:type] = guess_sequence_type
-      @pool       = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1
+      @pool             = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1
+      FileUtils.mkdir_p(@opt[:temp_dir])
+      extract_orf if @opt[:type] == :genetic
     end
 
     def run
-      iterate_input_file
+      input_file = @opt[:type] == :protein ? @opt[:input_file] : @opt[:orf]
+      iterate_input_file(input_file)
       @sorted_sequences = @sequences.sort_by(&:score).reverse
       Output.to_fasta(@opt[:input_file], @sorted_sequences, @opt[:type])
       Output.to_html(@opt[:input_file])
+      remove_temp_dir
     end
 
     private
 
-    def iterate_input_file
-      biofastafile = Bio::FlatFile.open(Bio::FastaFormat, @opt[:input_file])
-      biofastafile.each_entry do |entry|
+    # Uses getorf from EMBOSS package to extract all ORF
+    def extract_orf(input = @opt[:input_file], minsize = 90)
+      @opt[:orf] = File.join(@opt[:temp_dir], 'input.orf.fa')
+      system "getorf -sequence #{input} -outseq #{@opt[:orf]}" \
+             " -minsize #{minsize} >/dev/null 2>&1"
+    end
+
+    def iterate_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) }
         else
@@ -48,49 +54,18 @@ module NpSearch
     end
 
     def initialise_seqs(entry)
-      if @opt[:type] == :protein
-        initialise_protein_seq(entry.entry_id, entry.aaseq)
-      else
-        initialise_transcriptomic_seq(entry.entry_id, entry.naseq)
-      end
-    end
-
-    def initialise_protein_seq(id, seq)
-      sp = Signalp.analyse_sequence(seq)
-      return unless sp[:sp] == 'Y'
-      seq = Sequence.new(id, seq, sp)
-      ScoreSequence.run(seq)
+      return if entry.aaseq.length > @opt[:max_seq_length]
+      sp = Signalp.analyse_sequence(entry.aaseq)
+      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
     end
 
-    def initialise_transcriptomic_seq(id, naseq)
-      (1..6).each do |f|
-        translated_seq = naseq.translate(f)
-        orfs = translated_seq.to_s.scan(/(?=(M\w{#{MIN_ORF_SIZE},}))./).flatten
-        initialise_orfs(id, orfs, f)
-      end
-    end
-
-    def initialise_orfs(id, orfs, frame)
-      orfs.each do |orf|
-        sp = Signalp.analyse_sequence(orf)
-        next if sp[:sp] == 'N'
-        seq = Sequence.new(id, orf, sp, frame)
-        ScoreSequence.run(seq)
-        @sequences << seq
-        # 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
-
-    def guess_sequence_type
-      fasta_content = IO.binread(@opt[:input_file])
-      # removing non-letter and ambiguous characters
-      cleaned_sequence = fasta_content.gsub(/[^A-Z]|[NX]/i, '')
-      return nil if cleaned_sequence.length < 10 # conservative
-      type = Bio::Sequence.new(cleaned_sequence).guess(0.9)
-      (type == Bio::Sequence::NA) ? :nucleotide : :protein
+    def remove_temp_dir
+      return unless File.directory?(@opt[:temp_dir])
+      FileUtils.rm_rf(@opt[:temp_dir])
     end
   end
 end

data/npsearch.gemspec

@@ -16,7 +16,7 @@ Gem::Specification.new do |s|
                     ' For more information: https://github.com/wurmlab/npsearch'
   s.summary       = 'Search for neuropeptides based on the common' \
                     ' neuropeptides markers'
-  s.homepage      = 'https://github.com/IsmailM/NeuroPeptideSearch'
+  s.homepage      = 'https://github.com/wurmlab/npsearch'
   s.license       = 'AGPL'
 
   s.files         = `git ls-files -z`.split("\x0")
@@ -28,6 +28,7 @@ Gem::Specification.new do |s|
   s.add_development_dependency 'bundler', '~> 1.6'
   s.add_development_dependency 'rake', '~>10.3'
   s.add_development_dependency 'coveralls'
+  s.add_development_dependency 'minitest', '~> 5.4'
 
   s.add_dependency 'bio', '~> 1.4'
   s.add_dependency 'slim', '~> 3.0'

data/templates/contents.slim

@@ -29,9 +29,9 @@ html lang="en"
           p.sequence
             span.id
               - if @opt[:type] == :protein
-                | >#{seq.id}
+                | >#{seq.defline}
               - elsif @opt[:type] == :nucleotide
-                | >#{seq.id}-(frame:#{seq.translated_frame})
+                | >#{seq.defline}-(frame:#{seq.translated_frame})
             br
             span.seq== seq.html_seq
       br
@@ -50,5 +50,5 @@ html lang="en"
         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 
+        a href="https://github.com/wurmlab/npsearch" target="_blank"  NpSearch 
         | v#{NpSearch::VERSION}

data/test/files/mixed_content.fa

@@ -0,0 +1,167 @@
+>isotig00006  gene=isogroup00003  length=1747  numContigs=6
+AGTTAAAAGTTGAAAAATTGGTGACCATATTTTGACACTCTAGCATATTTGGGAGCTATA
+TACTGATTTGGGTTTCACCATGCACAGATGAGGTATATACATAAGTTGAAAGCCTGCAGC
+TCTATATTAAAGGCATTGAAGACtcGCCcAAaccgtgTGcgcccTCTGAAAAaGTTAACT
+TTCcGTTgCTTGCAaGTGAAGTTTtcTtCTTGTCGCTACAAAATGCAGACAGTAATGAAA
+
+>isotig00007  gene=isogroup00003  length=1749  numContigs=5
+TGTGTGTGTGTGGTGCTTCCccTCTAGGGCTGTAAATTTCAAAGGAACCTTGCGCAAGAA
+CAGtAGCTTGCGaCGTTTTTCAAaaCCAGAGGTTCTGAACTGAACTGTACTGACTACTGT
+AGGGtacTTAAaGGCATTGAAGACTCGCCcAAaCCatgTGCCGCGctttGAAAAAGTTAA
+CTTTCCGTTGCTTGCAAATGAcGTTTtcTtCTtGTCgCTACAAAATGCAGACAGTAaTgA
+AACGTGATACcTtGTtATCTTTtATCTAgACctGAGATGtCcACGCTGCTATGTACACTG
+TGTTGTGGgTATTGACcGTAGCTGTATGTATtGACTGTACACTAGTGTCTAATtACCGAC
+GGTAGCAAGCTGTGTGTGTATTTTCTGGGATCaaTGGTGgTGTCTAACACTTCtGTTACA
+CCtCAtTcGAAACTAGGTCAGAtTAcCgGCATAGACGTTTCTTTGTGCcgAGTCtTCACA
+cccttttaaggagaagtattttatatcccattaaTAGAGAAAGAATTATGTTTCAATTGG
+TAGCATGCAACTTAAAAtTTTGCAAACaTTAGATACAATCAAACAATAACAAGGTTCATT
+ACAAGGttAAtCtacTGCCCTTTATTtCACATTaGTCTGTCACATCAGAAGgTCACAGCT
+TtCAaTAaTTATACAAACAAATtCCCTtGATGGgTGCTtGgTtAGATTCCTGCaatTTTC
+AAGTTTATCAATGTAATAAGTTCTGAATGTGGCAATGTGGaaGAAGCtTtGGGATAATCT
+GTGGATAAGACTGCCAGACTATCAACAAGATTCCACATCCATGCAACTCCAACTGCTTCC
+TTCACCTCCTTGCAGATGTACCACATGTCCaaAAAAAAGTCAGCATTGGTTAATGTAATT
+AAAATCTGGCTTCCTcCTGAGCTGGCAAATACACATGAATTGTCAAGTACAGAGGTCAGT
+GTGAAACCACTGAAAGATCTTCTCAGCTTTCAAGAAAACAAAGACTTGAAGCCAAATTGA
+CAGAGGCCACACTGATACCATTCCACTCTCATAAGATGAAGGTATCACACACACTTCATT
+TTGCTTCTGCGATGCAGTGCCTGGTAGACTGTGAGGgTCACCCAATGGATgtTTTAaCAa
+CTGCCtGGTTtAtAGAGCTCTGCAACAGATAATTCATCCTAaTGTCTAGTCGTCATCCTG
+TCATGGCCTTGAGCAAGTTGAACCCACTTCAACACAAAGCAGCTATTGAATTCTTGTCTA
+GGTACTGTcAAATCCACATCACCATCATTGCttGGTTCCAGCTaCGcTGACCATGaTAAA
+AGAGTACAATGAGGGTTTTTTAATTCACCCAACAGAGCTTGCATTCCAGTACCTTTGGGC
+AGCTGaaaaGATATTCAGAAaTTGTTATATATGAGTGTGTTTGTATGCATGCAtATGtGT
+GATTTtCTtGCTTTACAGAACAGCTCCaTTTTGATAAGCTAtgTAAcgtGgAAACCTGCC
+AATCAaTGTTtgAAataGGAcaGgCTGAAACGATTCTTAAATGAAAAGCTTAAtgaCTTc
+TTgCAtttttaTACATCACTGTTCAGGtAaGGCCAGTAAGGgCAGTATgAaGAAtAaGTA
+ACAATtAATAATTATCATTATGGCCATTTGCTGtcTGCATAAtAaCAAACTGAATGATGT
+CATCAGCCCTgTGCTCAGTTGACAgAACTGACAAGTAGGCACACaaTGTCAGTGTGATCC
+ATGAAACCT
+>isotig00008  gene=isogroup00003  length=1726  numContigs=6
+AGGTTTCATGGATCACACTGACAtTGTGTGCCTACTTGTCAGTTcTGTCAACTGAGCAcA
+GGGCTGATGACATCATTCAGTTTGttattATGCAggaCAGCAAATGGCCATAATGATAAT
+TATTAaTTGTTACTtaTTCTtcATACTGCCcTTACTGGCCTtaCCTGAACAGTGATGTAt
+caaaaTGcAAgAAGtcaTTAAGCTTTTCATTTAAGAATCGTTTCAGCctgTCCtaatTTt
+cAAaCAtTGATTGGCAGGTTTCcacgTTAcaTAGCTTATCAAAAtGGAGCTGTTCTGTAA
+AGCAAGaAAATCACaCATaTGCATGCATACAAACACACTCATATATAACAAtTTCTGAAT
+ATCTtttCAGCTGCCCAAAGGTACTGGAATGCAAGCTCTGTTGGGTGAATTAAAAAaCCc
+TCATTGTACTCTTTTATCATGGTCAGCGTAGCTGGAACCAGCAATGATGGTGATGTGGAT
+TTGACAGTACCTAGACAAGAATTCAATAGCTGCTTTGTGTTGAAGTGGGTTCAACTTGCT
+CAAGGCCATGACAGGATGACGACTAGACATtAGGATGAATTATCTGTTGCAGAGCTCTAT
+AAaCCAGGCAGTtGTtAAAaCATCCATTGGGTGACCcTCACAGTCTACCAGGCACTGCAT
+CGCAGAAGCAAAATGAAGTGTGTGTgATACCTTCATCTTATGAGAGTGGAATGGTATCAG
+TGTGGCCTCTGTCAATTTGGCTTCAAGTCTTTGTTTTCTTGAAAGCTGAGAaGATCTTTC
+AGTGGTTTCACACTGACCTCTGTACTTGACAATTCATGTGTATTTGCCAGCTCAGgAGGA
+AGCCAGATTTTAATTACATTAACCAATGCTGACTTTTTTttGGACATGTGGTACATCTGC
+AAGGAGGTGAAGGAAGCAGTTGGAGTTGCATGGATGTGGAATCTTGTTGATAGTCTGGCA
+GTCTTATCCACAGATTATCCCAAAGCTTCTCCACATTGCCACATTCAGAACTTATTACAT
+TGATAAACTTGAAAATtGCAGGAATCTAaCcAaGCACCcATCAaGGGAaTTTGTTTGTAT
+AATtATtGAAaGCTGTGACcTTCTGATGTGACAGACTAATGTGAAaTAAAGGgCAgtaGa
+TTaCCTTGTaaTGAACCttGTTATTGTTTGATTGTATCTAAtGTTTGCAaaTTTTAAGTT
+GCATGCTACCAATTGAAACATAATTCTTTCTCTAttaatgggatataaaatacttctcct
+taaaagggTGTgAaGACTcggCACAAAGAAACGTCtaTGCcGgtAaTCTGACCTAGTTTc
+gAatGaGGTGTAACagAAGTgTtAGACACcACCAttGATCCcAGAAAATACACACACAGC
+TTGCTACCGTCGGTAaTTAGACACTAGTGTACAGTCAaTACATACAGCTAcGgTCAATAC
+CCACAaCACAgTGTAcATAGCAGCGaTGgACATCTCAGGTCTAGATAAAAGATAaCAAGG
+TATCACGTTTCATtaCTGTCTGCATTTtGTAGCgaCAagAAGAAAAcgtCATTtGCAAGC
+AaTGgAAAGTtAACTTTTTCaGAGCGcagCAcGCgggTTGGGGCAAGTCTTCCAAGCCTT
+TAAGTtGACAtcTTGCCTTTGGCTATCCAGGgTGACAAGATGATACTAGCAGGTAgagtg
+actaattgagccctgtgtgagaaaccaatgcagaatctagcctagt
+>isotig00009  gene=isogroup00003  length=1827  numContigs=2
+TAGCTGTGATCTAGTGGATCTGACTGGCCTTTTGATTATTTCAGCacGATTCTCAGACTA
+CAGTTGTAAaCCTACTTCGACTACTACTACTActagtacTAACGGTGCAACGTTGTTATA
+AGTTTGCCAAAGGTGAAACTTTAGCCTTAGGACtGTGTTTATTTTATTTGCAGTCGCATT
+CgCCTAACTGTTTTCTGTTACTGGGTGCATTTAACTCACATTAATAGAGGATTTTtGACT
+AGTtCcTAGAGAGTGGTGTTTCTGTTTTACCACCATGGCAAAAAAGGGAAaGCCTCGCCC
+TGACCATAGGCCTCCTGCACACAACCCGCATTATGCTCATGATCCACCACCTTATTCACA
+ACAGCAACCACCACTTCAACAGCAGAACTATGCACAACAAATGCATCATGGTGGAGGTGG
+TGGAAATAGACAACATGCACGACcTAGACCTAGTCCACCTTCAGAAGTCAGTGACTGTGT
+CAAGTACTCCCTTTTCTtGTATAACTGCATCTTTTGgaTTGtCGGCCTTttCTTTATtGC
+AGCAGGTATCTGGgCATTTCACGATAGGGGTGTTTTTAATGAATTCCAGTCACTTAGTAC
+CAATGAGGTCTCCTTTCTCACTGATCCTGTTATTTGGCTGTTCGTCCTCGGAGGTGTAGT
+TTTCATGCTGGGAACCCTCGGATGTCTgGGGgCCCTCAGAGAAAaTATCTGCATGCTGAA
+GTGTTTTAGCATAATCATGGGGCTTATACTGCTGCTGGAAATTGGAGGTGGATGTGCGAT
+ATACTTCTATCGTGCACAGATTCAGGCACAGTTTCAAAAGTCCTTAACAGATGTGaCCAT
+AACAGATTACAGAGAAAATGCTGATTTCCAGGATCTCATAGACGCATTACAATCCGGTCT
+TTCTTGTTGTGGTGTCAATTCCTatGAAGACTGGGATAATAATATTTATTTCAACTGTAG
+TGGTCCTGCCAATAACCCTGAAGCcttGTGGTGTGCCTTtCTCCTGTTGTATACCGGATC
+AAGCAAGCGGAGTAGCCAACACCCAGTGCGGTTATGGAGTTCGTTCCCCCGAACAACAAA
+ATACTTTCCACACAAAGATTTACACCACTGGCTGTGCGGATATGTTTACAATGTGGATTA
+ATAGGTACCTATATTACATAGCAGGCATTGCTGGGGTCATTGTCTTGGTCGAGTtGTTTG
+GATTCTGTTTTGCACATTCCCTCATCAACGACATCAAACGCCAAAAGGCCCGCTGGGCGC
+ATCGATAATTCATTCCAGGATGTTGGTGgATGATGCTACTCAAGGGagAAGACTGACAGT
+GCCTTTtGGTCAaTATCGTGTAGCATCAGGAAGGAGGTAGTACCTCCTCAACTAACCaTA
+ACAGAATTTGTCCAGTTTGTAACATCGTCAAGAAATAAACAGACTTTTTTTACCATTAGG
+ACgTGATAATACTACCACGTAACCTCTCAAAGCACAAAAAGCAAAAAGCAAATATCTCCT
+TGTTTTAAAATTAGaagGTCTATCTCAGATAACAACCACAGAACATgTGGAGTTTTCCtT
+TATGCTATCATAAAGATATAAATATATATAAAATTGAGGTAGcATCtTGGCTACCCACCA
+AAATCATTTTTTTTCCAGTTTGaAACATCATGGAACATTTCAGAACAAAGATCATTTCAG
+TCGTTACCACACTCAAGAgaTTGCTGTcGTCAaCaTTTtGtaGCTTTTtAAtGTCTTGAT
+CTTCGTCGACATCGTCAATGTGTAAACTATTCTCGACGAGAGATTAGTGTCTAATACTGC
+GGGTgATTTGATATAAATCTCACTTGG
+>isotig00010  gene=isogroup00003  length=1650  numContigs=5
+TGAATGAGAAAtGAAATTTAGCGAAGAAATCACCTTGTAAATTAAAAACTAAAATGGCTT
+TCACACAAATTAaCAGTAAAtGgAGAATGTTTTTAAAGCAATATATGCAGTACAGCcATT
+CATTGGAAAACAGTAAcAAAaTACATTTATCTTGTtcATTTTtACctCctGCAAaacTTA
+cAaCcGTTAATTATGTAGATTGGATGGCACTAACAGGGTACTTGTCTTATCTGCCTATTG
+GATAATGTGGcATTAATACTACTGTGTATGGGCACTGAGGCTGAGAGTGCAGTAAGTTtA
+AAGGCATTGAAGACTCtCCCCGAaCcGCGtGCCGGGCTctGAAAAAGTtAaCTGCTCGCA
+AaTtAcGTTTtCTtCTTGTCaCTaCAAAaTGCAGACATTaaTGAAACGTGATACCTTGTt
+ATCTTTTATCTAGACCTGAGATGTCcAtCGCTGCTATgTACAcTGTGTTGTGGGTATTGA
+CcgTAGCTGTATGTATtGACTGTACACTAGTGTCTAATtACCGACGGTAGCAAGCTGTGT
+GTGTATTTTCTGGGATCaaTGGTGgTGTCTAACACTTCtGTTACACCtCAtTcGAAACTA
+GGTCAGAtTAcCgGCATAGACGTTTCTTTGTGCcgAGTCtTCACAcccttttaaggagaa
+gtattttatatcccattaaTAGAGAAAGAATTATGTTTCAATTGGTAGCATGCAACTTAA
+AAtTTTGCAAACaTTAGATACAATCAAACAATAACAAGGTTCATTACAAGGttAAtCtac
+TGCCCTTTATTtCACATTaGTCTGTCACATCAGAAGgTCACAGCTTtCAaTAaTTATACA
+AACAAATtCCCTtGATGGgTGCTtGgTtAGATTCCTGCaatTTTCAAGTTTATCAATGTA
+ATAAGTTCTGAATGTGGCAATGTGGaaGAAGCtTtGGGATAATCTGTGGATAAGACTGCC
+AGACTATCAACAAGATTCCACATCCATGCAACTCCAACTGCTTCCTTCACCTCCTTGCAG
+ATGTACCACATGTCCaaAAAAAAGTCAGCATTGGTTAATGTAATTAAAATCTGGCTTCCT
+cCTGAGCTGGCAAATACACATGAATTGTCAAGTACAGAGGTCAGTGTGAAACCACTGAAA
+GATCTTCTCAGCTTTCAAGAAAACAAAGACTTGAAGCCAAATTGACAGAGGCCACACTGA
+TACCATTCCACTCTCATAAGATGAAGGTATCACACACACTTCATTTTGCTTCTGCGATGC
+AGTGCCTGGTAGACTGTGAGGgTCACCCAATGGATgtTTTAaCAaCTGCCtGGTTtAtAG
+AGCTCTGCAACAGATAATTCATCCTAaTGTCTAGTCGTCATCCTGTCATGGCCTTGAGCA
+AGTTGAACCCACTTCAACACAAAGCAGCTATTGAATTCTTGTCTAGGTACTGTcAAATCC
+ACATCACCATCATTGCttGGTTCCAGCTaCGcTGACCATGaTAAAAGAGTACAATGAGGG
+TTTTTTAATTCACCCAACAGAGCTTGCATTCCAGTACCTTTGGGCAGCTGATATCCATTT
+TGTTCCTCGTATgCCTGTCAAAATCTGACATTctGagTCGCTTCGTTTGTTCGCAACGAG
+CACAGTGTGCAAAGctGCTATATATTGTCC
+>isotig00011  gene=isogroup00003  length=1525  numContigs=6
+ACATTCTTCAAGAGCTCTGCACCCACCAATCTAAAGTGACCAGCCAAGTGACTGACCTCA
+GGGCACAGTTAGCAGCTTTGACCACAGGATGAGCTATGTAACAACTGAAtgaaTGGTGTT
+CAtcGTTGATTGGGCAgTCAAAACAGCTGAATTTCTCTTGCGgAAGACATAAAGGCATTG
+AAGACtcGCCcAAaccGtGTGcgcccTCTGAAAAaGTTAACTTTctGTTgCTTGCAaGTG
+AAGTTTtcTtCTtGTCgCTACAAAATGCAGACAGTAaTgAAACGTGATACcTtGTtATCT
+TTtATCTAgACctGAGATGtCcACGCTGCTATGTACACTGTGTTGTGGgTATTGACcGTA
+GCTGTATGTATtGACTGTACACTAGTGTCTAATtACCGACGGTAGCAAGCTGTGTGTGTA
+TTTTCTGGGATCaaTGGTGgTGTCTAACACTTCtGTTACACCtCAtTcGAAACTAGGTCA
+GAtTAcCgGCATAGACGTTTCTTTGTGCcgAGTCtTCACAcccttttaaggagaagtatt
+ttatatcccattaaTAGAGAAAGAATTATGTTTCAATTGGTAGCATGCAACTTAAAAtTT
+TGCAAACaTTAGATACAATCAAACAATAACAAGGTTCATTACAAGGttAAtCtacTGCCC
+TTTATTtCACATTaGTCTGTCACATCAGAAGgTCACAGCTTtCAaTAaTTATACAAACAA
+ATtCCCTtGATGGgTGCTtGgTtAGATTCCTGCaatTTTCAAGTTTATCAATGTAATAAG
+TTCTGAATGTGGCAATGTGGaaGAAGCtTtGGGATAATCTGTGGATAAGACTGCCAGACT
+ATCAACAAGATTCCACATCCATGCAACTCCAACTGCTTCCTTCACCTCCTTGCAGATGTA
+CCACATGTCCaaAAAAAAGTCAGCATTGGTTAATGTAATTAAAATCTGGCTTCCTcCTGA
+GCTGGCAAATACACATGAATTGTCAAGTACAGAGGTCAGTGTGAAACCACTGAAAGATCT
+TCTCAGCTTTCAAGAAAACAAAGACTTGAAGCCAAATTGACAGAGGCCACACTGATACCA
+TTCCACTCTCATAAGATGAAGGTATCACACACACTTCATTTTGCTTCTGCGATGCAGTGC
+CTGGTAGACTGTGAGGgTCACCCAATGGATgtTTTAaCAaCTGCCtGGTTtAtAGAGCTC
+TGCAACAGATAATTCATCCTAaTGTCTAGTCGTCATCCTGTCATGGCCTTGAGCAAGTTG
+AACCCACTTCAACACAAAGCAGCTATTGAATTCTTGTCTAGGTACTGTcAAATCCACATC
+ACCATCATTGCttGGTTCCAGCTaCGcTGACCATGaTAAAAGAGTACAATGAGGGTTTTT
+TAATTCACCCAACAGAGCTTGCATTCCAGTACCTTTGGGCAGCTGATATCCATTTTGTTC
+CTCGTATgCCTGTCAAAATCTGACATTctGagTCGCTTCGTTTGTTCGCAACGAGCACAG
+TGTGCAAAGctGCTATATATTGTCC
+>isotig00001_f6
+FRIYKNYALQYVSKDAHLSLLWSAVTHLGTQYFGKTPFVLTYILLTECAVESCMEACIETLINNYEKDKLLPLQYYTSYFLCRHLAKCDYSKTDKILNVCQRNLMAFLLKINPFHLLRHRLAPNRMQPYEKVNFLLLASDVLFVSLQNADSNETRYIVIFSWTDVHRCTVCTLCCGCLQLYVLTVHCLITDGSKLCVYFLGSMVVSNTSVTPHSKLGQITAPFFLRESSHRIMIIGFSNLEPLTKCVTELIFLVTKKTLVHMRERYINMSIRGRVVYLLPDSADNSQLFENTLCYISSSFKAPKPNQQNKKPNEQRNCMTNVNFSKIELLKHISQHISHRANRTELELTVHCTFHFFLYLKVTTKLHRKTKTSSLHFNHKNIFALITKKIRYTIRQTLPYLKPLRLCSTLSVLNCLYSTVLTRQISIIKISKIYYIHNLKDVECLSGVKAGAFQSGPLFESLQDCMSSSYRVVENRQFIIMDVKYETKRLTSVSLRLANEASSRVPACRMTNTYIYITVMRNAYLPKRCSYTRKGSTHSHLLKVDVVVHVVYFHHLHHDAFVVHSSAVEVVVAVVNKVVDHEHNAGCVQEAYGQGEAFPFLPWWNRNTTLELVKNPLLMVKCTQQKTVRRMRLQIKTQSGSFTFGKLITTLHRYSKVYNCSLRIVLKSKGQSDPLDHS
+>isotig00002_f1
+MRNEIRRNHLVNKLKWLSHKLTVNGECFSNICSTAIHWKTVTKYIYLVHFYLLQNLQPLIMIGWHQGTCLICLLDNVALILLCMGTEAESAVSLKALKTLPEPRAGLKSLLANYVFFLSLQNADINETYLVIFYLDLRCPSLLCTLCCGYPLYVLTVHCLITDGSKLCVYFLGSMVVSNTSVTPHSKLGQITGIDVSLCRVFTPFGEVFYIPLIEKELCFNWHATNFANIRYNQTITRFITRLIYCPLFHISLSHQKVTAFNNYTNKFPWVLGIPAIFKFINVISSECGNVEEALGSVDKTARLSTRFHIHATPTASFTSLQMYHMSKKKSALVNVIKIWLPPELANTHELSSTEVSVKPLKDLLSFQENKDLKPNQRPHYHSTLIRRYHTHFILLLRCSAWTVRVTQWMFQLPGLSSATDNSSCLVVILSWPASTHFNTKQLLNSCLGTVKSTSPSLLGSSYADHDKRVQGFFNSPNRACIPVPLGSKDIQKLLYMSVFVCMHMCDFLALQNSSILISYVTWKPANQCLKDRLKRFLNEKLNDFLHFYTSLFRGQGQYEEVTINNYHYGHLLSAQTECHQPCAQLTELTSRHTMSVSMKP
+>isotig00008_f3
+VSWITLTLCAYLSVLSTEHRADDIIQFVIMQDSKWPLLIVTYSSYCPYWPYLNSDVSKCKKSLSFSFKNRFSLSFSNIDWQVSTLHSLSKWSCSVKQENHTYACIQTHSYITISEYLFSCPKVLECKLCWVNKTLIVLFYHGQRSWNQQWCGFDSTTRIQLLCVEVGSTCSRPQDDDTLGIICCRALTRQLLKHPLGDPHSLPGTASQKQNEVCVIPSSYESGMVSVWPLSIWLQVFVFLKAEKIFQWFHTDLCTQFMCICQLRRKPDFNYINQCLFFGHVVHLQGGEGSSWSCMDVESCSGSLIHRLSQSFSTLPHSELITLINLKIAGIPSTHQGNLFVLLKAVTFCDRLMNKGQITLTLLLFDCICLQILSCMLPIETFFLYWDIKYFSLKGCEDSAQRNVYAGNLTFRMRCNRSVRHHHSQKIHTQLATVGNTLVYSQYIQLRSIPTTQCTQRWTSQVIKDNKVSRFITVCILRQEENVICKQWKVNFFRAQHAGWGKSSKPLSHLAFGYPGQDDTSRSDLSPVETNAESSL
+>isotig00010_f3
+NEKNLAKKSPCKLKTKMAFTQINSKWRMFLKQYMQYSHSLENSNKIHLSCSFLPPAKLTTVNYVDWMALTGYLSYLPIGCGINTTVYGHGECSKFKGIEDSPRTACRALKKLTARKLRFLLVTTKCRHNVIPCYLLSRPEMSIAAMYTVLWVLTVAVCIDCTLVSNYRRQAVCVFSGINGGVHFCYTSFETRSDYRHRRFFVPSLHTLLRRSILYPINRERIMFQLVACNLKFCKHIQSNNNKVHYKVNLLPFISHSVTSEGHSFQLYKQIPLMGAWLDSCNFQVYQCNKFMWQCGRSFGIICGDCQTINKIPHPCNSNCFLHLLADVPHVQKKVSIGCNNLASSAGKYTIVKYRGQCETTERSSQLSRKQRLEAKLTEATLIPFHSHKMKVSHTLHFASAMQCLVDCEGHPMDVLTTAWFIELCNRFILMSSRHPVMALSKLNPLQHKAAIEFLSRYCQIHITIIAWFQLRPKSTMRVFFTQQSLHSSTFGQLISILFLVCLSKSDILSRFVCSQRAQCAKLLYIV
+>isotig00012_f3
+LKVEKLVTIFHSSIFGSYILIWVSPCTDEVYTVESLQLYIKGIEDSPKPCAPSEKVNFPLLASEVFFLSLQNADSNETYLVIFYLDLRCPRCYVHCVVGIDRSCMYLYTSVLPTVASCVCIFWDQWWCLTLLLHLIRNVRLPATFLCAESSHPFKEKYFISHRKNYVSIGSMQLKILQTLDTIKQQGSLQGSTALYFTLVCHIRRSQLSIIIQTNSLDGCLVRFLQFSSLSMVLNVAMWKKLWDNLWIRLPDYQQDSTSMQLQLLPSPPCRCTTCPKKSQHWLMLKSGFLLSWQIHMNCQVQRSVNHKIFSAFKKTKTSQIDRGHTDTIPLSDEGITHTSFCFCDAVPGRLGSPNGCFNNCLVYRALQQIIHPNVSSSCHGLEQVEPTSTQSSYILVVLSNPHHHHCLVPATLTMIKEYNEGFLIHPTELAFQYLWAADIHFVPRMPVKIHSESLRLFATSTVCKAAIYC
+>isotig00015_f4
+RRPYVARVKVINQWLSLELFLQIKVSTKKITVFEGGHRYERSTGQTRTILTAFHPISRTRIEPQTILHCGRTGHSSWDRGVEHTFTTMLPLYNTSFVSSMLPWCMEFCNQQKSLSSVSIATSIRAASMELQGVNVTFYCSVVRNHVCQHGVALKGCEDSRKKNVCRSDLVSNEVQKCTLPSIPENTNTACYRRLDTSVQSIHTATVNTHNTVYIAAMDISGLDKRQGITFHCLHFVVTRRKRNLRAVNFFRARHAVRGESSMPLNLLHSQPQCPYTVVLMPHYPIGRDKYPVSAIQSTLTVVSFAGGKNEQDKCILLLFSNEWLYCIYCFKNILHLLLICVKAILVFNLQGDFFAKFHFSF

data/test/test_argument_validator.rb

@@ -0,0 +1,50 @@
+require_relative 'test_helper'
+
+require 'npsearch/arg_validator'
+
+# Class to test the how well the CLI arguments are validated.
+class TestInputArgumentValidator < Minitest::Test
+  def setup
+    @c = NpSearch::ArgumentsValidators
+    @opt = { num_threads: 1, min_orf_length: 30 }
+  end
+
+  def test_assert_file_present
+    @c.send(:assert_file_present, 'existing file',
+            'test/files/genetic.fa', 1)
+    assert_raises(SystemExit) do
+      @c.send(:assert_file_present, 'non-existing file',
+              'test/files/nope_dont_exist.fa', 1)
+    end
+  end
+
+  def test_assert_input_file_not_empty
+    f = 'test/files/genetic.fa'
+    @c.send(:assert_input_file_not_empty, f)
+    f = 'test/files/empty_file.fa'
+    assert_raises(SystemExit) { @c.send(:assert_input_file_not_empty, f) }
+  end
+
+  def test_assert_input_file_probably_fasta
+    f = 'test/files/genetic.fa'
+    @c.send(:assert_input_file_probably_fasta, f)
+    f = 'test/files/not_fasta.fa'
+    assert_raises(SystemExit) { @c.send(:assert_input_file_probably_fasta, f) }
+  end
+
+  def test_assert_input_sequence
+    f = 'test/files/genetic.fa'
+    @c.send(:assert_input_sequence, f)
+    f = 'test/files/protein.fa'
+    @c.send(:assert_input_sequence, f)
+    f = 'test/files/mixed_content.fa'
+    assert_raises(SystemExit) { @c.send(:assert_input_sequence, f) }
+  end
+
+  def test_check_num_threads
+    [1, 50, 300].each do |t|
+      @c.send(:check_num_threads, t)
+    end
+    assert_equal(1, @c.send(:check_num_threads, -3))
+  end
+end

data/test/test_helper.rb

@@ -0,0 +1 @@
+require 'minitest/autorun'