RubyGems - npsearch - Versions diffs - 2.0.1 → 2.1.0 - Mend

npsearch 2.0.1 → 2.1.0

Files changed (28) hide show

checksums.yaml +4 -4
data/.gitignore +2 -1
data/README.md +3 -2
data/Rakefile +14 -5
data/bin/npsearch +45 -33
data/lib/npsearch/arg_validator.rb +70 -241
data/lib/npsearch/output.rb +6 -5
data/lib/npsearch/pool.rb +1 -1
data/lib/npsearch/scoresequence.rb +62 -60
data/lib/npsearch/sequence.rb +12 -9
data/lib/npsearch/signalp.rb +29 -10
data/lib/npsearch/version.rb +1 -1
data/lib/npsearch.rb +27 -52
data/npsearch.gemspec +2 -1
data/templates/contents.slim +3 -3
data/test/files/mixed_content.fa +167 -0
data/test/test_argument_validator.rb +50 -0
data/test/test_helper.rb +1 -0
data/test/test_sequence.rb +81 -0
data/test/test_sequence_scoring.rb +142 -0
metadata +27 -17
data/test/files/1_protein.fa +0 -204
data/test/files/2_orf.fa +0 -1330
data/test/files/3_signalp_out.txt +0 -667
data/test/files/4_secretome.fa +0 -6
data/test/files/5_output.fa +0 -6
data/test/files/5_output.html +0 -37
data/test/test_np_search.rb +0 -122

data/test/files/4_secretome.fa DELETED Viewed

@@ -1,6 +0,0 @@
->isotig00009_f2_3~~~ - S.P.=> Cleavage Site: 22:23 | D-value: 0.532
-MLKCFSIIMGLILLLEIGGGCA~~~IYFYRAQIQAQFQKSLTDVTITDYRENADFQDLIDALQSGLSCCGVNSYEDWDNNIYFNCSGPANNPEALWCAFLLLYTGSSKRSSQHPVRLWSSFPRTTKYFPHKDLHHWLCGYVYNVD
->isotig00009_f3_7~~~ - S.P.=> Cleavage Site: 16:17 | D-value: 0.643
-MKTGIIIFISTVVVLP~~~ITLKPCGVPFSCCIPDQASGVANTQCGYGVRSPEQQNTFHTKIYTTGCADMFTMWINRYLYYIAGIAGVIVLVELFGFCFAHSLINDIKRQKARWAHR
->isotig00016_f1_0~~~ - S.P.=> Cleavage Site: 23:24 | D-value: 0.592
-MNAGQIFIALMAQLFNACLLVSS~~~NFDSDIADSTLGKRSTGFVDTFGKRFVDSFGKRVDEFDYDHNGNYAEQSEQSSYISPQLKRGQKGLRSGSFIDAFGKRSSFQEVDEKRFADSFGKRFADSFGKRSPVGFVDTLGKRFAVSFGKRNTVGFVDTLGKRFADSFGKRSQQGFVDAFGKRYQGVY

data/test/files/5_output.fa DELETED Viewed

@@ -1,6 +0,0 @@
->isotig00009_f2_3~~~ - S.P.=> Cleavage Site: 22:23 | D-value: 0.532
-MLKCFSIIMGLILLLEIGGGCA~~~IYFYRAQIQAQFQKSLTDVTITDYRENADFQDLIDALQSGLSCCGVNSYEDWDNNIYFNCSGPANNPEALWCAFLLLYTGSSKRSSQHPVRLWSSFPRTTKYFPHKDLHHWLCGYVYNVD
->isotig00009_f3_7~~~ - S.P.=> Cleavage Site: 16:17 | D-value: 0.643
-MKTGIIIFISTVVVLP~~~ITLKPCGVPFSCCIPDQASGVANTQCGYGVRSPEQQNTFHTKIYTTGCADMFTMWINRYLYYIAGIAGVIVLVELFGFCFAHSLINDIKRQKARWAHR
->isotig00016_f1_0~~~ - S.P.=> Cleavage Site: 23:24 | D-value: 0.592
-MNAGQIFIALMAQLFNACLLVSS~~~NFDSDIADSTLGKRSTGFVDTFGKRFVDSFGKRVDEFDYDHNGNYAEQSEQSSYISPQLKRGQKGLRSGSFIDAFGKRSSFQEVDEKRFADSFGKRFADSFGKRSPVGFVDTLGKRFAVSFGKRNTVGFVDTLGKRFADSFGKRSQQGFVDAFGKRYQGVY

data/test/files/5_output.html DELETED Viewed

@@ -1,37 +0,0 @@
-<!DOCTYPE html>
-<html>
-  <head>
-    <title>Results</title>
-    <meta content='text/html; charset=utf-8' http-equiv='Content-Type'>
-    <style>
-      .id {font-weight: bold;}
-      .signalp {color:#007AC0; font-weight: bold;}
-      .motif {color:#00B050; font-weight: bold;}
-      .glycine {color:#FFC000; font-weight: bold;}
-      .phenylalanine {color:#FF00EB; font-weight: bold;}
-      .gkr {color:#FF0000; font-weight: bold;}
-      .cysteine {color:#00B050;}
-      p {word-wrap: break-word; font-family:Courier New, Courier, Mono;}
-    </style>
-  </head>
-  <body>
-    <p>
-      <span class='id'>isotig00009_f2_3</span>
-      <span>- S.P.=> Cleavage Site: 22:23 | D-value: 0.532</span>
-      <br>
-      <span class='signalp'>MLKCFSIIMGLILLLEIGGGCA</span><span>IYFYRAQIQAQFQKSLTDVTITDYRENADFQDLIDALQSGLS<span class="cysteine">C</span><span class="cysteine">C</span>GVNSYEDWDNNIYFN<span class="cysteine">C</span>SGPANNPEALW<span class="cysteine">C</span>AFLLLYTGSS<span class="motif">KR</span>SSQ<span class="motif">HPVR</span>LWSSFPRTTKYFPHKDLHHWL<span class="cysteine">C</span>GYVYNVD</span>
-    </p>
-    <p>
-      <span class='id'>isotig00009_f3_7</span>
-      <span>- S.P.=> Cleavage Site: 16:17 | D-value: 0.643</span>
-      <br>
-      <span class='signalp'>MKTGIIIFISTVVVLP</span><span>ITLKP<span class="cysteine">C</span>GVPFS<span class="cysteine">C</span><span class="cysteine">C</span>IPDQASGVANTQ<span class="cysteine">C</span>GYGVRSPEQQNTFHTKIYTTG<span class="cysteine">C</span>ADMFTMWINRYLYYIAGIAGVIVLVELFGF<span class="cysteine">C</span>FAHSLINDI<span class="motif">KR</span>QKARWAHR</span>
-    </p>
-    <p>
-      <span class='id'>isotig00016_f1_0</span>
-      <span>- S.P.=> Cleavage Site: 23:24 | D-value: 0.592</span>
-      <br>
-      <span class='signalp'>MNAGQIFIALMAQLFNACLLVSS</span><span>NFDSDIADSTL<span class="gkr">GKR</span>STGFVDTF<span class="gkr">GKR</span>FVDSF<span class="gkr">GKR</span>VDEFDYDHNGNYAEQSEQSSYISPQL<span class="motif">KR</span>GQ<span class="motif">KGLR</span>SGSFIDAF<span class="gkr">GKR</span>SSFQEVDE<span class="motif">KR</span>FADSF<span class="gkr">GKR</span>FADSF<span class="gkr">GKR</span>SPVGFVDTL<span class="gkr">GKR</span>FAVSF<span class="gkr">GKR</span>NTVGFVDTL<span class="gkr">GKR</span>FADSF<span class="gkr">GKR</span>SQQGFVDAF<span class="gkr">GKR</span>YQGVY</span>
-    </p>
-  </body>
-</html>

data/test/test_np_search.rb DELETED Viewed

@@ -1,122 +0,0 @@
-#!/usr/bin/env ruby
-require 'coveralls'
-Coveralls.wear!
-require 'bio'
-require 'test/unit'
-require 'npsearch'
-require 'npsearch/arg_validator'
-class InputChanged
-  # Changed to include the full entry definition rather than just the id. This
-  # was necessary for when testing individual parts since this is changed in
-  # pipeline
-  def read(input_file)
-    input_read = {}
-    biofastafile = Bio::FlatFile.open(Bio::FastaFormat, input_file)
-    biofastafile.each_entry do |entry|
-      # entry.definition used instead of entry.id
-      input_read[entry.definition] = entry.seq
-    end
-    input_read
-  end
-end
-class UnitTests < Test::Unit::TestCase
-  def setup # read all expected files
-    @dir                  = 'test/files'
-    @translation_test     = NpSearch::Translation.new
-    @analysis_test        = NpSearch::Analysis.new
-    @test_input1          = InputChanged.new
-    @test_arg_vldr        = NpSearch::ArgValidators.new(:is_verbose)
-    @test_vldr            = NpSearch::Validators.new
-    @test_input_read      = NpSearch::Input.read("#{@dir}/genetic.fa")
-    @expected_translation = NpSearch::Input.read("#{@dir}/1_protein.fa")
-    @expected_orf         = NpSearch::Input.read("#{@dir}/2_orf.fa")
-    @expected_sp_out_file = File.read("#{@dir}/3_signalp_out.txt")
-    @expected_secretome   = @test_input1.read("#{@dir}/4_secretome.fa")
-    @expected_output      = @test_input1.read("#{@dir}/5_output.fa")
-    @motif                = 'KK|KR|RR|R..R|R....R|R......R|' \
-                            'H..R|H....R|H......R|K..R|K....R|K......R'
-    @motif_ar             = %w(KR Kr kr)
-    @input_file_ar        = ["#{@dir}/genetic.fa", "#{@dir}/protein.fa"]
-    @input_file_ar_neg    = ["#{@dir}/empty_file.fa",
-                             "#{@dir}/missing_input.fa", "#{@dir}/not_fasta.fa"]
-    @cut_off_ar           = [622, 10, 2, 1]
-    @cut_off_ar_neg       = [-10, 'hello', -5, 0]
-  end
-  def test_motif
-    (0..2).each do |i|
-      test_run = @test_arg_vldr.arg(@motif_ar[i], @input_file_ar[0], @dir,
-                                    @cut_off_ar[0], FALSE, nil, 'help_banner')
-      assert_equal('genetic', test_run)
-    end
-  end
-  def test_input_file
-    test_run = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
-                                  @cut_off_ar[0], FALSE, nil, 'help_banner')
-    assert_equal('genetic', test_run)
-    test_run1 = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[1], @dir,
-                                   @cut_off_ar[0], FALSE, nil, 'help_banner')
-    assert_equal('protein', test_run1)
-    (0..2).each do |i|
-      test_run2 = lambda do
-        @test_arg_vldr.arg(@motif_ar[0], @input_file_ar_neg[i], @dir,
-                           @cut_off_ar[0], FALSE, nil, 'help_banner')
-      end
-      assert_raise(ArgumentError) { test_run2 }
-    end
-  end
-  def test_orf_min_length
-    (0..3).each do |i|
-      test_run = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
-                                    @cut_off_ar[i], FALSE, nil, 'help_banner')
-      assert_equal('genetic', test_run)
-    end
-    (0..3).each do |i|
-      test_run1 = lambda do
-        @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
-                           @cut_off_ar_neg[i], FALSE, nil, 'help_banner')
-      end
-      assert_raise(ArgumentError) { test_run1 }
-    end
-  end
-  # => Test if the output directory validator works, in ensuring whether an
-  #    output directory can be found.
-  def test_output_dir_validator
-    assert_equal(nil, @test_vldr.output_dir(@dir))
-  end
-  # => Test if the translation method works properly - assert that the produced
-  #    translation is equal to the expected translation hash
-  def test_translate
-    translation_hash_test = NpSearch::Translation.translate(@test_input_read)
-    assert_equal(@expected_translation, translation_hash_test)
-  end
-  # => Test if the extract_orf method works properly - assert that the produced
-  #    orf hash is equal to the expected orf hash.
-  # => In orf method, an array is produced while in the expected file read, an
-  #    array isn't produced, thus it s necessary to remove "[  ]" from both end.
-  def test_extract_orf
-    orf_hash_test = NpSearch::Translation.extract_orf(@expected_translation, 10)
-    assert_equal(@expected_orf.to_s, orf_hash_test.to_s.gsub('["', '"')
-                                                       .gsub('"]', '"'))
-  end
-  def test_parse
-    secretome = NpSearch::Analysis.parse("#{@dir}/3_signalp_out.txt",
-                                         @expected_orf, @motif)
-    assert_equal(@expected_secretome, secretome)
-  end
-  def test_flattener
-    flattened_output_test = NpSearch::Analysis.flattener(@expected_secretome)
-    assert_equal(@expected_output, flattened_output_test)
-  end
-end