mspire 0.4.9 → 0.5.0

data/specs/transmem/phobius_spec.rb

@@ -1,425 +0,0 @@
-require 'yaml'
-
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-# contains shared behavior that we need.
-require File.expand_path( File.dirname(__FILE__) + '/../transmem_spec_shared' )
-require 'fasta'
-
-require 'transmem/phobius'
-index_klass = Phobius::Index
-base_klass = Phobius
-
-describe index_klass do
-  before(:all) do
-    @phobius_file = Tfiles + '/phobius.small.small.txt'
-    @obj = Phobius::Index.new(@phobius_file)
-    @test_hash = {
-      'gi|16127995|ref|NP_414542.1| protein description' => 0, 
-      'gi|16127996|ref|NP_414543.1| protein description' => 0, 
-      'gi|16127997|ref|NP_414544.1| protein description' => 0, 
-      'gi|16127998|ref|NP_414545.1| protein description' => 0, 
-      'gi|16127999|ref|NP_414546.1| protein description' => 0, 
-      'gi|16128000|ref|NP_414547.1| protein description' => 0, 
-      'gi|16128001|ref|NP_414548.1| protein description' => 9, 
-      'gi|16128002|ref|NP_414549.1| protein description' => 0, 
-      'gi|16128003|ref|NP_414550.1| protein description' => 0, 
-      'gi|16128004|ref|NP_414551.1| protein description' => 6, 
-      'gi|16128005|ref|NP_414552.1| protein description' => 0, 
-      'gi|90111078|ref|NP_414553.2| protein description' => 0, 
-      'gi|16128007|ref|NP_414554.1| protein description' => 0, 
-      'gi|16128008|ref|NP_414555.1| protein description' => 0, 
-      'gi|16128009|ref|NP_414556.1| protein description' => 0, 
-      'gi|16128010|ref|NP_414557.1| protein description' => 0, 
-      'gi|16128011|ref|NP_414558.1| protein description' => 0, 
-      'gi|16128012|ref|NP_414559.1| protein description' => 1, 
-      'gi|49175991|ref|YP_025292.1| protein description' => 0, 
-      'gi|16128013|ref|NP_414560.1| protein description' => 11, 
-      'gi|16128014|ref|NP_414561.1| protein description' => 0, 
-      'gi|16128015|ref|NP_414562.1| protein description' => 0, 
-      'gi|16128016|ref|NP_414563.1| protein description' => 0, 
-      'gi|16128017|ref|NP_414564.1| protein description' => 0, 
-      'gi|16128018|ref|NP_414565.1| protein description' => 0, 
-      'gi|16128019|ref|NP_414566.1| protein description' => 0, 
-      'gi|16128020|ref|NP_414567.1| protein description' => 0, 
-      'gi|16128021|ref|NP_414568.1| protein description' => 4, 
-      'gi|16128022|ref|NP_414569.1| protein description' => 0, 
-      'gi|16128023|ref|NP_414570.1| protein description' => 0, 
-      'gi|16128024|ref|NP_414571.1| protein description' => 0, 
-      'gi|16128025|ref|NP_414572.1| protein description' => 0, 
-      'gi|16128026|ref|NP_414573.1| protein description' => 0, 
-      'gi|16128027|ref|NP_414574.1| protein description' => 0, 
-      'gi|90111079|ref|NP_414576.4| protein description' => 0, 
-      'gi|90111080|ref|NP_414577.2| protein description' => 0, 
-      'gi|16128030|ref|NP_414578.1| protein description' => 0, 
-      'gi|49175993|ref|NP_414579.3| protein description' => 0, 
-      'gi|16128032|ref|NP_414580.1| protein description' => 0, 
-      'gi|16128033|ref|NP_414581.1| protein description' => 0, 
-      'gi|16128034|ref|NP_414582.1| protein description' => 12,
-      'gi|90111081|ref|NP_414583.2| protein description' => 0, 
-      'gi|16128036|ref|NP_414584.1| protein description' => 0, 
-      'gi|16128037|ref|NP_414585.1| protein description' => 0, 
-      'gi|16128038|ref|NP_414586.1| protein description' => 0, 
-      'gi|16128039|ref|NP_414587.1| protein description' => 12,
-      'gi|16128040|ref|NP_414588.1| protein description' => 0, 
-      'gi|16128041|ref|NP_414589.1| protein description' => 13,
-      'gi|16128042|ref|NP_414590.1| protein description' => 0, 
-      'gi|16128043|ref|NP_414591.1| protein description' => 0,
-    }
-    @ref_to_key = { 'gi|16127905|ref|NP_414542.1| thr operon leader peptide [Escherichia coli K12]' => 'gi|16127905|ref|NP_414542.1|',
-      'SWN:PWP1_HUMAN PERIODIC TRYPTOPHAN PROTEIN 1 HOMOLOG' => 'SWN:PWP1_HUMAN',
-      'MY:B|/-"[super]"duper!@#$%^&*(wil) and other stuff' => 'MY:B|/-[super]duper!@#$%^&*(wil)'}
-  end
-  it_should_behave_like 'a transmem index'
-end
-
-describe "a phobius parser", :shared => true do
-  it 'parses a phobius file into a hash structure' do
-    @file_to_hash.exist_as_a_file?.should be_true
-    hash = @class.default_index(@file_to_hash)
-    hash.should == @structure_to_create
-  end
-end
-
-describe base_klass, "parsing the 'short' file format" do
-  before(:all) do
-    @class = base_klass
-    @file_to_hash = Tfiles + '/phobius.small.small.txt'
-    @structure_to_create = YAML.load(PhobiusSupportingFile::MY_YAML1)
-  end
-  it_should_behave_like 'a phobius parser'
-end
-
-
-describe index_klass, 'on small mock set' do
-  before(:all) do
-    phobius_file = Tfiles + '/phobius.small.small.txt'
-    fasta_file = Tfiles + '/small.fasta'
-    # Note that it needs a fasta object to do this!
-    @obj = index_klass.new(phobius_file, Fasta.new(fasta_file))
-    @tm_test = {
-      :mykey => 'gi|16128001|ref|NP_414548.1|',
-
-      # "MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGLTSFQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVICVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNAAAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAEFVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQLADIIMACMAITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE"
-      # transmembrane sequences:
-      # LWGSVMIYLLFGAGCWFTF
-      # LAARVGSGNLAGVALAITAG
-      # FWMWVAAFIGMATSFAECSLAQLY
-      # LGMRWMGVLFAVFLLIAYGI
-      # FPPLVTGIILAVFTLLAIT
-      # GFVPLMAIIWVLTSLVICVMNIG
-      # IVQMIGIFIDTLVICTASAMLILLA
-      # VLMGSWGAEFVTLVVILFAFSSIVANYIY
-      # IIMACMAITNLTAILLLSPVVHTIA
-      :seqs => %w(VLWG LAIT LAG),
-      :exps => 
-      {
-        :number => [3.0, 4.0, (2.0+3)/2],
-        :fraction => [3.0/4, 4.0/4, ((2.0+3)/2)/3 ],
-      }
-    }
-  end
-  it_should_behave_like "a calculator of transmembrane overlap"
-end
-
-
-module PhobiusSupportingFile
-  MY_YAML1 =<<END
---- 
-gi|16128042|ref|NP_414590.1|: 
-  :signal_peptide: true
-  :num_certain_transmembrane_segments: 0
-gi|16128017|ref|NP_414564.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128015|ref|NP_414562.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128038|ref|NP_414586.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|90111081|ref|NP_414583.2|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128022|ref|NP_414569.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128020|ref|NP_414567.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128009|ref|NP_414556.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128000|ref|NP_414547.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128043|ref|NP_414591.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128032|ref|NP_414580.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128030|ref|NP_414578.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128014|ref|NP_414561.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128005|ref|NP_414552.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128003|ref|NP_414550.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16127999|ref|NP_414546.1|: 
-  :signal_peptide: true
-  :num_certain_transmembrane_segments: 0
-gi|16128037|ref|NP_414585.1|: 
-  :signal_peptide: true
-  :num_certain_transmembrane_segments: 0
-gi|16128021|ref|NP_414568.1|: 
-  :transmembrane_segments: 
-  - :start: 12
-    :stop: 31
-  - :start: 70
-    :stop: 88
-  - :start: 100
-    :stop: 117
-  - :start: 137
-    :stop: 157
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 4
-gi|16128008|ref|NP_414555.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|90111080|ref|NP_414577.2|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|90111079|ref|NP_414576.4|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128026|ref|NP_414573.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128004|ref|NP_414551.1|: 
-  :transmembrane_segments: 
-  - :start: 12
-    :stop: 31
-  - :start: 37
-    :stop: 56
-  - :start: 63
-    :stop: 84
-  - :start: 96
-    :stop: 116
-  - :start: 123
-    :stop: 143
-  - :start: 149
-    :stop: 169
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 6
-gi|16128036|ref|NP_414584.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128034|ref|NP_414582.1|: 
-  :transmembrane_segments: 
-  - :start: 12
-    :stop: 30
-  - :start: 50
-    :stop: 71
-  - :start: 91
-    :stop: 116
-  - :start: 145
-    :stop: 163
-  - :start: 195
-    :stop: 216
-  - :start: 228
-    :stop: 251
-  - :start: 263
-    :stop: 286
-  - :start: 318
-    :stop: 335
-  - :start: 347
-    :stop: 366
-  - :start: 406
-    :stop: 425
-  - :start: 446
-    :stop: 466
-  - :start: 472
-    :stop: 495
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 12
-gi|16128007|ref|NP_414554.1|: 
-  :signal_peptide: true
-  :num_certain_transmembrane_segments: 0
-gi|16127998|ref|NP_414545.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16127996|ref|NP_414543.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128041|ref|NP_414589.1|: 
-  :transmembrane_segments: 
-  - :start: 6
-    :stop: 24
-  - :start: 31
-    :stop: 49
-  - :start: 55
-    :stop: 72
-  - :start: 84
-    :stop: 111
-  - :start: 117
-    :stop: 135
-  - :start: 147
-    :stop: 169
-  - :start: 181
-    :stop: 202
-  - :start: 214
-    :stop: 233
-  - :start: 239
-    :stop: 258
-  - :start: 270
-    :stop: 290
-  - :start: 296
-    :stop: 315
-  - :start: 327
-    :stop: 348
-  - :start: 360
-    :stop: 378
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 13
-gi|16128039|ref|NP_414587.1|: 
-  :transmembrane_segments: 
-  - :start: 20
-    :stop: 42
-  - :start: 54
-    :stop: 74
-  - :start: 86
-    :stop: 104
-  - :start: 110
-    :stop: 132
-  - :start: 144
-    :stop: 166
-  - :start: 172
-    :stop: 193
-  - :start: 242
-    :stop: 263
-  - :start: 283
-    :stop: 303
-  - :start: 310
-    :stop: 329
-  - :start: 335
-    :stop: 358
-  - :start: 370
-    :stop: 390
-  - :start: 402
-    :stop: 421
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 12
-gi|49175993|ref|NP_414579.3|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128025|ref|NP_414572.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128023|ref|NP_414570.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128012|ref|NP_414559.1|: 
-  :transmembrane_segments: 
-  - :start: 25
-    :stop: 44
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 1
-gi|16128033|ref|NP_414581.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128019|ref|NP_414566.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|49175991|ref|YP_025292.1|: 
-  :signal_peptide: true
-  :num_certain_transmembrane_segments: 0
-gi|16127997|ref|NP_414544.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16127995|ref|NP_414542.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128040|ref|NP_414588.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128024|ref|NP_414571.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128013|ref|NP_414560.1|: 
-  :transmembrane_segments: 
-  - :start: 12
-    :stop: 39
-  - :start: 59
-    :stop: 79
-  - :start: 91
-    :stop: 114
-  - :start: 126
-    :stop: 145
-  - :start: 154
-    :stop: 175
-  - :start: 181
-    :stop: 200
-  - :start: 207
-    :stop: 238
-  - :start: 258
-    :stop: 276
-  - :start: 288
-    :stop: 312
-  - :start: 324
-    :stop: 351
-  - :start: 363
-    :stop: 380
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 11
-gi|16128011|ref|NP_414558.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|90111078|ref|NP_414553.2|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128002|ref|NP_414549.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128027|ref|NP_414574.1|: 
-  :signal_peptide: true
-  :num_certain_transmembrane_segments: 0
-gi|16128018|ref|NP_414565.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128016|ref|NP_414563.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128010|ref|NP_414557.1|: 
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 0
-gi|16128001|ref|NP_414548.1|: 
-  :transmembrane_segments: 
-  - :start: 12
-    :stop: 30
-  - :start: 68
-    :stop: 87
-  - :start: 93
-    :stop: 116
-  - :start: 137
-    :stop: 156
-  - :start: 176
-    :stop: 194
-  - :start: 206
-    :stop: 228
-  - :start: 297
-    :stop: 321
-  - :start: 342
-    :stop: 370
-  - :start: 414
-    :stop: 438
-  :signal_peptide: false
-  :num_certain_transmembrane_segments: 9
-END
-
-end