mspire 0.2.4 → 0.3.0

data/specs/transmem/phobius_spec.rb

@@ -0,0 +1,423 @@
+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.should exist
+    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