bio 1.2.1 → 1.3.0

data/test/data/rpsblast/misc.rpsblast

@@ -0,0 +1,193 @@
+RPS-BLAST 2.2.18 [Mar-02-2008]
+
+Database: Pfam.v.22.0 
+           9318 sequences; 1,769,994 total letters
+
+Searching..................................................done
+
+Query= TestSequence mixture of globin and rhodopsin (computationally
+randomly concatenated)
+         (495 letters)
+
+
+
+                                                                 Score    E
+Sequences producing significant alignments:                      (bits) Value
+
+gnl|CDD|84466 pfam00042, Globin, Globin..                             110   2e-25
+gnl|CDD|84429 pfam00001, 7tm_1, 7 transmembrane receptor (rhodop...    91   2e-19
+gnl|CDD|87195 pfam06976, DUF1300, Protein of unknown function (D...    37   0.003
+
+>gnl|CDD|84466 pfam00042, Globin, Globin..
+          Length = 110
+
+ Score =  110 bits (277), Expect = 2e-25
+ Identities = 50/110 (45%), Positives = 69/110 (62%), Gaps = 5/110 (4%)
+
+Query: 148 EKQLITGLWGKV--NVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHG 205
+           +K L+   WGKV  N  E GAE LARL   YP T+ +F  FG+LS+  A+  +P  +AHG
+Sbjct: 1   QKALVKASWGKVKGNAPEIGAEILARLFTAYPDTKAYFPKFGDLSTAEALKSSPKFKAHG 60
+
+Query: 206 KKVLTSFGDAVKNLDN---IKNTFSQLSELHCDKLHVDPENFRLLGDILI 252
+           KKVL + G+AVK+LD+   +K    +L   H  + HVDP NF+L G+ L+
+Sbjct: 61  KKVLAALGEAVKHLDDDGNLKAALKKLGARHAKRGHVDPANFKLFGEALL 110
+
+
+>gnl|CDD|84429 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family). This
+           family contains, amongst other G-protein-coupled
+           receptors (GCPRs), members of the opsin family, which
+           have been considered to be typical members of the
+           rhodopsin superfamily. They share several motifs, mainly
+           the seven transmembrane helices, GCPRs of the rhodopsin
+           superfamily. All opsins bind a chromophore, such as
+           11-cis-retinal. The function of most opsins other than
+           the photoisomerases is split into two steps: light
+           absorption and G-protein activation. Photoisomerases, on
+           the other hand, are not coupled to G-proteins - they are
+           thought to generate and supply the chromophore that is
+           used by visual opsins..
+          Length = 258
+
+ Score = 90.8 bits (225), Expect = 2e-19
+ Identities = 37/162 (22%), Positives = 76/162 (46%), Gaps = 10/162 (6%)
+
+Query: 299 HAIMGVAFTWVMALACAAPPLAGWSRY-IPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV 357
+            A + +   WV+AL  + PPL       + EG   +C ID+          S+ +   ++
+Sbjct: 100 RAKVLILLVWVLALLLSLPPLLFSWLRTVEEGNVTTCLIDFPEESLLR---SYTLLSTLL 156
+
+Query: 358 HFTIPMIIIFFCYGQLVFTV----KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWV 413
+            F +P+++I  CY +++ T+    +  A+  +       +E++  +M++++V+ F++CW+
+Sbjct: 157 GFVLPLLVILVCYTRILRTLRRRARSGASIARSLKRRSSSERKAAKMLLVVVVVFVLCWL 216
+
+Query: 414 PYASVAFY--IFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIY 453
+           PY  V     +         P  + I  + A   +  NP+IY
+Sbjct: 217 PYHIVLLLDSLCLLSIIRVLPTALLITLWLAYVNSCLNPIIY 258
+
+
+
+ Score = 73.4 bits (180), Expect = 3e-14
+ Identities = 32/86 (37%), Positives = 47/86 (54%)
+
+Query: 55  NFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEG 114
+           N L + V ++ K+LRTP N  LLNLAVADL  +L      LY  + G + FG   C L G
+Sbjct: 2   NLLVILVILRTKRLRTPTNIFLLNLAVADLLFLLTLPPWALYYLVGGDWPFGDALCKLVG 61
+
+Query: 115 FFATLGGEIALWSLVVLAIERYVVVC 140
+               + G  ++  L  ++I+RY+ + 
+Sbjct: 62  ALFVVNGYASILLLTAISIDRYLAIV 87
+
+
+>gnl|CDD|87195 pfam06976, DUF1300, Protein of unknown function (DUF1300). This
+           family represents a conserved region approximately 80
+           residues long within a number of proteins of unknown
+           function that seem to be specific to C. elegans. Some
+           family members contain more than one copy of this
+           region..
+          Length = 336
+
+ Score = 37.1 bits (86), Expect = 0.003
+ Identities = 32/145 (22%), Positives = 58/145 (40%), Gaps = 7/145 (4%)
+
+Query: 336 IDYYTLKPEVNNESFVIYMFV--VHFT-IPMIIIFFCYGQLVFTVKEAAAQQQESATTQK 392
+           I+Y     E+   S+ I + +  + F  IP II+      L+F +K+       S+T+  
+Sbjct: 192 IEYIIETTELFGSSYEILLLIEGILFKLIPSIILPIATILLIFQLKKNKKVSSRSSTSSS 251
+
+Query: 393 AEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVI 452
+           +    T++V  + I+FLI  VP   +    F         + +   A      +  N  I
+Sbjct: 252 SNDRSTKLVTFVTISFLIATVPLGILYLIKFFVFEYEGLVMIIDKLAIIFTFLSTINGTI 311
+
+Query: 453 YIM----MNKQFRNCMLTTICCGKN 473
+           + +    M+ Q+RN +       K 
+Sbjct: 312 HFLICYFMSSQYRNTVREMFGRKKK 336
+
+
+Query= randomseq3
+         (1087 letters)
+
+ ***** No hits found ******
+
+
+Query= gi|6013469|gb|AAD49229.2|AF159462_1 EHEC factor for adherence
+[Escherichia coli]
+         (3223 letters)
+
+
+
+                                                                 Score    E
+Sequences producing significant alignments:                      (bits) Value
+
+gnl|CDD|86672 pfam04488, Gly_transf_sug, Glycosyltransferase sug...    84   1e-16
+gnl|CDD|84583 pfam00175, NAD_binding_1, Oxidoreductase NAD-bindi...    37   0.019
+
+>gnl|CDD|86672 pfam04488, Gly_transf_sug, Glycosyltransferase sugar-binding region
+           containing DXD motif. The DXD motif is a short conserved
+           motif found in many families of glycosyltransferases,
+           which add a range of different sugars to other sugars,
+           phosphates and proteins. DXD-containing
+           glycosyltransferases all use nucleoside diphosphate
+           sugars as donors and require divalent cations, usually
+           manganese. The DXD motif is expected to play a
+           carbohydrate binding role in sugar-nucleoside
+           diphosphate and manganese dependent
+           glycosyltransferases..
+          Length = 86
+
+ Score = 84.2 bits (208), Expect = 1e-16
+ Identities = 33/85 (38%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
+
+Query: 505 RISIKDVNSLTSLSKSENNHNYQTEMLLRWNYPAA-SDLLRMYILKEHGGIYTDTDMMPA 563
+              I     L SL    N + +  EM LRW Y AA SD LR  IL ++GGIY DTD++P 
+Sbjct: 1   YDVILVTPDLESLFIDTNAYPWFQEMFLRWPYNAAASDFLRYAILYKYGGIYLDTDVIPL 60
+
+Query: 564 YSKQVIFKIMMQTN-GDNRFLEDLK 587
+            S  V+  I         R  E L 
+Sbjct: 61  KSLDVLINIEGSNFLDGERSFERLN 85
+
+
+>gnl|CDD|84583 pfam00175, NAD_binding_1, Oxidoreductase NAD-binding domain. Xanthine
+            dehydrogenases, that also bind FAD/NAD, have essentially
+            no similarity..
+          Length = 110
+
+ Score = 37.2 bits (86), Expect = 0.019
+ Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 3/82 (3%)
+
+Query: 959  IKGFLASNPHTKINILYSNKTEHNIFIKDLFSFAVMENELRDIINNMSKDKTPENWEGRV 1018
+            +K  L     T++ ++Y N+TE ++ +++       +   R  +  +    T + W GR 
+Sbjct: 16   LKALLEDEDGTEVYLVYGNRTEDDLLLREELEELAKKYPGRLKVVAVVSR-TDDGWYGRK 74
+
+Query: 1019 MLQRYLELKMKDHLSLQSSQEA 1040
+                  +  +++HLSL    + 
+Sbjct: 75   G--YVTDALLEEHLSLIDLDDT 94
+
+
+  Database: Pfam.v.22.0
+    Posted date:  Nov 8, 2007  6:06 PM
+  Number of letters in database: 1,769,994
+  Number of sequences in database:  9318
+  
+Lambda     K      H
+   0.327    0.139    0.439 
+
+Gapped
+Lambda     K      H
+   0.267   0.0632    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Sequences: 9318
+Number of Hits to DB: 28,279,060
+Number of extensions: 2147710
+Number of successful extensions: 3028
+Number of sequences better than 2.0e-02: 3
+Number of HSP's gapped: 3016
+Number of HSP's successfully gapped: 20
+Length of database: 1,769,994
+Neighboring words threshold: 11
+Window for multiple hits: 40
+X1: 15 ( 7.1 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 40 (21.7 bits)
+S2: 77 (33.6 bits)

data/test/functional/bio/appl/test_pts1.rb

@@ -0,0 +1,115 @@
+#
+# = test/functional/bio/appl/test_pts1.rb - Unit test for Bio::PTS1 with network connection
+#
+# Copyright::   Copyright (C) 2006 
+#               Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/pts1'
+
+
+module Bio
+
+  class FuncTestPTS1 < Test::Unit::TestCase
+
+    def setup
+      @seq =<<END
+>AB000464
+MRTGGDNAGPSHSHIKRLPTSGLSTWLQGTQTCVLHLPTGTRPPAHHPLLGYSSRRSYRL
+LENPAAGCWARFSFCQGAAWDWDLEGVQWLRALAGGVSTAPSAPPGNLVFLSVSIFLCGS
+LLLETCPAYFSSLDPD*
+END
+      @serv = Bio::PTS1.new
+    end
+
+
+    def test_function_set
+      @serv.function("GENERAL")
+      assert_equal("GENERAL", @serv.function)
+    end
+
+    def test_function_show
+      assert_equal("METAZOA-specific", @serv.function)
+    end
+
+    def test_function_set_number_1
+      @serv.function(1)
+      assert_equal("METAZOA-specific", @serv.function)
+    end
+
+    def test_function_set_number_2
+      @serv.function(2)
+      assert_equal("FUNGI-specific", @serv.function)
+    end
+
+    def test_function_set_number_3
+      @serv.function(3)
+      assert_equal("GENERAL", @serv.function)
+    end
+
+
+    def test_exec
+      report = @serv.exec(@seq)
+      assert_equal(Bio::PTS1::Report, report.class)
+    end
+
+    def test_exec_with_faa
+      report = @serv.exec(Bio::FastaFormat.new(@seq))
+      assert_equal(Bio::PTS1::Report, report.class)
+    end
+
+  end
+
+  class FuncTestPTS1Report < Test::Unit::TestCase
+    def setup
+      serv = Bio::PTS1.new
+      seq = ">hoge\nAVSFLSMRRARL\n"
+      @report = serv.exec(seq)
+    end
+    
+
+    def test_output_size
+      assert_equal(1634, @report.output.size)
+    end
+
+    def test_entry_id
+      assert_equal("hoge", @report.entry_id)
+    end
+
+    def test_prediction
+      assert_equal("Targeted", @report.prediction)
+    end
+    
+    def test_cterm
+      assert_equal("AVSFLSMRRARL", @report.cterm)
+    end
+    
+    def test_score
+      assert_equal("7.559", @report.score)
+    end
+
+    def test_fp
+      assert_equal("2.5e-04", @report.fp)
+    end
+    
+    def test_sppta
+      assert_equal("-5.833", @report.sppta)
+    end
+    
+    def test_spptna
+      assert_equal("-1.698", @report.spptna)
+    end
+
+    def test_profile
+      assert_equal("15.091", @report.profile)
+    end
+  end
+end

data/test/functional/bio/io/test_ensembl.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: test_ensembl.rb,v 1.5 2007/11/10 16:57:43 nakao Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -40,6 +40,13 @@ class FuncTestEnsemblHuman < Test::Unit::TestCase
   def test_server
     assert_equal("http://www.ensembl.org", @serv.server)
   end
+end
+
+class FuncTestEnsemblHumanExportView < Test::Unit::TestCase
+  def setup
+    @serv = Bio::Ensembl.new('Homo_sapiens',
+                             'http://jul2008.archive.ensembl.org')
+  end
 
   def test_fna_exportview
     seq = ">4 dna:chromosome chromosome:NCBI36:4:1149206:1149209:1\nGAGA\n"
@@ -72,82 +79,80 @@ class FuncTestEnsemblHuman < Test::Unit::TestCase
     assert_equal(fna10, fna)
   end
 
-   def test_gff_exportview
-     line = ["chromosome:NCBI36:4:1149206:1149209:1", 
-             "Ensembl", 
-             "Gene", 
-             "-839",
-             "2747", 
-             ".", 
-             "+",
-             ".",
-             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding\n"].join("\t")  + "\n"
-     line = ["4", 
-             "Ensembl", 
-             "Gene", 
-             "1148366", 
-             "1151952", 
-             ".", 
-             "+", 
-             "1", 
-             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding"].join("\t") + "\n"
+   def test_gff_exportview_for_empty_result
      gff = @serv.exportview(4, 1149206, 1149209, ['gene'])
+     assert_equal('', gff)
+   end
+
+   def test_gff_exportview
+     # OR1A1 (Olfactory receptor 1A1)
+     lines = [ [ "17",
+                 "Ensembl",
+                 "Gene",
+                 "3065665",
+                 "3066594",
+                 ".",
+                 "+",
+                 "1",
+                 "gene_id=ENSG00000172146; transcript_id=ENST00000304094; exon_id=ENSE00001137815; gene_type=KNOWN_protein_coding"
+               ],
+               [ "17",
+                 "Vega",
+                 "Gene",
+                 "3065665",
+                 "3066594",
+                 ".",
+                 "+",
+                 "1",
+                 "gene_id=OTTHUMG00000090637; transcript_id=OTTHUMT00000207292; exon_id=OTTHUME00001080001; gene_type=KNOWN_protein_coding"
+               ]
+             ]
+     line = lines.collect { |x| x.join("\t") + "\n" }.join('')
+     gff = @serv.exportview(17, 3065665, 3066594, ['gene'])
      assert_equal(line, gff)
    end
 
-   def test_gff_exportview_with_named_args
-     line = ["chromosome:NCBI36:4:1149206:1149209:1",
-             "Ensembl",
-             "Gene",
-             "-839",
-             "2747",
-             ".",
-             "+",
-             ".",
-             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding"].join("\t") + "\n"
-     line = ["4", 
-             "Ensembl", 
-             "Gene", 
-             "1148366", 
-             "1151952", 
-             ".", 
-             "+", 
-             "1", 
-             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding"].join("\t") + "\n"
+   def test_gff_exportview_with_named_args_for_empty_result
      gff = @serv.exportview(:seq_region_name => 4,
                             :anchor1 => 1149206,
                             :anchor2 => 1149209, 
                             :options => ['gene'])
+     assert_equal('', gff)
+   end 
+
+   def test_gff_exportview_with_named_args
+     # OR1A1 (Olfactory receptor 1A1)
+     lines = [ [ "17",
+                 "Ensembl",
+                 "Gene",
+                 "3065665",
+                 "3066594",
+                 ".",
+                 "+",
+                 "1",
+                 "gene_id=ENSG00000172146; transcript_id=ENST00000304094; exon_id=ENSE00001137815; gene_type=KNOWN_protein_coding"
+               ],
+               [ "17",
+                 "Vega",
+                 "Gene",
+                 "3065665",
+                 "3066594",
+                 ".",
+                 "+",
+                 "1",
+                 "gene_id=OTTHUMG00000090637; transcript_id=OTTHUMT00000207292; exon_id=OTTHUME00001080001; gene_type=KNOWN_protein_coding"
+               ]
+             ]
+     line = lines.collect { |x| x.join("\t") + "\n" }.join('')
+     gff = @serv.exportview(:seq_region_name => 17,
+                            :anchor1 => 3065665,
+                            :anchor2 => 3066594, 
+                            :options => ['gene'])
      assert_equal(line, gff)
    end 
 
-   def test_tab_exportview_with_named_args
-     line = [["seqname",
-             "source",
-             "feature",
-             "start",
-             "end",
-             "score",
-             "strand",
-             "frame",
-             "gene_id",
-             "transcript_id",
-             "exon_id",
-             "gene_type"].join("\t"),
-             ["chromosome:NCBI36:4:1149206:1149209:1",
-              "Ensembl",
-              "Gene",
-              "-839",
-              "2747",
-              ".",
-              "+",
-              ".",
-              "ENSG00000206158",
-              "ENST00000382964",
-              "ENSE00001494097",
-              "KNOWN_protein_coding"].join("\t") + "\n"
-     ].join("\n")
-     line = [["seqname",
+   def test_tab_exportview_with_named_args_for_empty_result
+     line = ["seqname",
              "source",
              "feature",
              "start",
@@ -158,20 +163,7 @@ class FuncTestEnsemblHuman < Test::Unit::TestCase
              "gene_id",
              "transcript_id",
              "exon_id",
-             "gene_type"].join("\t"),
-             ["4",
-              "Ensembl",
-              "Gene",
-              "1148366",
-              "1151952",
-              ".",
-              "+",
-              "1",
-              "ENSG00000206158",
-              "ENST00000382964",
-              "ENSE00001494097",
-              "KNOWN_protein_coding"].join("\t") + "\n"
-     ].join("\n")
+             "gene_type"].join("\t") + "\n"
      gff = @serv.exportview(:seq_region_name => 4,
                             :anchor1 => 1149206,
                             :anchor2 => 1149209, 
@@ -180,6 +172,57 @@ class FuncTestEnsemblHuman < Test::Unit::TestCase
      assert_equal(line, gff)
    end 
 
+   def test_tab_exportview_with_named_args
+     # OR1A1 (Olfactory receptor 1A1)
+     lines = [ [ "seqname",
+                 "source",
+                 "feature",
+                 "start",
+                 "end",
+                 "score",
+                 "strand",
+                 "frame",
+                 "gene_id",
+                 "transcript_id",
+                 "exon_id",
+                 "gene_type"
+               ],
+               [ "17",
+                 "Ensembl",
+                 "Gene",
+                 "3065665",
+                 "3066594",
+                 ".",
+                 "+",
+                 "1",
+                 "ENSG00000172146",
+                 "ENST00000304094",
+                 "ENSE00001137815",
+                 "KNOWN_protein_coding"
+               ],
+               [ "17",
+                 "Vega",
+                 "Gene",
+                 "3065665",
+                 "3066594",
+                 ".",
+                 "+",
+                 "1",
+                 "OTTHUMG00000090637",
+                 "OTTHUMT00000207292",
+                 "OTTHUME00001080001",
+                 "KNOWN_protein_coding"
+               ]
+             ]
+     line = lines.collect { |x| x.join("\t") + "\n" }.join('')
+     gff = @serv.exportview(:seq_region_name => 17,
+                            :anchor1 => 3065665,
+                            :anchor2 => 3066594, 
+                            :options => ['gene'],
+                            :format => 'tab')
+     assert_equal(line, gff)
+   end 
+
 
 end