bio 1.0.0 → 1.1.0

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

@@ -0,0 +1,103 @@
+#
+# test/functional/bio/io/test_ensembl.rb - Functional test for Bio::Ensembl
+#
+# Copyright::   Copyright (C) 2007
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id: test_ensembl.rb,v 1.4 2007/04/05 23:35:42 trevor Exp $
+#
+
+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/io/ensembl'
+
+module Bio
+
+class FuncTestEnsembl < Test::Unit::TestCase
+  def setup
+    @serv = Bio::Ensembl.new('Homo_sapiens')
+  end
+  
+  def test_class
+    assert_equal(Bio::Ensembl, @serv.class)
+  end
+end
+
+class FuncTestEnsemblHuman < Test::Unit::TestCase
+  def setup
+    @serv = Bio::Ensembl.human
+  end 
+
+  def test_organism
+    assert_equal("Homo_sapiens", @serv.organism)
+  end
+  
+  def test_server
+    assert_equal("http://www.ensembl.org", @serv.server)
+  end
+
+  def test_fna_exportview
+    seq = ">4 dna:chromosome chromosome:NCBI36:4:1149206:1149209:1\nGAGA\n"
+    fna = @serv.exportview(4, 1149206, 1149209)
+    assert_equal(seq, fna)
+  end
+
+  def test_fasta_exportview_with_hash_4th_params
+    fna = @serv.exportview(4, 1149206, 1149209, :upstream => 10)
+    fna10 = @serv.exportview(4, 1149196, 1149209)
+    assert_equal(fna10, fna)
+  end
+
+  def test_fna_exportview_with_named_args
+    seq = ">4 dna:chromosome chromosome:NCBI36:4:1149206:1149209:1\nGAGA\n"
+    fna = @serv.exportview(:seq_region_name => 4,
+                           :anchor1 => 1149206,
+                           :anchor2 => 1149209)
+    assert_equal(seq, fna)
+  end 
+
+  def test_fasta_exportview_with_named_args_and_hash_4th_params
+    fna = @serv.exportview(:seq_region_name => 4, 
+                           :anchor1 => 1149206, 
+                           :anchor2 => 1149209, 
+                           :upstream => 10)
+    fna10 = @serv.exportview(:seq_region_name => 4, 
+                             :anchor1 => 1149196, 
+                             :anchor2 => 1149209)
+    assert_equal(fna10, fna)
+  end
+
+   def test_gff_exportview
+     line = "chromosome:NCBI36:4:1149206:1149209:1\tEnsembl\tGene\t-839\t2747\t.\t+\t.\tgene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding\n"
+     gff = @serv.exportview(4, 1149206, 1149209, ['gene'])
+     assert_equal(line, gff)
+   end
+
+   def test_gff_exportview_with_named_args
+     line = "chromosome:NCBI36:4:1149206:1149209:1\tEnsembl\tGene\t-839\t2747\t.\t+\t.\tgene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding\n"
+     gff = @serv.exportview(:seq_region_name => 4,
+                            :anchor1 => 1149206,
+                            :anchor2 => 1149209, 
+                            :options => ['gene'])
+     assert_equal(line, gff)
+   end 
+
+   def test_tab_exportview_with_named_args
+     line = "seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\nchromosome:NCBI36:4:1149206:1149209:1\tEnsembl\tGene\t-839\t2747\t.\t+\t.\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n"
+     gff = @serv.exportview(:seq_region_name => 4,
+                            :anchor1 => 1149206,
+                            :anchor2 => 1149209, 
+                            :options => ['gene'],
+                            :format => 'tab')
+     assert_equal(line, gff)
+   end 
+
+
+end
+
+end # module Bio

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

@@ -1,23 +1,11 @@
 #
-# test/functional/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
+# test/functional/bio/io/test_soapwsdl.rb - Functional test for SOAP/WSDL
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2005,2007
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_soapwsdl.rb,v 1.2 2006/01/20 12:04:03 k Exp $ 
+#  $Id: test_soapwsdl.rb,v 1.4 2007/04/05 23:35:42 trevor Exp $ 
 #
 
 require 'pathname'

data/test/unit/bio/appl/bl2seq/test_report.rb

@@ -4,9 +4,9 @@
 #
 #  Copyright::   Copyright (C) 2006 
 #                Mitsuteru C. Nakao <n@bioruby.org>
-#  License::     Ruby's
+#  License::     The Ruby License
 #
-#  $Id: test_report.rb,v 1.2 2006/02/23 22:25:30 nakao Exp $
+#  $Id: test_report.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/appl/blast/test_report.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/blast/test_report.rb - Unit test for Bio::Blast::Report
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_report.rb,v 1.3 2006/02/03 17:21:51 nakao Exp $
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/appl/blast/test_xmlparser.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/blast/test_xmlparser.rb - Unit test for Bio::Blast::Report
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_xmlparser.rb,v 1.4 2006/02/03 17:21:51 nakao Exp $
+#  $Id: test_xmlparser.rb,v 1.7 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'
@@ -39,6 +26,7 @@ module Bio
 
     def self.output
       File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
+#      File.open(File.join(TestDataBlast, '2.2.15.blastp.m7')).read 
     end
   end
 

data/test/unit/bio/appl/genscan/test_report.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/genscan/test_report.rb - Unit test for Bio::Genscan::Report
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_report.rb,v 1.2 2005/11/22 08:31:47 nakao Exp $
+#  $Id: test_report.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/appl/hmmer/test_report.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/hmmer/test_report.rb - Unit test for Bio::HMMER::Report
 #
-#   Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_report.rb,v 1.1 2006/02/02 17:10:08 nakao Exp $
+#  $Id: test_report.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/appl/iprscan/test_report.rb

@@ -0,0 +1,338 @@
+#
+# test/unit/bio/appl/iprscan/test_report.rb - Unit test for Bio::InterProScan::Report
+#
+#   Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
+#
+#  $Id: test_report.rb,v 1.7 2007/07/18 11:11:57 nakao Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/iprscan/report'
+
+
+module Bio
+  class TestIprscanData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 5)).cleanpath.to_s
+    TestDataIprscan = Pathname.new(File.join(bioruby_root, "test", "data", "iprscan")).cleanpath.to_s
+    def self.raw_format
+      File.open(File.join(TestDataIprscan, "merged.raw"))
+    end
+
+    def self.txt_format
+      File.open(File.join(TestDataIprscan, "merged.txt"))
+    end
+
+  end
+  
+  
+  class TestIprscanPTxtReport < Test::Unit::TestCase
+
+    def setup
+      test_entry=<<-END
+slr0002\t860
+InterPro\tIPR001264\tGlycosyl transferase, family 51
+BlastProDom\tPD001895\tsp_Q55683_SYNY3_Q55683\t2e-37\t292-370
+HMMPfam\tPF00912\tTransglycosyl\t8e-104\t204-372
+InterPro\tIPR001460\tPenicillin-binding protein, transpeptidase domain
+HMMPfam\tPF00905\tTranspeptidase\t5.7e-30\t451-742
+InterPro\tNULL\tNULL
+ProfileScan\tPS50310\tALA_RICH\t10.224\t805-856
+//
+END
+      @obj = Bio::Iprscan::Report.parse_ptxt_entry(test_entry)
+    end 
+   
+ 
+    def test_query_id
+      assert_equal('slr0002', @obj.query_id)
+    end
+
+    def test_query_length
+      assert_equal(860, @obj.query_length)
+    end
+
+    def test_matches_size
+      assert_equal(4, @obj.matches.size)
+    end
+    
+    def test_match_ipr_id
+      assert_equal('IPR001264', @obj.matches.first.ipr_id)
+    end
+
+    def test_match_ipr_description
+      assert_equal('Glycosyl transferase, family 51', @obj.matches.first.ipr_description)
+    end
+
+    def test_match_method
+      assert_equal('BlastProDom', @obj.matches.first.method_name)
+    end
+
+    def test_match_accession
+      assert_equal('PD001895', @obj.matches.first.accession)
+    end
+
+    def test_match_description
+      assert_equal('sp_Q55683_SYNY3_Q55683', @obj.matches.first.description)
+    end
+
+    def test_match_evalue
+      assert_equal('2e-37', @obj.matches.first.evalue)
+    end
+
+    def test_match_match_start
+      assert_equal(292, @obj.matches.first.match_start)
+    end
+
+    def test_match_match_end
+      assert_equal(370, @obj.matches.first.match_end)
+    end
+
+  end # TestIprscanPTxtReport
+
+
+  class TestIprscanTxtEntry < Test::Unit::TestCase
+    def setup
+      test_txt = Bio::TestIprscanData.txt_format.read.split(/\n\nSequence/)[0]
+      @obj = Bio::Iprscan::Report.parse_txt_entry(test_txt)
+    end 
+
+    def test_iprscan_report_class
+      assert_equal(Bio::Iprscan::Report, @obj.class)
+    end
+ 
+    def test_query_id
+      assert_equal('Q9RHD9', @obj.query_id)
+    end
+
+    def test_query_length
+      assert_equal(267, @obj.query_length)
+    end
+
+    def test_matches_size
+      assert_equal(16, @obj.matches.size)
+    end
+    
+    def test_match_ipr_id
+      assert_equal('IPR000110', @obj.matches.first.ipr_id)
+    end
+
+    def test_match_ipr_description
+      assert_equal('Ribosomal protein S1', @obj.matches.first.ipr_description)
+    end
+
+    def test_match_method
+      assert_equal('FPrintScan', @obj.matches.first.method_name)
+    end
+
+    def test_match_accession
+      assert_equal('PR00681', @obj.matches.first.accession)
+    end
+
+    def test_match_description
+      assert_equal('RIBOSOMALS1', @obj.matches.first.description)
+    end
+
+    def test_match_evalue
+      assert_equal('1.5e-17', @obj.matches.first.evalue)
+    end
+
+    def test_match_status
+      assert_equal('T', @obj.matches.first.status)
+    end
+
+    def test_match_date
+      assert_equal(nil, @obj.matches.first.date)
+    end
+
+    def test_match_match_start
+      assert_equal(6, @obj.matches.first.match_start)
+    end
+
+    def test_match_match_end
+      assert_equal(27, @obj.matches.first.match_end)
+    end
+
+    def test_match_go_terms
+      ary = [["Molecular Function", "RNA binding", "GO:0003723"], 
+             ["Molecular Function", "structural constituent of ribosome", "GO:0003735"], 
+             ["Cellular Component", "ribosome", "GO:0005840"], 
+             ["Biological Process", "protein biosynthesis", "GO:0006412"]]
+      assert_equal(ary, @obj.matches.first.go_terms)
+    end
+  end # TestIprscanTxtEntry
+
+
+  class TestIprscanTxtEntryList < Test::Unit::TestCase
+    def setup
+      test_txt = Bio::TestIprscanData.txt_format.read.split(/\n\nSequence/)[0]
+      @obj = Bio::Iprscan::Report.parse_txt_entry(test_txt)
+    end 
+    
+    def test_to_hash
+      hsh = {"IPR008994" => [12, 13, 14].map {|x| @obj.matches[x] },
+             "IPR000110" => [0, 1, 2].map {|x| @obj.matches[x] },
+             "IPR003029" => [3, 4, 5, 6, 7, 8, 9, 10, 11].map {|x| @obj.matches[x] },
+             "NULL" => [15].map {|x| @obj.matches[x] }}
+      assert_equal(hsh.keys.sort, @obj.to_hash.keys.sort)
+      assert_equal(hsh, @obj.to_hash)
+    end
+
+    def test_to_hash_match?
+      @obj.to_hash.each do |ipr_id, matches|
+        matches.each do |match|
+          assert_equal(ipr_id, match.ipr_id)
+        end
+      end
+    end
+  end # TestIprscanTxtEntryList
+
+
+  class TestIprscanTxtReport < Test::Unit::TestCase
+    def setup
+      @test_txt = Bio::TestIprscanData.txt_format
+    end 
+
+    def test_parse_txt 
+      Bio::Iprscan::Report.parse_txt(@test_txt) do |report|
+        assert_equal(Bio::Iprscan::Report, report.class)
+      end
+    end
+
+
+  end # TestIprscanTxtReport
+
+
+
+  class TestIprscanRawReport < Test::Unit::TestCase
+    def setup
+      test_raw = Bio::TestIprscanData.raw_format
+      entry = ''
+      @obj = []
+      while line = test_raw.gets
+        if entry.split("\t").first == line.split("\t").first
+          entry << line
+        elsif entry != '' and entry.split("\t").first != line.split("\t").first
+          @obj << Bio::Iprscan::Report.parse_raw_entry(entry)
+          entry = ''
+        else
+          entry << line
+        end
+      end
+      @obj << Bio::Iprscan::Report.parse_raw_entry(entry)
+    end
+
+    def test_self_reports_in_raw
+      io = File.open(File.join(Bio::TestIprscanData::TestDataIprscan, 
+                               "merged.raw"))
+      result = []
+      Bio::Iprscan::Report.parse_raw(io) {|x| result << x }
+      assert_equal(@obj.size, result.size)
+      assert_equal(@obj.first.query_id, result.first.query_id)      
+      assert_equal(@obj.first.query_id, result.first.query_id)            
+      assert_equal(@obj[2].query_id, result[2].query_id)      
+      assert_equal(@obj.last.query_id, result.last.query_id)      
+    end
+    
+    def test_obj
+      assert_equal(3, @obj.size)
+    end
+    
+    def test_query_id
+      assert_equal('Q9RHD9', @obj.first.query_id)
+    end
+
+    def test_entry_id
+      assert_equal('Q9RHD9', @obj.first.entry_id)
+    end
+
+    def test_query_length
+      assert_equal(267, @obj.first.query_length)
+    end
+    
+    def test_match_query_id
+      assert_equal('Q9RHD9', @obj.first.matches.first.query_id)
+    end
+    
+    def test_match_crc64
+      assert_equal('D44DAE8C544CB7C1', @obj.first.matches.first.crc64)
+    end
+    
+    def test_match_query_length
+      assert_equal(267, @obj.first.matches.first.query_length)
+    end
+    
+    def test_match_method
+      assert_equal('HMMPfam', @obj.first.matches.first.method_name)
+    end
+    
+    def test_match_accession
+      assert_equal('PF00575', @obj.first.matches.first.accession)
+    end
+    
+    def test_match_description
+      assert_equal('S1', @obj.first.matches.first.description)
+    end
+    
+    def test_match_match_start
+      assert_equal(1, @obj.first.matches.first.match_start)
+    end
+    
+    def test_match_match_end
+      assert_equal(55, @obj.first.matches.first.match_end)
+    end
+    
+    def test_match_evalue
+      assert_equal('3.3E-6', @obj.first.matches.first.evalue)
+    end
+    
+    def test_match_status
+      assert_equal('T', @obj.first.matches.first.status)
+    end
+
+    def test_match_date
+      assert_equal('11-Nov-2005', @obj.first.matches.first.date)
+    end
+
+    def test_match_ipr_id
+      assert_equal('IPR003029', @obj.first.matches.first.ipr_id)
+    end
+
+    def test_match_ipr_description
+      assert_equal('RNA binding S1', @obj.first.matches.first.ipr_description)
+    end
+
+    def test_match_go_terms
+      ary = ["Biological Process:phosphorylation (GO:0016310)", 
+             "Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)"]
+      assert_equal(ary,
+                   @obj.last.matches.last.go_terms)
+    end
+
+  end
+
+  class TestIprscanReport < Test::Unit::TestCase
+    def setup
+      @test_txt = Bio::TestIprscanData.txt_format.read.split(/\n\nSequence/)[0]
+      @obj = Bio::Iprscan::Report.parse_txt_entry(@test_txt)
+      @test_raw = Bio::TestIprscanData.raw_format.read.split("RS16_ECOLI")[0]
+    end 
+
+    def test_to_raw
+#      assert_equal(@test_raw.split("\n").sort, 
+#                   @obj.format_raw.split("\n").sort)      
+    end
+
+    def test_output_raw
+#      assert_equal(@test_raw.split("\n").sort, 
+#                   @obj.output(:raw).split("\n").sort)      
+#      assert_equal(@test_raw.split("\n").sort, 
+#                   @obj.output('raw').split("\n").sort)      
+    end
+
+  end # TestIprscanReport
+
+end