jandot-bio 1.2.1

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

@@ -0,0 +1,342 @@
+#
+# test/unit/bio/appl/hmmer/test_report.rb - Unit test for Bio::HMMER::Report
+#
+# Copyright::  Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_report.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/hmmer/report'
+
+
+module Bio
+
+  class TestHMMERReportData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+    TestDataHMMER = Pathname.new(File.join(bioruby_root, 'test', 'data', 'HMMER')).cleanpath.to_s
+
+    def self.hmmpfam
+      File.open(File.join(TestDataHMMER, 'hmmpfam.out')).read 
+    end
+
+    def self.output
+      self.hmmpfam
+    end
+
+    def self.hmmsearch
+      File.open(File.join(TestDataHMMER, 'hmmsearch.out')).read 
+    end
+  end
+
+
+  class TestHMMERReportClassMethods < Test::Unit::TestCase
+    def test_reports_ary
+      ary = Bio::HMMER.reports(Bio::TestHMMERReportData.output)
+      assert_equal(Array, ary.class)
+    end
+
+    def test_reports_ary
+      Bio::HMMER.reports(Bio::TestHMMERReportData.output).each do |report|
+        assert_equal(Bio::HMMER::Report, report.class)
+      end
+    end
+  end
+
+  
+  class TestHMMERReportConstants < Test::Unit::TestCase
+    def test_rs
+      assert_equal("\n//\n", Bio::HMMER::Report::RS)
+      assert_equal("\n//\n", Bio::HMMER::Report::DELIMITER)
+    end
+  end
+
+    
+  class TestHMMERReportHmmpfam < Test::Unit::TestCase
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.hmmpfam)
+    end
+    
+    def test_program
+      assert_equal(Hash, @obj.program.class)
+      assert_equal("hmmpfam - search one or more sequences against HMM database", @obj.program['name'])
+      assert_equal("HMMER 2.3.2 (Oct 2003)", @obj.program['version'])
+      assert_equal("Copyright (C) 1992-2003 HHMI/Washington University School of Medicine", @obj.program['copyright'])
+      assert_equal("Freely distributed under the GNU General Public License (GPL)", @obj.program['license'])
+    end
+
+    def test_parameter
+      assert_equal(Hash, @obj.parameter.class)
+      assert_equal("/Users/nakao/Sites/iprscan/tmp/20050517/iprscan-20050517-16244071/chunk_1/iprscan-20050517-16244071.nocrc", @obj.parameter["Sequence file"])
+      assert_equal("/Users/nakao/Sites/iprscan/data/Pfam", @obj.parameter['HMM file'])
+    end
+
+    def test_query_info
+      assert_equal(Hash, @obj.query_info.class)
+      assert_equal("104K_THEPA", @obj.query_info["Query sequence"])
+      assert_equal("[none]", @obj.query_info["Accession"])
+      assert_equal("[none]", @obj.query_info["Description"])
+    end
+
+    def test_hits
+      assert_equal(Bio::HMMER::Report::Hit, @obj.hits.first.class)
+    end
+
+    def test_hsps
+      assert_equal(Bio::HMMER::Report::Hsp, @obj.hsps.first.class)
+    end
+
+    def test_histogram
+      assert_equal(nil, @obj.histogram)
+    end
+
+    def test_statistical_detail
+      assert_equal(nil, @obj.statistical_detail)
+    end
+
+    def test_total_seq_searched
+      assert_equal(nil, @obj.total_seq_searched)
+    end
+
+    def test_whole_seq_top_hits
+      assert_equal(nil, @obj.whole_seq_top_hits)
+    end
+
+    def test_domain_top_hits
+      assert_equal(nil, @obj.domain_top_hits)
+    end
+
+    def test_each
+      @obj.each do |hit|
+        assert_equal(Bio::HMMER::Report::Hit, hit.class)
+      end
+    end
+
+    def test_each_hit
+      @obj.each_hit do |hit|
+        assert_equal(Bio::HMMER::Report::Hit, hit.class)
+      end
+    end
+  end 
+
+
+  class TestHMMERReportHit < Test::Unit::TestCase
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.output).hits.first
+    end
+
+    def test_hit
+      assert_equal(Bio::HMMER::Report::Hit, @obj.class)
+    end
+
+    def test_hsps
+      assert_equal(Bio::HMMER::Report::Hsp, @obj.hsps.first.class)
+    end
+
+    def test_accession
+      assert_equal("PF04385.4", @obj.accession)
+    end
+    def test_target_id
+      assert_equal("PF04385.4", @obj.target_id)
+    end
+    def test_hit_id
+      assert_equal("PF04385.4", @obj.hit_id)
+    end
+    def test_entry_id
+      assert_equal("PF04385.4", @obj.entry_id)
+    end
+
+    def test_description
+      assert_equal("Domain of unknown function, DUF529", @obj.description)
+    end
+    def test_definition
+      assert_equal("Domain of unknown function, DUF529", @obj.definition)
+    end
+
+    def test_score
+      assert_equal(259.3, @obj.score)
+    end
+    def test_bit_score
+      assert_equal(259.3, @obj.bit_score)
+    end
+
+    def test_evalue
+      assert_equal(6.6e-75, @obj.evalue)
+    end
+
+    def test_num
+      assert_equal(4, @obj.num)
+    end
+    
+    def test_each
+      @obj.each do |hsp|
+        assert_equal(Bio::HMMER::Report::Hsp, hsp.class)
+      end
+    end
+
+    def test_each_hsp
+      @obj.each_hsp do |hsp|
+        assert_equal(Bio::HMMER::Report::Hsp, hsp.class)
+      end
+    end
+
+    def test_target_def
+      assert_equal("<4> Domain of unknown function, DUF529", @obj.target_def)
+    end
+
+    def test_append_hsp
+      hsp = @obj.hsps.first
+      assert_equal(5, @obj.append_hsp(hsp).size)
+    end
+  end
+
+  class TestHMMERReportHsp < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.output).hits.first.hsps.first
+    end
+
+    def test_hsp
+      assert_equal(Bio::HMMER::Report::Hsp, @obj.class)
+    end
+    
+    def test_accession
+      assert_equal("PF04385.4", @obj.accession)
+    end
+
+    def test_domain
+      assert_equal("1/4", @obj.domain)
+    end
+
+    def test_seq_f
+      assert_equal(36, @obj.seq_f)
+    end
+
+    def test_seq_t
+      assert_equal(111, @obj.seq_t)
+    end
+
+    def test_seq_ft
+      assert_equal("..", @obj.seq_ft)
+    end
+
+    def test_hmm_f
+      assert_equal(1, @obj.hmm_f)
+    end
+
+    def test_hmm_t
+      assert_equal(80, @obj.hmm_t)
+    end
+
+    def test_score
+      assert_equal(65.0, @obj.score)
+    end
+    def test_bit_score
+      assert_equal(65.0, @obj.bit_score)
+    end
+
+    def test_evalue
+      assert_equal(2.0e-16, @obj.evalue)
+    end
+
+    def test_midline
+      assert_equal("t+D+n++++    f  +v+++g+++ + ++ ++v+++++++Gn+v+We++   + +l++ ++++++++++++++++ +++", @obj.midline)
+    end
+
+    def test_hmmseq
+      assert_equal("tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvWeseddpefglivtlsfyldsnkfLvlllintak", @obj.hmmseq)
+    end
+
+    def test_flatseq
+      assert_equal("TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENA---STPLYTGAIVTNNDGPYMAYVEVLGDP", @obj.flatseq)
+    end
+
+    def test_query_frame
+      assert_equal(1, @obj.query_frame)
+    end
+
+    def test_target_frame
+      assert_equal(1, @obj.target_frame)
+    end
+
+    def test_csline
+      assert_equal(nil, @obj.csline)
+    end
+
+    def test_rfline
+      assert_equal(nil, @obj.rfline)
+    end
+
+    def test_set_alignment
+    end
+
+    def test_query_seq
+      assert_equal("TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENA---STPLYTGAIVTNNDGPYMAYVEVLGDP", @obj.query_seq)
+    end
+
+    def test_target_seq
+      assert_equal("tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvWeseddpefglivtlsfyldsnkfLvlllintak", @obj.target_seq)
+    end
+
+    def test_target_from
+      assert_equal(1, @obj.target_from)
+    end
+
+    def test_targat_to
+      assert_equal(80, @obj.target_to)
+    end
+
+    def test_query_from
+      assert_equal(36, @obj.query_from)
+    end
+
+    def test_query_to
+      assert_equal(111, @obj.query_to)
+    end
+  end
+
+  class TestHMMERReportHmmsearch < Test::Unit::TestCase
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.hmmsearch)
+    end
+
+    def test_histogram
+      hist = "score    obs    exp  (one = represents 1 sequences)\n-----    ---    ---\n  377      1      0|="
+      assert_equal(hist, @obj.histogram)
+    end
+    
+    def test_statistical_detail
+      hash = {"P(chi-square)" => 0.0, "chi-sq statistic" => 0.0, "lambda" => 0.7676, "mu" => -10.6639}
+      assert_equal(hash, @obj.statistical_detail)
+      hash.keys.each do |key|
+        assert_equal(hash[key], @obj.statistical_detail[key])
+      end
+    end
+    
+    def test_total_seq_searched
+      assert_equal(1, @obj.total_seq_searched)
+    end
+
+    def test_whole_seq_top_hit
+      hash = {"Total memory" => "16K", "Satisfying E cutoff" => 1, "Total hits" => 1}
+      assert_equal(hash, @obj.whole_seq_top_hits)
+      hash.keys.each do |key|
+        assert_equal(hash[key], @obj.whole_seq_top_hits[key])
+      end
+    end
+
+    def test_domain_top_hits
+      hash = {"Total memory" => "17K", "Satisfying E cutoff" => 1, "Total hits" => 1}
+      assert_equal(hash, @obj.domain_top_hits)
+      hash.keys.each do |key|
+        assert_equal(hash[key], @obj.domain_top_hits[key])
+      end
+    end
+  end
+
+end # module Bio

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