bio 0.7.1 → 1.0.0

data/sample/any2fasta.rb

@@ -0,0 +1,59 @@
+#!/usr/bin/env ruby
+#
+# any2fasta.rb - convert input file into FASTA format using a regex
+#                filter
+#
+#   Copyright (C) 2006 Pjotr Prins <p@bioruby.org>
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program 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 General Public License for more details.
+#
+#  $Id: any2fasta.rb,v 1.1 2006/02/17 14:59:27 pjotr Exp $
+#
+
+require 'bio/io/flatfile'
+
+include Bio
+
+usage = <<USAGE
+
+Usage: any2fasta.rb [regex] infiles
+
+  Examples:
+
+    Output all sequences containing GATC or GATT ignoring case:
+		
+	  any2fasta.rb "/GAT[CT]/i" *.seq > reduced.fasta
+		
+USAGE
+
+if ARGV.size == 0
+  print usage
+	exit 1
+end
+
+# ---- Valid regular expression - if it is not a file
+regex = ARGV[0]
+if regex=~/^\// and !File.exist?(regex)
+  ARGV.shift
+else
+  regex = nil
+end
+
+ARGV.each do | fn |
+  ff = Bio::FlatFile.auto(fn)
+  ff.each_entry do |entry|
+	  if regex != nil
+		  next if eval("entry.seq !~ #{regex}")
+		end
+  	print entry.seq.to_fasta(entry.definition,70)
+	end
+end
+

data/test/data/HMMER/hmmpfam.out

@@ -0,0 +1,64 @@
+hmmpfam - search one or more sequences against HMM database
+HMMER 2.3.2 (Oct 2003)
+Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+HMM file:                 /Users/nakao/Sites/iprscan/data/Pfam
+Sequence file:            /Users/nakao/Sites/iprscan/tmp/20050517/iprscan-20050517-16244071/chunk_1/iprscan-20050517-16244071.nocrc
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query sequence: 104K_THEPA
+Accession:      [none]
+Description:    [none]
+
+Scores for sequence family classification (score includes all domains):
+Model    Description                                    Score    E-value  N 
+-------- -----------                                    -----    ------- ---
+PF04385.4 Domain of unknown function, DUF529             259.3    6.6e-75   4
+
+Parsed for domains:
+Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
+-------- ------- ----- -----    ----- -----      -----  -------
+PF04385.4   1/4      36   111 ..     1    80 []    65.0    2e-16
+PF04385.4   2/4     149   224 ..     1    80 []    64.7  2.5e-16
+PF04385.4   3/4     265   343 ..     1    80 []    64.6  2.7e-16
+PF04385.4   4/4     379   456 ..     1    80 []    65.0    2e-16
+
+Alignments of top-scoring domains:
+PF04385.4: domain 1 of 4, from 36 to 111: score 65.0, E = 2e-16
+                   *->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+                      t+D+n++++    f  +v+++g+++ + ++ ++v+++++++Gn+v+W
+  104K_THEPA    36    TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIW 81   
+
+                   eseddpefglivtlsfyldsnkfLvlllintak<-*
+                   e++   + +l++ ++++++++++++++++ +++   
+  104K_THEPA    82 ENA---STPLYTGAIVTNNDGPYMAYVEVLGDP    111  
+
+PF04385.4: domain 2 of 4, from 149 to 224: score 64.7, E = 2.5e-16
+                   *->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+                      +L++ ++ +++k+ + ++a+ng ++vt++p++G+ +++++++n++++
+  104K_THEPA   149    SLNMAFQLENNKYEVETHAKNGANMVTFIPRNGHICKMVYHKNVRIY 195  
+
+                   eseddpefglivtlsfyldsnkfLvlllintak<-*
+                   ++     ++++vt++++++ +++L+l+++ +     
+  104K_THEPA   196 KA----TGNDTVTSVVGFFRGLRLLLINVFSID    224  
+
+PF04385.4: domain 3 of 4, from 265 to 343: score 64.6, E = 2.7e-16
+                   *->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+                       +Dl+ +++ +++f+ + a+++ ++++++p++G+++tk++dG++v++
+  104K_THEPA   265    PVDLDIKDIDYTMFHLADATYHEPCFKIIPNTGFCITKLFDGDQVLY 311  
+
+                   eseddpefglivtlsfyldsnkfLvlllintak<-*
+                   es+ + + ++i  +++y+++n ++++l++n+++   
+  104K_THEPA   312 ESFNP-LIHCINEVHIYDRNNGSIICLHLNYSP    343  
+
+PF04385.4: domain 4 of 4, from 379 to 456: score 65.0, E = 2e-16
+                   *->tLDlndtgstlkqfdykvalngdivvty.tpkpGvkftkitdGnevv
+                      +LD+n  ++++k+ +++  +n d  +t+ tp+p+  + +++dG+ev+
+  104K_THEPA   379    ELDVN--FISDKDLYVAALTNADLNYTMvTPRPHRDVIRVSDGSEVL 423  
+
+                   WeseddpefglivtlsfyldsnkfLvlllintak<-*
+                   W++e+  ++ l++++++++d++ +Lv+l+i++     
+  104K_THEPA   424 WYYEGL-DNFLVCAWIYVSDGVASLVHLRIKDRI    456  
+
+//

data/test/data/HMMER/hmmsearch.out

@@ -0,0 +1,88 @@
+hmmsearch - search a sequence database with a profile HMM
+HMMER 2.2g (August 2001)
+Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+HMM file:                   /sw/share/hmmer/demo/7tm_1 [7tm_1]
+Sequence database:          /sw/share/hmmer/demo/P08908.fasta
+per-sequence score cutoff:  [none]
+per-domain score cutoff:    [none]
+per-sequence Eval cutoff:   <= 10        
+per-domain Eval cutoff:     [none]
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query HMM:   7tm_1
+Accession:   PF00001
+Description: 7 transmembrane receptor (rhodopsin family)
+  [HMM has been calibrated; E-values are empirical estimates]
+
+Scores for complete sequences (score includes all domains):
+Sequence             Description                        Score    E-value  N 
+--------             -----------                        -----    ------- ---
+sp|P08908|5H1A_HUMAN 5-hydroxytryptamine 1A receptor    377.1   5.5e-130   1
+
+Parsed for domains:
+Sequence             Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
+--------             ------- ----- -----    ----- -----      -----  -------
+sp|P08908|5H1A_HUMAN   1/1      53   400 ..     1   275 []   377.1 5.5e-130
+
+Alignments of top-scoring domains:
+sp|P08908|5H1A_HUMAN: domain 1 of 1, from 53 to 400: score 377.1, E = 5.5e-130
+                   *->GNlLVilvilrtkklrtptnifilNLAvADLLflltlppwalyylvg
+                      GN+ V+++i+++++l++++n++i++LAv+DL+++++++p+a++y v 
+  sp|P08908|    53    GNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVL 99   
+
+                   gsedWpfGsalCklvtaldvvnmyaSillLtaISiDRYlAIvhPlryrrr
+                   +   W++G++ C+l++aldv+++++Sil+L+aI++DRY+AI++P+ y ++
+  sp|P08908|   100 N--KWTLGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK 147  
+
+                   rtsprrAkvvillvWvlalllslPpllfswvktveegngtlnvnvtvCli
+                   rt prrA+++i+l+W++++l+s+Pp +++w++++  +         +C+i
+  sp|P08908|   148 RT-PRRAAALISLTWLIGFLISIPP-MLGWRTPEDRSD------PDACTI 189  
+
+                   dfpeestasvstwlvsyvllstlvgFllPllvilvcYtrIlrtlrkrark
+                   + +++           y+++st+++F++Pll++lv+Y+rI+r++r r rk
+  sp|P08908|   190 SKDHG-----------YTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK 228  
+
+                   gas...............................................
+                    + + ++++ +++++ ++ ++++++ ++++++++ + + +++ ++    +
+  sp|P08908|   229 TVKkvektgadtrhgaspapqpkksvngesgsrnwrlgveskaggalcan 278  
+
+                   ..................................................
+                   +  ++++++   +  + ++ ++++++ + +++ ++++  + + +++++++
+  sp|P08908|   279 gavrqgddgaalevievhrvgnskehlplpseagptpcapasferknern 328  
+
+                   .....kkrsskerkaaktllvvvvvFvlCWlPyfivllldtlc.lsiims
+                    + ++k+   +erk++ktl++++++F+lCWlP+fiv+l+ ++c++s++m 
+  sp|P08908|   329 aeakrKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCeSSCHM- 377  
+
+                   stCelervlptallvtlwLayvNsclNPiIY<-*
+                           +  +  +++wL+y+Ns lNP+IY   
+  sp|P08908|   378 --------PTLLGAIINWLGYSNSLLNPVIY    400  
+
+
+Histogram of all scores:
+score    obs    exp  (one = represents 1 sequences)
+-----    ---    ---
+  377      1      0|=                                                          
+
+
+% Statistical details of theoretical EVD fit:
+              mu =   -10.6639
+          lambda =     0.7676
+chi-sq statistic =     0.0000
+  P(chi-square)  =          0
+
+Total sequences searched: 1
+
+Whole sequence top hits:
+tophits_s report:
+     Total hits:           1
+     Satisfying E cutoff:  1
+     Total memory:         16K
+
+Domain top hits:
+tophits_s report:
+     Total hits:           1
+     Satisfying E cutoff:  1
+     Total memory:         17K

data/test/data/aaindex/DAYM780301

@@ -0,0 +1,30 @@
+H DAYM780301
+D Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
+R
+A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
+T A model of evolutionary change in proteins
+J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff,
+  M.O., ed.), National Biomedical Research Foundation, Washington, D.C.,
+  p.352 (1978)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+      2.
+     -2.      6.
+      0.      0.      2.
+      0.     -1.      2.      4.
+     -2.     -4.     -4.     -5.     12.
+      0.      1.      1.      2.     -5.      4.
+      0.     -1.      1.      3.     -5.      2.      4.
+      1.     -3.      0.      1.     -3.     -1.      0.      5.
+     -1.      2.      2.      1.     -3.      3.      1.     -2.      6.
+     -1.     -2.     -2.     -2.     -2.     -2.     -2.     -3.     -2.      5.
+     -2.     -3.     -3.     -4.     -6.     -2.     -3.     -4.     -2.      2.      6.
+     -1.      3.      1.      0.     -5.      1.      0.     -2.      0.     -2.     -3.      5.
+     -1.      0.     -2.     -3.     -5.     -1.     -2.     -3.     -2.      2.      4.      0.      6.
+     -4.     -4.     -4.     -6.     -4.     -5.     -5.     -5.     -2.      1.      2.     -5.      0.      9.
+      1.      0.     -1.     -1.     -3.      0.     -1.     -1.      0.     -2.     -3.     -1.     -2.     -5.      6.
+      1.      0.      1.      0.      0.     -1.      0.      1.     -1.     -1.     -3.      0.     -2.     -3.      1.      2.
+      1.     -1.      0.      0.     -2.     -1.      0.      0.     -1.      0.     -2.      0.     -1.     -3.      0.      1.      3.
+     -6.      2.     -4.     -7.     -8.     -5.     -7.     -7.     -3.     -5.     -2.     -3.     -4.      0.     -6.     -2.     -5.     17.
+     -3.     -4.     -2.     -4.      0.     -4.     -4.     -5.      0.     -1.     -1.     -4.     -2.      7.     -5.     -3.     -3.      0.     10.
+      0.     -2.     -2.     -2.     -2.     -2.     -2.     -1.     -2.      4.      2.     -2.      2.     -1.     -1.     -1.      0.     -6.     -2.      4.
+//

data/test/data/aaindex/PRAM900102

@@ -0,0 +1,20 @@
+H PRAM900102
+D Relative frequency in alpha-helix (Prabhakaran, 1990)
+R LIT:1614053b PMID:2390062
+A Prabhakaran, M.
+T The distribution of physical, chemical and conformational properties in 
+  signal and nascent peptides
+J Biochem. J. 269, 691-696 (1990) Original reference of these three data: 
+  Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, 
+  W.H., ed.), San Francisco P.235 (1983)
+C LEVM780101    1.000  LEVM780104    0.964  PALJ810101    0.943
+  KANM800101    0.942  ISOY800101    0.929  MAXF760101    0.924
+  ROBB760101    0.916  GEIM800101    0.912  GEIM800104    0.907
+  RACS820108    0.904  PALJ810102    0.902  PALJ810109    0.898
+  NAGK730101    0.894  CRAJ730101    0.887  CHOP780201    0.873
+  TANS770101    0.854  KANM800103    0.850  QIAN880107    0.829
+  QIAN880106    0.827  BURA740101    0.805  NAGK730103   -0.809
+I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
+    1.29    0.96    0.90    1.04    1.11    1.27    1.44    0.56    1.22    0.97
+    1.30    1.23    1.47    1.07    0.52    0.82    0.82    0.99    0.72    0.91
+//

data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq

@@ -0,0 +1,53 @@
+Query= CD8A_HUMAN P01732 T-cell surface glycoprotein CD8 alpha chain
+precursor (T-lymphocyte differentiation antigen T8/Leu-2).
+         (235 letters)
+
+>CD8B_HUMAN P10966 T-cell surface glycoprotein CD8 beta chain
+           precursor (Antigen CD8B).
+          Length = 210
+
+ Score = 29.6 bits (65), Expect = 5e-05
+ Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
+
+Query: 39  VELKCQVLLSNPTSGCSWLFQ---PRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLG 95
+           V L C+  +S       WL Q   P   +      L+ S       E ++ ++ +  R  
+Sbjct: 37  VMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLALWDSAKGTIHGEEVEQEKIAVFRDA 96
+
+Query: 96  DTFVLTLSDFRRENEGYYFCSALSNSIMYF 125
+             F+L L+  + E+ G YFC  + +  + F
+Sbjct: 97  SRFILNLTSVKPEDSGIYFCMIVGSPELTF 126
+
+
+Lambda     K      H
+   0.323    0.137    0.436 
+
+Gapped
+Lambda     K      H
+   0.267   0.0410    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 102
+Number of Sequences: 0
+Number of extensions: 5
+Number of successful extensions: 3
+Number of sequences better than 10.0: 1
+Number of HSP's better than 10.0 without gapping: 1
+Number of HSP's successfully gapped in prelim test: 0
+Number of HSP's that attempted gapping in prelim test: 0
+Number of HSP's gapped (non-prelim): 1
+length of query: 235
+length of database: 210
+effective HSP length: 22
+effective length of query: 213
+effective length of database: 188
+effective search space:    40044
+effective search space used:    40044
+T: 11
+A: 40
+X1: 16 ( 7.5 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 20 (12.2 bits)
+S2: 20 (12.3 bits)

data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq

@@ -0,0 +1,37 @@
+Query= CD8A_HUMAN P01732 T-cell surface glycoprotein CD8 alpha chain
+precursor (T-lymphocyte differentiation antigen T8/Leu-2).
+         (235 letters)
+
+Lambda     K      H
+   0.323    0.137    0.436 
+
+Gapped
+Lambda     K      H
+   0.267   0.0410    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 175
+Number of Sequences: 0
+Number of extensions: 8
+Number of successful extensions: 0
+Number of sequences better than 1.0e-05: 0
+Number of HSP's better than  0.0 without gapping: 0
+Number of HSP's successfully gapped in prelim test: 0
+Number of HSP's that attempted gapping in prelim test: 0
+Number of HSP's gapped (non-prelim): 0
+length of query: 235
+length of database: 393
+effective HSP length: 27
+effective length of query: 208
+effective length of database: 366
+effective search space:    76128
+effective search space used:    76128
+T: 11
+A: 40
+X1: 16 ( 7.5 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 41 (22.0 bits)
+S2: 74 (33.1 bits)

data/test/data/blast/{eco:b0002.faa.m0 → b0002.faa.m0}

@@ -12,7 +12,7 @@ aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal)
 aspartate kinase (A)
          (820 letters)
 
-Database: eco:b0002.faa 
+Database: b0002.faa 
            1 sequences; 820 total letters
 
 Searching.done
@@ -88,7 +88,7 @@ Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
 Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
 
 
-  Database: eco:b0002.faa
+  Database: b0002.faa
     Posted date:  Aug 7, 2005  7:29 AM
   Number of letters in database: 820
   Number of sequences in database:  1

data/test/data/blast/{eco:b0002.faa.m7 → b0002.faa.m7}

@@ -4,7 +4,7 @@
   <BlastOutput_program>blastp</BlastOutput_program>
   <BlastOutput_version>blastp 2.2.10 [Oct-19-2004]</BlastOutput_version>
   <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db>eco:b0002.faa</BlastOutput_db>
+  <BlastOutput_db>b0002.faa</BlastOutput_db>
   <BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
   <BlastOutput_query-def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</BlastOutput_query-def>
   <BlastOutput_query-len>820</BlastOutput_query-len>

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

@@ -0,0 +1,134 @@
+#
+# test/unit/bio/appl/bl2seq/test_report.rb - Unit test for 
+# Bio::Blast::Bl2seq::Report
+#
+#  Copyright::   Copyright (C) 2006 
+#                Mitsuteru C. Nakao <n@bioruby.org>
+#  License::     Ruby's
+#
+#  $Id: test_report.rb,v 1.2 2006/02/23 22:25:30 nakao 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/bl2seq/report'
+
+
+module Bio
+  class TestBl2seqReportData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+    TestDataBl2seq = Pathname.new(File.join(bioruby_root, 'test', 'data', 'bl2seq')).cleanpath.to_s
+
+    def self.output(format = 7)
+      case format
+      when 'empty'
+        File.open(File.join(TestDataBl2seq, 'cd8a_p53_e-5blastp.bl2seq')).read 
+      when 'blastp'
+        File.open(File.join(TestDataBl2seq, 'cd8a_cd8b_blastp.bl2seq')).read 
+      when 'blastn'
+      when 'blastx'
+      when 'tblastn'
+      when 'tblastx'
+      end
+    end
+  end
+
+
+  class TestBl2seqReportConstants < Test::Unit::TestCase
+    def test_rs
+      rs = nil
+      assert_equal(nil, Bio::Blast::Bl2seq::Report::RS)
+      assert_equal(nil, Bio::Blast::Bl2seq::Report::DELIMITER)
+    end
+  end
+
+
+  class TestBl2seqReport < Test::Unit::TestCase
+
+    def setup
+      @empty = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('empty'))
+      @blastp = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('blastp'))
+    end
+
+    def test_new
+      assert(@empty)
+      assert(@blastp)
+    end
+
+    def test_undefed_methods
+      methods = ['format0_parse_header',
+                 'program',
+                 'version',
+                 'version_number',
+                 'version_date',
+                 'message',
+                 'converged?',
+                 'reference',
+                 'db']
+      
+      methods.each do |x|
+        assert_nil(@empty.methods.include?(x))
+      end
+
+      methods.each do |x|
+        assert_nil(@blastp.methods.include?(x))
+      end
+    end
+
+    #  TestF0dbstat < Test::Unit::TestCase
+
+    def test_db_num
+      assert_equal(0, @empty.db_num)
+      assert_equal(0, @blastp.db_num)
+    end
+
+    def test_db_len
+      assert_equal(393, @empty.db_len)
+      assert_equal(210, @blastp.db_len)
+    end
+
+#    TestIteration < Test::Unit::TestCase
+    def test_undefed_methods
+      methods = ['message',
+                 'pattern_in_database',
+                 'pattern',
+                 'pattern_positions',
+                 'hits_found_again',
+                 'hits_newly_found',
+                 'hits_for_pattern',
+                 'parse_hitlist',
+                 'converged?']
+
+      methods.each do |x|
+        assert_equal(false, @empty.iterations.first.methods.include?(x), "undifined? : #{x}")
+      end
+
+      methods.each do |x|
+        assert_equal(false, @blastp.iterations.first.methods.include?(x), "undefined? : #{x}")
+      end
+    end
+  end
+
+
+  class TestBl2seqReportHit < Test::Unit::TestCase
+    def setup
+      @empty = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('empty'))
+      @blastp = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('blastp'))
+      @empty_hit = @empty.hits.first
+      @blastp_hit = @blastp.hits.first
+    end
+
+    def test_empty_hits
+      assert_equal(0, @empty.hits.size)
+    end
+
+    def test_hits
+      assert_equal(Bio::Blast::Bl2seq::Report::Hit, @blastp.hits.first.class)
+      assert_equal(1, @blastp.hits.size)
+    end
+  end
+
+end # module Bio