RubyGems - bio - Versions diffs - 1.4.3.0001 → 1.5.0 - Mend

bio 1.4.3.0001 → 1.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (158) hide show

checksums.yaml +7 -0
data/.travis.yml +39 -33
data/BSDL +22 -0
data/COPYING +2 -2
data/COPYING.ja +36 -36
data/ChangeLog +2404 -1025
data/KNOWN_ISSUES.rdoc +15 -55
data/README.rdoc +17 -23
data/RELEASE_NOTES.rdoc +246 -183
data/Rakefile +3 -2
data/bin/br_biofetch.rb +29 -5
data/bioruby.gemspec +15 -32
data/bioruby.gemspec.erb +10 -20
data/doc/ChangeLog-1.4.3 +1478 -0
data/doc/RELEASE_NOTES-1.4.3.rdoc +204 -0
data/doc/Tutorial.rd +0 -6
data/doc/Tutorial.rd.html +7 -12
data/doc/Tutorial.rd.ja +960 -1064
data/doc/Tutorial.rd.ja.html +977 -1067
data/gemfiles/Gemfile.travis-jruby1.8 +2 -1
data/gemfiles/Gemfile.travis-jruby1.9 +2 -4
data/gemfiles/Gemfile.travis-rbx +13 -0
data/gemfiles/Gemfile.travis-ruby1.8 +2 -1
data/gemfiles/Gemfile.travis-ruby1.9 +2 -4
data/gemfiles/Gemfile.travis-ruby2.2 +9 -0
data/lib/bio.rb +10 -43
data/lib/bio/alignment.rb +8 -14
data/lib/bio/appl/blast.rb +1 -2
data/lib/bio/appl/blast/format0.rb +18 -7
data/lib/bio/appl/blast/remote.rb +0 -9
data/lib/bio/appl/blast/report.rb +1 -1
data/lib/bio/appl/clustalw/report.rb +3 -1
data/lib/bio/appl/genscan/report.rb +1 -2
data/lib/bio/appl/iprscan/report.rb +1 -2
data/lib/bio/appl/meme/mast.rb +4 -4
data/lib/bio/appl/meme/mast/report.rb +1 -1
data/lib/bio/appl/paml/codeml.rb +2 -2
data/lib/bio/appl/paml/codeml/report.rb +1 -0
data/lib/bio/appl/paml/common.rb +1 -1
data/lib/bio/appl/sosui/report.rb +1 -2
data/lib/bio/command.rb +62 -2
data/lib/bio/data/aa.rb +13 -31
data/lib/bio/data/codontable.rb +1 -2
data/lib/bio/db/biosql/biosql_to_biosequence.rb +1 -0
data/lib/bio/db/biosql/sequence.rb +1 -1
data/lib/bio/db/embl/common.rb +1 -1
data/lib/bio/db/embl/embl.rb +5 -4
data/lib/bio/db/embl/format_embl.rb +3 -3
data/lib/bio/db/embl/sptr.rb +9 -1444
data/lib/bio/db/embl/swissprot.rb +12 -29
data/lib/bio/db/embl/trembl.rb +13 -30
data/lib/bio/db/embl/uniprot.rb +12 -29
data/lib/bio/db/embl/uniprotkb.rb +1455 -0
data/lib/bio/db/fasta.rb +17 -0
data/lib/bio/db/fasta/defline.rb +1 -3
data/lib/bio/db/fastq.rb +1 -1
data/lib/bio/db/genbank/ddbj.rb +9 -5
data/lib/bio/db/genbank/refseq.rb +11 -3
data/lib/bio/db/gff.rb +3 -4
data/lib/bio/db/go.rb +5 -6
data/lib/bio/db/kegg/module.rb +4 -5
data/lib/bio/db/kegg/pathway.rb +4 -5
data/lib/bio/db/kegg/reaction.rb +1 -1
data/lib/bio/db/nexus.rb +3 -2
data/lib/bio/db/pdb/pdb.rb +2 -2
data/lib/bio/db/phyloxml/phyloxml_elements.rb +82 -59
data/lib/bio/db/phyloxml/phyloxml_parser.rb +2 -2
data/lib/bio/db/phyloxml/phyloxml_writer.rb +1 -2
data/lib/bio/db/sanger_chromatogram/chromatogram.rb +1 -2
data/lib/bio/db/transfac.rb +1 -1
data/lib/bio/io/das.rb +40 -41
data/lib/bio/io/fastacmd.rb +0 -16
data/lib/bio/io/fetch.rb +111 -55
data/lib/bio/io/flatfile/buffer.rb +4 -5
data/lib/bio/io/hinv.rb +2 -3
data/lib/bio/io/ncbirest.rb +43 -6
data/lib/bio/io/pubmed.rb +76 -81
data/lib/bio/io/togows.rb +33 -10
data/lib/bio/map.rb +1 -1
data/lib/bio/pathway.rb +1 -1
data/lib/bio/sequence/compat.rb +1 -1
data/lib/bio/sequence/na.rb +63 -12
data/lib/bio/shell.rb +0 -2
data/lib/bio/shell/core.rb +5 -6
data/lib/bio/shell/interface.rb +3 -4
data/lib/bio/shell/irb.rb +1 -2
data/lib/bio/shell/plugin/entry.rb +2 -3
data/lib/bio/shell/plugin/seq.rb +7 -6
data/lib/bio/shell/setup.rb +1 -2
data/lib/bio/tree.rb +2 -2
data/lib/bio/util/contingency_table.rb +0 -2
data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +2 -2
data/lib/bio/util/sirna.rb +76 -16
data/lib/bio/version.rb +8 -9
data/sample/benchmark_clustalw_report.rb +47 -0
data/sample/biofetch.rb +248 -151
data/setup.rb +6 -7
data/test/data/clustalw/example1-seqnos.aln +58 -0
data/test/network/bio/appl/blast/test_remote.rb +1 -15
data/test/network/bio/appl/test_blast.rb +0 -12
data/test/network/bio/io/test_pubmed.rb +49 -0
data/test/network/bio/io/test_togows.rb +0 -1
data/test/network/bio/test_command.rb +65 -2
data/test/unit/bio/appl/bl2seq/test_report.rb +0 -1
data/test/unit/bio/appl/blast/test_report.rb +110 -48
data/test/unit/bio/appl/clustalw/test_report.rb +67 -51
data/test/unit/bio/appl/sim4/test_report.rb +46 -17
data/test/unit/bio/appl/test_blast.rb +2 -2
data/test/unit/bio/db/embl/test_embl.rb +0 -1
data/test/unit/bio/db/embl/test_embl_rel89.rb +0 -1
data/test/unit/bio/db/embl/{test_sptr.rb → test_uniprotkb.rb} +111 -115
data/test/unit/bio/db/embl/{test_uniprot_new_part.rb → test_uniprotkb_new_part.rb} +11 -11
data/test/unit/bio/db/genbank/test_genbank.rb +10 -4
data/test/unit/bio/db/pdb/test_pdb.rb +14 -8
data/test/unit/bio/db/test_fasta.rb +41 -1
data/test/unit/bio/db/test_fastq.rb +14 -4
data/test/unit/bio/db/test_gff.rb +2 -2
data/test/unit/bio/db/test_phyloxml.rb +30 -30
data/test/unit/bio/db/test_phyloxml_writer.rb +2 -2
data/test/unit/bio/io/flatfile/test_autodetection.rb +1 -2
data/test/unit/bio/io/flatfile/test_buffer.rb +7 -1
data/test/unit/bio/io/flatfile/test_splitter.rb +1 -1
data/test/unit/bio/io/test_togows.rb +3 -2
data/test/unit/bio/sequence/test_dblink.rb +1 -1
data/test/unit/bio/sequence/test_na.rb +3 -1
data/test/unit/bio/test_alignment.rb +1 -2
data/test/unit/bio/test_command.rb +5 -4
data/test/unit/bio/test_db.rb +4 -2
data/test/unit/bio/test_pathway.rb +25 -10
data/test/unit/bio/util/test_sirna.rb +22 -22
metadata +656 -1430
data/doc/KEGG_API.rd +0 -1843
data/doc/KEGG_API.rd.ja +0 -1834
data/extconf.rb +0 -2
data/lib/bio/appl/blast/ddbj.rb +0 -131
data/lib/bio/db/kegg/taxonomy.rb +0 -280
data/lib/bio/io/dbget.rb +0 -194
data/lib/bio/io/ddbjrest.rb +0 -344
data/lib/bio/io/ddbjxml.rb +0 -458
data/lib/bio/io/ebisoap.rb +0 -158
data/lib/bio/io/ensembl.rb +0 -229
data/lib/bio/io/higet.rb +0 -73
data/lib/bio/io/keggapi.rb +0 -363
data/lib/bio/io/ncbisoap.rb +0 -156
data/lib/bio/io/soapwsdl.rb +0 -119
data/lib/bio/shell/plugin/keggapi.rb +0 -181
data/lib/bio/shell/plugin/soap.rb +0 -87
data/sample/dbget +0 -37
data/sample/demo_ddbjxml.rb +0 -212
data/sample/demo_kegg_taxonomy.rb +0 -92
data/sample/demo_keggapi.rb +0 -502
data/sample/psortplot_html.rb +0 -214
data/test/network/bio/io/test_ddbjrest.rb +0 -47
data/test/network/bio/io/test_ensembl.rb +0 -230
data/test/network/bio/io/test_soapwsdl.rb +0 -53
data/test/unit/bio/io/test_ddbjxml.rb +0 -81
data/test/unit/bio/io/test_ensembl.rb +0 -111
data/test/unit/bio/io/test_soapwsdl.rb +0 -33

data/sample/psortplot_html.rb DELETED

@@ -1,214 +0,0 @@
-#!/usr/bin/env ruby
-#
-# psortplot_html.rb - A KEGG API demo script. Generates a HTML file of
-#                     genes marked by PSORT II predictions onto a
-#                     KEGG/PATHWAY map.
-#
-#  Usage:
-#
-#   % ruby psortplot_html.rb
-#   % cat sce00010_psort2.html
-#   % ruby psortplot_html.rb path:eco00010
-#   % cat eco00010_psort2.html
-#
-# Copyright::  Copyright (C) 2005
-#              Mitsuteru C. Nakao <n@bioruby.org>
-# License::    The Ruby License
-#
-#  $Id: psortplot_html.rb,v 1.3 2007/04/05 23:35:42 trevor Exp $
-#
-require 'bio'
-class KEGG
-  DBGET_BASEURI = 'http://kegg.com/dbget-bin'
-  WWW_BGET_BASEURI = DBGET_BASEURI + '/www_bget'
-  WWW_PATHWAY_BASEURI = DBGET_BASEURI + '/get_pathway'
-  # path := path:sce00010
-  def self.link_pathway(path0)
-    path, path = path0.split(':')
-    org_name = path.scan(/(^\w{3})/).to_s
-    mapno = path.sub(org_name, '')
-    str = "<a href='#{WWW_PATHWAY_BASEURI}?org_name=#{org_name}&mapno=#{mapno}'>#{path0}</a>"
-  end
-  # ec_num := ec:1.2.3.4
-  def self.link_ec(ec_num)
-    ec = ec_num.sub(/^ec:/, '')
-    str = "<a href='#{WWW_BGET_BASEURI}?enzyme+#{ec}'>#{ec_num}</a>"
-    return str
-  end
-  # gene := eco:b0002
-  def self.link_genes(gene)
-    org_name, gene_name = gene.split(':')
-    str = "<a href='#{WWW_BGET_BASEURI}?#{org_name}+#{gene_name}'>#{gene}</a>"
-    return str
-  end
-end
-class PSORT
-  COLOR_Palette = {
-    'csk' => "#FF0000",   # 'cytoskeletal'
-    'cyt' => "#FF8000",   # 'cytoplasmic'
-    'nuc' => "#FFFF00",   # 'nuclear'
-    'mit' => "#80FF00",   # 'mitochondrial'
-    'ves' => "#00FF00",	# 'vesicles of secretory system'
-    'end' => "#00FF80",	# 'endoplasmic reticulum'
-    'gol' => "#00FFFF",	# 'Golgi'
-    'vac' => "#0080FF",	# 'vacuolar'
-    'pla' => "#0000FF",	# 'plasma membrane'
-    'pox' => "#8000FF",	# 'peroxisomal'
-    'exc' => "#FF00FF",	# 'extracellular, including cell wall'
-    '---' => "#FF0080"	# 'other'
-  }
-end
-keggapi = Bio::KEGG::API.new
-psort2serv = Bio::PSORT::PSORT2.imsut
-# Obtains a list of genes on specified pathway
-pathway = ARGV.shift || "path:sce00010"
-genes = keggapi.get_genes_by_pathway(pathway)
-scl = Hash.new # protein subcelluler localizations
-ec = Hash.new  # EC numbers
-serial = 0
-sync_default = $stdout.sync
-$stdout.sync = true
-genes.each do |gene|
-  print "#{(serial += 1).to_s.rjust(genes.size.to_s.size)}\t#{gene}\t"
-  # Obtains amino acid sequence from KEGG GENES entry
-  aaseq = keggapi.get_aaseqs([gene])
-  # Predicts protein subcellualr localization
-  result = psort2serv.exec(aaseq)
-  scl[gene] = result.pred
-  print "#{scl[gene]}\t"
-  # Obtains the EC number from KEGG GENES entry
-  ec[gene] = keggapi.get_enzymes_by_gene(gene)
-  puts "#{ec[gene].inspect}"
-end
-$stdout.sync = sync_default
-fg_list = Array.new
-bg_list = Array.new
-genes.each do |gene|
-  fg_list << "#FF0000"
-  bg_list << PSORT::COLOR_Palette[scl[gene]]
-end
-# coloring KEGG pathway according to gene's localization
-url = keggapi.color_pathway_by_objects(pathway, genes, fg_list, bg_list)
-puts "#{url} downloaded."
-# remove "path:" prefix from pathway_id
-path_code = pathway.sub(/^path:/, '')
-# save the result image
-image_file = "#{path_code}_psort2.gif"
-begin
-  keggapi.save_image(url, image_file)
-end
-# create html with a color palette
-html = <<END
-<html>
-<head>
-<title>PSORT II prediction protein subcellular localization map of KEGG/PATHWAY (#{pathway})</title>
-<style>
-table { border-collapse: collapse; }
-td { border: 1px solid black; padding: 5px; }
-td.outer { border: none; vertical-align: top; }
-</style>
-</head>
-<body>
-<h1><li><a href="http://psort.ims.u-tokyo.ac.jp/helpwww2.html">PSORT II</a> prediction protein subcellular localization map of <a href="http://kegg.com/kegg/pathway.html">KEGG/PATHWAY</a> (<a href="">#{KEGG.link_pathway(pathway)})</h1>
-<table>
-<tr>
-  <td class=outer>
-    <table>
-    <tr>
-      <th></th>
-      <th>EC</th>
-      <th>Gene</th>
-      <th>Localization</th>
-    </tr>
-END
-# generate gene table with localization
-names = Bio::PSORT::PSORT2::SclNames
-multi_genes = Hash.new(0)
-ec.values.flatten.sort.uniq.each do |ec_num|
-  ec.find_all {|x| x[1].include?(ec_num) }.each do |gene|
-    gene = gene[0]
-    loc = scl[gene]
-    color = PSORT::COLOR_Palette[loc]
-    name = names[loc]
-    multi_genes[gene] += 1
-    html += <<END
-    <tr>
-      <td>#{multi_genes[gene]}</td>
-      <td>#{KEGG.link_ec(ec_num)}</td>
-      <td>#{KEGG.link_genes(gene)}</td>
-      <td bgcolor="#{color}">#{name}</td>
-    </tr>
-END
-  end
-end
-html += <<END
-    </table>
-  </td>
-  <td class=outer>
-    <table>
-    <tr>
-      <th>Code</th>
-      <th>Color</th>
-    </tr>
-END
-# generate color code table also
-PSORT::COLOR_Palette.sort.each do |code, color|
-  html += <<END
-    <tr>
-      <td>#{code}</td>
-      <td bgcolor="#{color}">#{names[code]}</td>
-    </tr>
-END
-end
-html += <<END
-    </table>
-  </td>
-</tr>
-</table>
-<br>
-<img src="#{image_file}">
-</body>
-</html>
-END
-# save generated HTML file
-html_file = "#{path_code}_psort2.html"
-File.open(html_file, "w+") do |file|
-  file.puts html
-end
-puts "Open #{html_file}"

data/test/network/bio/io/test_ddbjrest.rb DELETED

@@ -1,47 +0,0 @@
-#
-# test/functional/bio/io/test_ddbjrest.rb - Functional test for Bio::DDBJ::REST
-#
-# Copyright::   Copyright (C) 2011
-#               Naohisa Goto <ng@bioruby.org>
-# License::     The Ruby License
-#
-# loading helper routine for testing bioruby
-require 'pathname'
-load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
-                            'bioruby_test_helper.rb')).cleanpath.to_s
-# libraries needed for the tests
-require 'bio/io/ddbjrest'
-require 'test/unit'
-module Bio
-module NetTestDDBJREST
-  class TestDDBJ < Test::Unit::TestCase
-    def setup
-      @obj = Bio::DDBJ::REST::DDBJ.new
-    end
-    def test_countBasePair
-      text = @obj.countBasePair("AF237819")
-      expected = {
-        "a" => 47,
-        "t" => 38,
-        "g" => 48,
-        "c" => 38
-      }
-      h = {}
-      text.each_line do |line|
-        base, count, percent = line.split(/\t/)
-        count = count.to_i
-        h[base] = count if count > 0
-      end
-      assert_equal(expected, h)
-    end
-  end #class TestDDBJ
-end #module NetTestDDBJREST
-end #module Bio

data/test/network/bio/io/test_ensembl.rb DELETED

@@ -1,230 +0,0 @@
-#
-# 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
-#
-#  $Id:$
-#
-# loading helper routine for testing bioruby
-require 'pathname'
-load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
-                            'bioruby_test_helper.rb')).cleanpath.to_s
-# libraries needed for the tests
-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
-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"
-    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_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_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_for_empty_result
-     line = ["seqname",
-             "source",
-             "feature",
-             "start",
-             "end",
-             "score",
-             "strand",
-             "frame",
-             "gene_id",
-             "transcript_id",
-             "exon_id",
-             "gene_type"].join("\t") + "\n"
-     gff = @serv.exportview(:seq_region_name => 4,
-                            :anchor1 => 1149206,
-                            :anchor2 => 1149209,
-                            :options => ['gene'],
-                            :format => 'tab')
-     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
-end # module Bio