RubyGems - bio - Versions diffs - 1.2.1 → 1.3.0 - Mend

bio 1.2.1 → 1.3.0

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 (259) hide show

data/ChangeLog +3421 -0
data/KNOWN_ISSUES.rdoc +88 -0
data/README.rdoc +252 -0
data/README_DEV.rdoc +285 -0
data/Rakefile +143 -0
data/bin/bioruby +0 -0
data/bin/br_biofetch.rb +0 -0
data/bin/br_bioflat.rb +12 -1
data/bin/br_biogetseq.rb +0 -0
data/bin/br_pmfetch.rb +4 -3
data/bioruby.gemspec +477 -0
data/bioruby.gemspec.erb +117 -0
data/doc/Changes-0.7.rd +7 -0
data/doc/Changes-1.3.rdoc +239 -0
data/doc/Tutorial.rd +296 -184
data/doc/Tutorial.rd.html +1031 -0
data/doc/Tutorial.rd.ja +111 -45
data/doc/Tutorial.rd.ja.html +2225 -0
data/doc/bioruby.css +281 -0
data/extconf.rb +2 -0
data/lib/bio.rb +29 -4
data/lib/bio/appl/blast.rb +306 -121
data/lib/bio/appl/blast/ddbj.rb +142 -0
data/lib/bio/appl/blast/format0.rb +35 -25
data/lib/bio/appl/blast/format8.rb +2 -2
data/lib/bio/appl/blast/genomenet.rb +263 -0
data/lib/bio/appl/blast/ncbioptions.rb +220 -0
data/lib/bio/appl/blast/remote.rb +106 -0
data/lib/bio/appl/blast/report.rb +260 -9
data/lib/bio/appl/blast/rexml.rb +12 -5
data/lib/bio/appl/blast/rpsblast.rb +277 -0
data/lib/bio/appl/blast/wublast.rb +133 -12
data/lib/bio/appl/blast/xmlparser.rb +35 -18
data/lib/bio/appl/blat/report.rb +46 -5
data/lib/bio/appl/emboss.rb +62 -13
data/lib/bio/appl/fasta.rb +9 -11
data/lib/bio/appl/genscan/report.rb +3 -3
data/lib/bio/appl/hmmer.rb +1 -1
data/lib/bio/appl/hmmer/report.rb +10 -10
data/lib/bio/appl/paml/baseml.rb +95 -0
data/lib/bio/appl/paml/baseml/report.rb +32 -0
data/lib/bio/appl/paml/codeml.rb +242 -0
data/lib/bio/appl/paml/codeml/rates.rb +67 -0
data/lib/bio/appl/paml/codeml/report.rb +67 -0
data/lib/bio/appl/paml/common.rb +348 -0
data/lib/bio/appl/paml/common_report.rb +38 -0
data/lib/bio/appl/paml/yn00.rb +103 -0
data/lib/bio/appl/paml/yn00/report.rb +32 -0
data/lib/bio/appl/psort.rb +2 -2
data/lib/bio/appl/pts1.rb +5 -5
data/lib/bio/appl/tmhmm/report.rb +10 -1
data/lib/bio/command.rb +297 -41
data/lib/bio/compat/features.rb +157 -0
data/lib/bio/compat/references.rb +128 -0
data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
data/lib/bio/db/biosql/sequence.rb +508 -0
data/lib/bio/db/embl/common.rb +28 -12
data/lib/bio/db/embl/embl.rb +107 -9
data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
data/lib/bio/db/embl/format_embl.rb +190 -0
data/lib/bio/db/embl/sptr.rb +15 -16
data/lib/bio/db/fantom.rb +6 -8
data/lib/bio/db/fasta.rb +10 -507
data/lib/bio/db/fasta/defline.rb +532 -0
data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
data/lib/bio/db/fasta/format_fasta.rb +97 -0
data/lib/bio/db/genbank/common.rb +25 -8
data/lib/bio/db/genbank/format_genbank.rb +187 -0
data/lib/bio/db/genbank/genbank.rb +36 -1
data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
data/lib/bio/db/gff.rb +1791 -119
data/lib/bio/db/kegg/glycan.rb +2 -6
data/lib/bio/db/lasergene.rb +3 -3
data/lib/bio/db/medline.rb +4 -1
data/lib/bio/db/newick.rb +10 -10
data/lib/bio/db/pdb/chain.rb +6 -2
data/lib/bio/db/pdb/pdb.rb +12 -3
data/lib/bio/db/rebase.rb +7 -8
data/lib/bio/db/soft.rb +3 -3
data/lib/bio/feature.rb +1 -88
data/lib/bio/io/biosql/biodatabase.rb +64 -0
data/lib/bio/io/biosql/bioentry.rb +29 -0
data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
data/lib/bio/io/biosql/bioentry_path.rb +12 -0
data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
data/lib/bio/io/biosql/biosequence.rb +11 -0
data/lib/bio/io/biosql/comment.rb +7 -0
data/lib/bio/io/biosql/config/database.yml +20 -0
data/lib/bio/io/biosql/dbxref.rb +13 -0
data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
data/lib/bio/io/biosql/location.rb +32 -0
data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
data/lib/bio/io/biosql/ontology.rb +10 -0
data/lib/bio/io/biosql/reference.rb +9 -0
data/lib/bio/io/biosql/seqfeature.rb +32 -0
data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
data/lib/bio/io/biosql/taxon.rb +12 -0
data/lib/bio/io/biosql/taxon_name.rb +9 -0
data/lib/bio/io/biosql/term.rb +27 -0
data/lib/bio/io/biosql/term_dbxref.rb +11 -0
data/lib/bio/io/biosql/term_path.rb +12 -0
data/lib/bio/io/biosql/term_relationship.rb +13 -0
data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
data/lib/bio/io/biosql/term_synonym.rb +10 -0
data/lib/bio/io/das.rb +7 -7
data/lib/bio/io/ddbjxml.rb +57 -0
data/lib/bio/io/ensembl.rb +2 -2
data/lib/bio/io/fetch.rb +28 -14
data/lib/bio/io/flatfile.rb +17 -853
data/lib/bio/io/flatfile/autodetection.rb +545 -0
data/lib/bio/io/flatfile/buffer.rb +237 -0
data/lib/bio/io/flatfile/index.rb +17 -7
data/lib/bio/io/flatfile/indexer.rb +30 -12
data/lib/bio/io/flatfile/splitter.rb +297 -0
data/lib/bio/io/hinv.rb +442 -0
data/lib/bio/io/keggapi.rb +2 -2
data/lib/bio/io/ncbirest.rb +733 -0
data/lib/bio/io/pubmed.rb +34 -80
data/lib/bio/io/registry.rb +2 -2
data/lib/bio/io/sql.rb +178 -357
data/lib/bio/io/togows.rb +458 -0
data/lib/bio/location.rb +106 -11
data/lib/bio/pathway.rb +120 -14
data/lib/bio/reference.rb +115 -101
data/lib/bio/sequence.rb +164 -183
data/lib/bio/sequence/adapter.rb +108 -0
data/lib/bio/sequence/common.rb +22 -45
data/lib/bio/sequence/compat.rb +2 -2
data/lib/bio/sequence/dblink.rb +54 -0
data/lib/bio/sequence/format.rb +254 -77
data/lib/bio/sequence/format_raw.rb +23 -0
data/lib/bio/shell.rb +3 -1
data/lib/bio/shell/core.rb +2 -2
data/lib/bio/shell/plugin/entry.rb +33 -4
data/lib/bio/shell/plugin/ncbirest.rb +64 -0
data/lib/bio/shell/plugin/togows.rb +40 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/bioruby_generator.rb +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/_classes.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/_log.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/_methods.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/_modules.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/_variables.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby-bg.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby-gem.png +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby-link.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby.css +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby_controller.rb +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/bioruby_helper.rb +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/commands.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/history.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/index.rhtml +0 -0
data/lib/bio/shell/rails/vendor/plugins/{generators → bioruby/generators}/bioruby/templates/spinner.gif +0 -0
data/lib/bio/tree.rb +4 -2
data/lib/bio/util/color_scheme.rb +2 -2
data/lib/bio/util/contingency_table.rb +2 -2
data/lib/bio/util/restriction_enzyme.rb +2 -2
data/lib/bio/util/restriction_enzyme/single_strand.rb +6 -5
data/lib/bio/version.rb +25 -0
data/rdoc.zsh +8 -0
data/sample/any2fasta.rb +0 -0
data/sample/biofetch.rb +0 -0
data/sample/dbget +0 -0
data/sample/demo_sequence.rb +158 -0
data/sample/enzymes.rb +0 -0
data/sample/fasta2tab.rb +0 -0
data/sample/fastagrep.rb +72 -0
data/sample/fastasort.rb +54 -0
data/sample/fsplit.rb +0 -0
data/sample/gb2fasta.rb +2 -3
data/sample/gb2tab.rb +0 -0
data/sample/gbtab2mysql.rb +0 -0
data/sample/genes2nuc.rb +0 -0
data/sample/genes2pep.rb +0 -0
data/sample/genes2tab.rb +0 -0
data/sample/genome2rb.rb +0 -0
data/sample/genome2tab.rb +0 -0
data/sample/goslim.rb +0 -0
data/sample/gt2fasta.rb +0 -0
data/sample/na2aa.rb +34 -0
data/sample/pmfetch.rb +0 -0
data/sample/pmsearch.rb +0 -0
data/sample/ssearch2tab.rb +0 -0
data/sample/tfastx2tab.rb +0 -0
data/sample/vs-genes.rb +0 -0
data/setup.rb +1596 -0
data/test/data/blast/blastp-multi.m7 +188 -0
data/test/data/command/echoarg2.bat +1 -0
data/test/data/paml/codeml/control_file.txt +30 -0
data/test/data/paml/codeml/output.txt +78 -0
data/test/data/paml/codeml/rates +217 -0
data/test/data/rpsblast/misc.rpsblast +193 -0
data/test/data/soft/GDS100_partial.soft +0 -0
data/test/data/soft/GSE3457_family_partial.soft +0 -0
data/test/functional/bio/appl/test_pts1.rb +115 -0
data/test/functional/bio/io/test_ensembl.rb +123 -80
data/test/functional/bio/io/test_togows.rb +267 -0
data/test/functional/bio/sequence/test_output_embl.rb +51 -0
data/test/functional/bio/test_command.rb +301 -0
data/test/runner.rb +17 -1
data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
data/test/unit/bio/appl/blast/test_report.rb +753 -35
data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
data/test/unit/bio/appl/test_blast.rb +135 -4
data/test/unit/bio/appl/test_fasta.rb +2 -2
data/test/unit/bio/appl/test_pts1.rb +1 -64
data/test/unit/bio/db/embl/test_common.rb +15 -15
data/test/unit/bio/db/embl/test_embl.rb +4 -4
data/test/unit/bio/db/embl/test_embl_rel89.rb +5 -5
data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
data/test/unit/bio/db/embl/test_sptr.rb +38 -1
data/test/unit/bio/db/pdb/test_pdb.rb +2 -2
data/test/unit/bio/db/test_gff.rb +1151 -25
data/test/unit/bio/db/test_medline.rb +127 -0
data/test/unit/bio/db/test_nexus.rb +5 -1
data/test/unit/bio/db/test_prosite.rb +4 -4
data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
data/test/unit/bio/io/test_ddbjxml.rb +8 -3
data/test/unit/bio/io/test_fastacmd.rb +5 -5
data/test/unit/bio/io/test_flatfile.rb +357 -106
data/test/unit/bio/io/test_soapwsdl.rb +2 -2
data/test/unit/bio/io/test_togows.rb +161 -0
data/test/unit/bio/sequence/test_common.rb +210 -11
data/test/unit/bio/sequence/test_compat.rb +3 -3
data/test/unit/bio/sequence/test_dblink.rb +58 -0
data/test/unit/bio/sequence/test_na.rb +2 -2
data/test/unit/bio/test_command.rb +111 -50
data/test/unit/bio/test_feature.rb +29 -1
data/test/unit/bio/test_location.rb +566 -6
data/test/unit/bio/test_pathway.rb +91 -65
data/test/unit/bio/test_reference.rb +67 -13
data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -3
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -4
data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +3 -3
data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +3 -3
data/test/unit/bio/util/test_restriction_enzyme.rb +3 -3
metadata +202 -167
data/test/unit/bio/appl/blast/test_xmlparser.rb +0 -388

data/doc/Tutorial.rd.html ADDED

@@ -0,0 +1,1031 @@
+<?xml version="1.0" ?>
+<!DOCTYPE html
+  PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>doc/Tutorial.rd</title>
+<link href="bioruby.css" type="text/css" rel="stylesheet" />
+</head>
+<body>
+<h1><a name="label-0" id="label-0">BioRuby Tutorial</a></h1><!-- RDLabel: "BioRuby Tutorial" -->
+<p>Editor: PjotrPrins &lt;p .at. bioruby.org&gt;</p>
+<ul>
+<li>Copyright (C) 2001-2003 KATAYAMA Toshiaki &lt;k .at. bioruby.org&gt;</li>
+<li>Copyright (C) 2005-2008 Pjotr Prins, Naohisa Goto and others</li>
+</ul>
+<p>The latest version resides in the CVS repository ./doc/<a href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&amp;cvsroot=bioruby&amp;content-type=text/plain">Tutorial.rd</a>. This one was updated:</p>
+<pre>$Id: Tutorial.rd,v 1.22 2008/05/19 12:22:05 pjotr Exp $ </pre>
+<p>in preparation for the <a href="http://hackathon.dbcls.jp/">BioHackathlon 2008</a></p>
+<h2><a name="label-1" id="label-1">Introduction</a></h2><!-- RDLabel: "Introduction" -->
+<p>This is a tutorial for using Bioruby. A basic knowledge of Ruby is required.
+If you want to know more about the programming langauge Ruby we recommend the
+excellent book <a href="http://www.pragprog.com/titles/ruby">Programming Ruby</a>
+by Dave Thomas and Andy Hunt - some of it is online
+<a href="http://www.rubycentral.com/pickaxe/">here</a>.</p>
+<p>For BioRuby you need to install Ruby and the BioRuby package on your computer</p>
+<p>You can check whether Ruby is installed on your computer and what
+version it has with the</p>
+<pre>% ruby -v</pre>
+<p>command. Showing something like:</p>
+<pre>ruby 1.8.5 (2006-08-25) [powerpc-linux]</pre>
+<p>If you see no such thing you'll have to install Ruby using your installation
+manager. For more information see the
+<a href="http://www.ruby-lang.org/en/">Ruby</a> website.</p>
+<p>Once Ruby is works download and install Bioruby using the links on the
+<a href="http://bioruby.org/">Bioruby</a> website.</p>
+<p>A lot of BioRuby's documentation exists in the source code and unit tests. To
+really dive in you will need the latest source code tree. The embedded rdoc
+documentation can be viewed online at
+<a href="http://bioruby.org/rdoc/">bioruby's rdoc</a>. But first lets start!</p>
+<h2><a name="label-2" id="label-2">Trying Bioruby</a></h2><!-- RDLabel: "Trying Bioruby" -->
+<p>Bioruby comes with its own shell. After unpacking the sources run the
+following command</p>
+<pre>./bin/bioruby  or
+ruby -I lib bin/bioruby</pre>
+<p>and you should see a prompt</p>
+<pre>bioruby&gt;</pre>
+<p>Now test the following:</p>
+<pre>bioruby&gt; seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+==&gt; "atgcatgcaaaa"
+bioruby&gt; seq.complement
+==&gt; "ttttgcatgcat"</pre>
+<p>See the the Bioruby shell section below for more tweaking. If you have trouble running
+examples also check the section below on trouble shooting. You can also post a
+question to the mailing list. BioRuby developers usually try to help.</p>
+<h2><a name="label-3" id="label-3">Working with nucleic / amino acid sequences (Bio::Sequence class)</a></h2><!-- RDLabel: "Working with nucleic / amino acid sequences (Bio::Sequence class)" -->
+<p>The Bio::Sequence class allows the usual sequence transformations and
+translations.  In the example below the DNA sequence "atgcatgcaaaa" is
+converted into the complemental strand, spliced into a subsequence,
+next the nucleic acid composition is calculated and the sequence is
+translated into the amino acid sequence, the molecular weight
+calculated, and so on. When translating into amino acid sequences the
+frame can be specified and optionally the condon table selected (as
+defined in codontable.rb).</p>
+<pre>bioruby&gt; seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+==&gt; "atgcatgcaaaa"
+# complemental sequence (Bio::Sequence::NA object)
+bioruby&gt; seq.complement
+==&gt; "ttttgcatgcat"
+bioruby&gt; seq.subseq(3,8) # gets subsequence of positions 3 to 8
+==&gt; "gcatgc"
+bioruby&gt; seq.gc_percent
+==&gt; 33
+bioruby&gt; seq.composition
+==&gt; {"a"=&gt;6, "c"=&gt;2, "g"=&gt;2, "t"=&gt;2}
+bioruby&gt; seq.translate
+==&gt; "MHAK"
+bioruby&gt; seq.translate(2)        # translate from frame 2
+==&gt; "CMQ"
+bioruby&gt; seq.translate(1,11)     # codon table 11
+==&gt; "MHAK"
+bioruby&gt; seq.translate.codes
+==&gt; ["Met", "His", "Ala", "Lys"]
+bioruby&gt; seq.translate.names
+==&gt; ["methionine", "histidine", "alanine", "lysine"]
+bioruby&gt;  seq.translate.composition
+==&gt; {"K"=&gt;1, "A"=&gt;1, "M"=&gt;1, "H"=&gt;1}
+bioruby&gt; seq.translate.molecular_weight
+==&gt; 485.605
+bioruby&gt; seq.complement.translate
+==&gt; "FCMH"</pre>
+<p>get a random sequence with the same NA count:</p>
+<pre>bioruby&gt; counts = {'a'=&gt;seq.count('a'),'c'=&gt;seq.count('c'),'g'=&gt;seq.count('g'),'t'=&gt;seq.count('t')}
+==&gt; {"a"=&gt;6, "c"=&gt;2, "g"=&gt;2, "t"=&gt;2}
+bioruby!&gt; randomseq = Bio::Sequence::NA.randomize(counts)
+==!&gt; "aaacatgaagtc"
+bioruby!&gt; print counts
+a6c2g2t2
+bioruby!&gt; p counts
+{"a"=&gt;6, "c"=&gt;2, "g"=&gt;2, "t"=&gt;2}</pre>
+<p>The p, print and puts methods are standard Ruby ways of outputting to
+the screen. If you want to know more about standard Ruby commands you
+can use the 'ri' command on the command line (or the help command in
+Windows). For example</p>
+<pre>% ri puts
+% ri p
+% ri File.open</pre>
+<p>Nucleic acid sequence is an object of Bio::Sequence::NA class, and
+amino acid sequence is an object of Bio::Sequence::AA class.  Shared
+methods are in the parent Bio::Sequence class.</p>
+<p>As Bio::Sequence class inherits Ruby's String class, you can use
+String class methods. For example, to get a subsequence, you can
+not only use subseq(from, to) but also String#[].</p>
+<p>Please take note that the Ruby's string's are base 0 - i.e. the first letter
+has index 0, for example:</p>
+<pre>bioruby&gt; s = 'abc'
+==&gt; "abc"
+bioruby&gt; s[0].chr
+==&gt; "a"
+bioruby&gt; s[0..1]
+==&gt; "ab"</pre>
+<p>So when using String methods, you should subtract 1 from positions
+conventionally used in biology.  (subseq method will throw an exception if you
+specify positions smaller than or equal to 0 for either one of the "from" or
+"to".)</p>
+<p>The window_search(window_size, step_size) method shows a typical Ruby
+way of writing concise and clear code using 'closures'. Each sliding
+window creates a subsequence which is supplied to the enclosed block
+through a variable named +s+.</p>
+<p>Show average percentage of GC content for 20 bases (stepping the default one base at a time)</p>
+<pre>bioruby&gt; seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
+==&gt; "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
+bioruby&gt; a=[]; seq.window_search(20) { |s| a.push s.gc_percent }
+bioruby&gt; a
+==&gt; [30, 35, 40, 40, 35, 35, 35, 30, 25, 30, 30, 30, 35, 35, 35, 35, 35, 40, 45, 45, 45, 45, 40, 35, 40, 40, 40, 40, 40, 35, 35, 35, 30, 30, 30]</pre>
+<p>Since the class of each subsequence is the same as original sequence
+(Bio::Sequence::NA or Bio::Sequence::AA or Bio::Sequence), you can
+use all methods on the subsequence. For example,</p>
+<p>Shows translation results for 15 bases shifting a codon at a time</p>
+<pre>bioruby&gt; a = []
+bioruby&gt; seq.window_search(15, 3) do |s|
+bioruby&gt;   a.push s.translate
+bioruby&gt; end
+bioruby&gt; a
+==&gt; ["MHAIK", "HAIKL", "AIKLI", "IKLIP", "KLIPI", "LIPIR", "IPIRS", "PIRSS", "IRSSR", "RSSRS", "SSRSS", "SRSSK", "RSSKK", "SSKKK"]</pre>
+<p>Finally, the window_search method returns the last leftover
+subsequence. This allows for example</p>
+<p>Divide a genome sequence into sections of 10000bp and
+output FASTA formatted sequences (line width 60 chars). The 1000bp at the
+start and end of each subsequence overlapped. At the 3' end of the sequence
+the leftover is also added:</p>
+<pre>i = 1
+textwidth=60
+remainder = seq.window_search(10000, 9000) do |s|
+  puts s.to_fasta("segment #{i}", textwidth)
+  i += 1
+end
+if remainder
+  puts remainder.to_fasta("segment #{i}", textwidth)
+end</pre>
+<p>If you don't want the overlapping window, set window size and stepping
+size to equal values.</p>
+<p>Other examples</p>
+<p>Count the codon usage</p>
+<pre>bioruby&gt; codon_usage = Hash.new(0)
+bioruby&gt; seq.window_search(3, 3) do |s|
+bioruby&gt;   codon_usage[s] += 1
+bioruby&gt; end
+bioruby&gt; codon_usage
+==&gt; {"cat"=&gt;1, "aaa"=&gt;3, "cca"=&gt;1, "att"=&gt;2, "aga"=&gt;1, "atc"=&gt;1, "cta"=&gt;1, "gca"=&gt;1, "cga"=&gt;1, "tca"=&gt;3, "aag"=&gt;1, "tcc"=&gt;1, "atg"=&gt;1}</pre>
+<p>Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)</p>
+<pre>bioruby&gt; a = []
+bioruby&gt; seq.window_search(10, 10) do |s|
+bioruby&gt;   a.push s.molecular_weight
+bioruby&gt; end
+bioruby&gt; a
+==&gt; [3096.2062, 3086.1962, 3056.1762, 3023.1262, 3073.2262]</pre>
+<p>In most cases, sequences are read from files or retrieved from databases.
+For example:</p>
+<pre>require 'bio'
+input_seq = ARGF.read       # reads all files in arguments
+my_naseq = Bio::Sequence::NA.new(input_seq)
+my_aaseq = my_naseq.translate
+puts my_aaseq</pre>
+<p>Save the program as na2aa.rb. Prepare a nucleic acid sequence
+described below and saves it as my_naseq.txt:</p>
+<pre>gtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctg
+atgccgcacgtaggcctgataagacgcggacagcgtcgcatcaggcatcttgtgcaaatg
+tcggatgcggcgtga</pre>
+<p>na2aa.rb translates a nucleic acid sequence to a protein sequence.
+For example, translates my_naseq.txt:</p>
+<pre>% ruby na2aa.rb my_naseq.txt</pre>
+<p>or use a pipe!</p>
+<pre>% cat my_naseq.txt|ruby na2aa.rb</pre>
+<p>Outputs</p>
+<pre>VAIFPKAMTGAKNQSSDICLMPHVGLIRRGQRRIRHLVQMSDAA*</pre>
+<p>You can also write this, a bit fanciful, as a one-liner script.</p>
+<pre>% ruby -r bio -e 'p Bio::Sequence::NA.new($&lt;.read).translate' my_naseq.txt</pre>
+<p>In the next section we will retrieve data from databases instead of using raw
+sequence files. One generic example of the above can be found in
+./sample/na2aa.rb.</p>
+<h2><a name="label-4" id="label-4">Parsing GenBank data (Bio::GenBank class)</a></h2><!-- RDLabel: "Parsing GenBank data (Bio::GenBank class)" -->
+<p>We assume that you already have some GenBank data files. (If you don't,
+download some .seq files from ftp://ftp.ncbi.nih.gov/genbank/)</p>
+<p>As an example we fetch the ID, definition and sequence of each entry
+from the GenBank format and convert it to FASTA. This is also an example
+script in the BioRuby distribution.</p>
+<p>A first attempt could be to use the Bio::GenBank class for reading in
+the data:</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+# Read all lines from STDIN split by the GenBank delimiter
+while entry = gets(Bio::GenBank::DELIMITER)
+  gb = Bio::GenBank.new(entry)      # creates GenBank object
+  print "&gt;#{gb.accession} "         # Accession
+  puts gb.definition                # Definition
+  puts gb.naseq                     # Nucleic acid sequence
+                                    # (Bio::Sequence::NA object)
+end</pre>
+<p>But that has the disadvantage the code is tied to GenBank input. A more
+generic method is to use Bio::FlatFile which allows you to use different
+input formats:</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
+ff.each_entry do |gb|
+  definition = "#{gb.accession} #{gb.definition}"
+  puts gb.naseq.to_fasta(definition, 60)
+end</pre>
+<p>For example, in turn, reading FASTA format files:</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
+ff.each_entry do |f|
+  puts "definition : " + f.definition
+  puts "nalen      : " + f.nalen.to_s
+  puts "naseq      : " + f.naseq
+end</pre>
+<p>In above two scripts, the first arguments of Bio::FlatFile.new are
+database classes of BioRuby. This is expanded on in a later section.</p>
+<p>Again another option is to use the Bio::DB.open class:</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+ff = Bio::GenBank.open("gbvrl1.seq")
+ff.each_entry do |gb|
+  definition = "#{gb.accession} #{gb.definition}"
+  puts gb.naseq.to_fasta(definition, 60)
+end</pre>
+<p>Next, we are going to parse the GenBank 'features', which is normally
+very complicated:</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
+# iterates over each GenBank entry
+ff.each_entry do |gb|
+  # shows accession and organism
+  puts "# #{gb.accession} - #{gb.organism}"
+  # iterates over each element in 'features'
+  gb.features.each do |feature|
+    position = feature.position
+    hash = feature.assoc            # put into Hash
+    # skips the entry if "/translation=" is not found
+    next unless hash['translation']
+    # collects gene name and so on and joins it into a string
+    gene_info = [
+      hash['gene'], hash['product'], hash['note'], hash['function']
+    ].compact.join(', ')
+    # shows nucleic acid sequence
+    puts "&gt;NA splicing('#{position}') : #{gene_info}"
+    puts gb.naseq.splicing(position)
+    # shows amino acid sequence translated from nucleic acid sequence
+    puts "&gt;AA translated by splicing('#{position}').translate"
+    puts gb.naseq.splicing(position).translate
+    # shows amino acid sequence in the database entry (/translation=)
+    puts "&gt;AA original translation"
+    puts hash['translation']
+  end
+end</pre>
+<p>Note: In this example Feature#assoc method makes a Hash from a
+feature object. It is useful because you can get data from the hash
+by using qualifiers as keys.
+(But there is a risk some information is lost when two or more
+qualifiers are the same. Therefore an Array is returned by
+Feature#feature)</p>
+<p>Bio::Sequence#splicing splices subsequence from nucleic acid sequence
+according to location information used in GenBank, EMBL and DDBJ.</p>
+<p>When the specified translation table is different from the default
+(universal), or when the first codon is not "atg" or the protein
+contains selenocysteine, the two amino acid sequences will differ.</p>
+<p>The Bio::Sequence#splicing method takes not only DDBJ/EMBL/GenBank
+feature style location text but also Bio::Locations object. For more
+information about location format and Bio::Locations class, see
+bio/location.rb.</p>
+<p>Splice according to location string used in a GenBank entry</p>
+<pre>naseq.splicing('join(2035..2050,complement(1775..1818),13..345')</pre>
+<p>Generate Bio::Locations object and pass the splicing method</p>
+<pre>locs = Bio::Locations.new('join((8298.8300)..10206,1..855)')
+naseq.splicing(locs)</pre>
+<p>You can also use the splicing method for amino acid sequences
+(Bio::Sequence::AA objects).</p>
+<p>Splicing peptide from a protein (e.g. signal peptide)</p>
+<pre>aaseq.splicing('21..119')</pre>
+<h3><a name="label-5" id="label-5">More databases</a></h3><!-- RDLabel: "More databases" -->
+<p>Databases in BioRuby are essentially accessed like that of GenBank
+with classes like Bio::GenBank, Bio::KEGG::GENES. A full list can be found in
+the ./lib/bio/db directory of the BioRuby source tree.</p>
+<p>In many cases the Bio::DatabaseClass acts as a factory pattern
+and recognises the database type automatically - returning a
+parsed object. For example using Bio::FlatFile</p>
+<p>Bio::FlatFile class as described above. The first argument of the
+Bio::FlatFile.new is database class name in BioRuby (such as Bio::GenBank,
+Bio::KEGG::GENES and so on).</p>
+<pre>ff = Bio::FlatFile.new(Bio::DatabaseClass, ARGF)</pre>
+<p>Isn't it wonderful that Bio::FlatFile automagically recognizes each
+database class?</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+ff = Bio::FlatFile.auto(ARGF)
+ff.each_entry do |entry|
+  p entry.entry_id          # identifier of the entry
+  p entry.definition        # definition of the entry
+  p entry.seq               # sequence data of the entry
+end</pre>
+<p>An example that can take any input, filter using a regular expression to output
+to a FASTA file can be found in sample/any2fasta.rb. With this technique it is
+possible to write a Unix type grep/sort pipe for sequence information. One
+example using scripts in the BIORUBY sample folder:</p>
+<pre>fastagrep.rb '/At|Dm/' database.seq | fastasort.rb</pre>
+<p>greps the database for Arabidopsis and Drosophila entries and sorts the output
+to FASTA.</p>
+<p>Other methods to extract specific data from database objects can be
+different between databases, though some methods are common (see the
+guidelines for common methods as described in bio/db.rb).</p>
+<ul>
+<li>entry_id --&gt; gets ID of the entry</li>
+<li>definition --&gt; gets definition of the entry</li>
+<li>reference --&gt; gets references as Bio::Reference object</li>
+<li>organism --&gt; gets species</li>
+<li>seq, naseq, aaseq --&gt; returns sequence as corresponding sequence object</li>
+</ul>
+<p>Refer to the documents of each database to find the exact naming
+of the included methods.</p>
+<p>In principal BioRuby uses the following conventions: when a method
+name is plural the method returns some object as an Array. For
+example, some classes have a "references" method which returns
+multiple Bio::Reference objects as an Array. And some classes have a
+"reference" method which returns a single Bio::Reference object.</p>
+<h3><a name="label-6" id="label-6">Alignments (Bio::Alignment)</a></h3><!-- RDLabel: "Alignments (Bio::Alignment)" -->
+<p>Bio::Alignment class in bio/alignment.rb is a container class like Ruby's Hash,
+Array and BioPerl's Bio::SimpleAlign.  A very simple example is:</p>
+<pre>bioruby&gt; seqs = [ 'atgca', 'aagca', 'acgca', 'acgcg' ]
+bioruby&gt; seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
+# creates alignment object
+bioruby&gt; a = Bio::Alignment.new(seqs)
+bioruby&gt; a.consensus
+==&gt; "a?gc?"
+# shows IUPAC consensus
+a.consensus_iupac
+==&gt; "ahgcr"
+# iterates over each seq
+a.each { |x| p x }
+# ==&gt;
+#    "atgca"
+#    "aagca"
+#    "acgca"
+#    "acgcg"
+# iterates over each site
+a.each_site { |x| p x }
+# ==&gt;
+#    ["a", "a", "a", "a"]
+#    ["t", "a", "c", "c"]
+#    ["g", "g", "g", "g"]
+#    ["c", "c", "c", "c"]
+#    ["a", "a", "a", "g"]
+# doing alignment by using CLUSTAL W.
+# clustalw command must be installed.
+factory = Bio::ClustalW.new
+a2 = a.do_align(factory)</pre>
+<h2><a name="label-7" id="label-7">Restriction Enzymes (Bio::RE)</a></h2><!-- RDLabel: "Restriction Enzymes (Bio::RE)" -->
+<p>BioRuby has extensive support for restriction enzymes (REs). It contains a full
+library of commonly used REs (from REBASE) which can be used to cut single
+stranded RNA or dubbel stranded DNA into fragments. To list all enzymes:</p>
+<pre>rebase = Bio::RestrictionEnzyme.rebase
+rebase.each do |enzyme_name, info|
+  p enzyme_name
+end</pre>
+<p>and cut a sequence with an enzyme follow up with:</p>
+<pre>res = seq.cut_with_enzyme('EcoRII', {:max_permutations =&gt; 0},
+  {:view_ranges =&gt; true})
+if res.kind_of? Symbol #error
+   err = Err.find_by_code(res.to_s)
+   unless err
+     err = Err.new(:code =&gt; res.to_s)
+   end
+end
+res.each do |frag|
+   em = EnzymeMatch.new
+   em.p_left = frag.p_left
+   em.p_right = frag.p_right
+   em.c_left = frag.c_left
+   em.c_right = frag.c_right
+   em.err = nil
+   em.enzyme = ar_enz
+   em.sequence = ar_seq
+   p em
+ end</pre>
+<h2><a name="label-8" id="label-8">Sequence homology search by using the FASTA program (Bio::Fasta)</a></h2><!-- RDLabel: "Sequence homology search by using the FASTA program (Bio::Fasta)" -->
+<p>Let's start with a query.pep file which contains a sequence in FASTA
+format.  In this example we are going to execute a homology search
+from a remote internet site or on your local machine. Note that you
+can use the ssearch program instead of fasta when you use them in your
+local machine.</p>
+<h3><a name="label-9" id="label-9">using FASTA in local machine</a></h3><!-- RDLabel: "using FASTA in local machine" -->
+<p>Install the fasta program on your machine (the command name looks like
+fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
+First, you must prepare your FASTA-formatted database sequence file
+target.pep and FASTA-formatted query.pep. </p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+# Creates FASTA factory object ("ssearch" instead of
+# "fasta34" can also work)
+factory = Bio::Fasta.local('fasta34', ARGV.pop)
+(EDITOR's NOTE: not consistent pop command)
+ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
+# Iterates over each entry. the variable "entry" is a
+# Bio::FastaFormat object:
+ff.each do |entry|
+  # shows definition line (begins with '&gt;') to the standard error output
+  $stderr.puts "Searching ... " + entry.definition
+  # executes homology search. Returns Bio::Fasta::Report object.
+  report = factory.query(entry)
+  # Iterates over each hit
+  report.each do |hit|
+    # If E-value is smaller than 0.0001
+    if hit.evalue &lt; 0.0001
+      # shows identifier of query and hit, E-value, start and
+      # end positions of homologous region
+      print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
+      p hit.lap_at
+    end
+  end
+end</pre>
+<p>We named above script as f_search.rb. You can execute as follows:</p>
+<pre>% ./f_search.rb query.pep target.pep &gt; f_search.out</pre>
+<p>In above script, the variable "factory" is a factory object for executing
+FASTA many times easily. Instead of using Fasta#query method,
+Bio::Sequence#fasta method can be used.</p>
+<pre>seq = "&gt;test seq\nYQVLEEIGRGSFGSVRKVIHIPTKKLLVRKDIKYGHMNSKE"
+seq.fasta(factory)</pre>
+<p>When you want to add options to FASTA command, you can set the
+third argument of Bio::Fasta.local method. For example, setting ktup to 1
+and getting top-10 hits:</p>
+<pre>factory = Bio::Fasta.local('fasta34', 'target.pep', '-b 10')
+factory.ktup = 1</pre>
+<p>Bio::Fasta#query returns Bio::Fasta::Report object.
+We can get almost all information described in FASTA report text
+with the Report object. For example, getting information for hits:</p>
+<pre>report.each do |hit|
+  puts hit.evalue           # E-value
+  puts hit.sw               # Smith-Waterman score (*)
+  puts hit.identity         # % identity
+  puts hit.overlap          # length of overlapping region
+  puts hit.query_id         # identifier of query sequence
+  puts hit.query_def        # definition(comment line) of query sequence
+  puts hit.query_len        # length of query sequence
+  puts hit.query_seq        # sequence of homologous region
+  puts hit.target_id        # identifier of hit sequence
+  puts hit.target_def       # definition(comment line) of hit sequence
+  puts hit.target_len       # length of hit sequence
+  puts hit.target_seq       # hit of homologous region of hit sequence
+  puts hit.query_start      # start position of homologous
+                            # region in query sequence
+  puts hit.query_end        # end position of homologous region
+                            # in query sequence
+  puts hit.target_start     # start posiotion of homologous region
+                            # in hit(target) sequence
+  puts hit.target_end       # end position of homologous region
+                            # in hit(target) sequence
+  puts hit.lap_at           # array of above four numbers
+end</pre>
+<p>Most of above methods are common with the Bio::Blast::Report described
+below. Please refer to document of Bio::Fasta::Report class for
+FASTA-specific details.</p>
+<p>If you need original output text of FASTA program you can use the "output"
+method of the factory object after the "query" method.</p>
+<pre>report = factory.query(entry)
+puts factory.output</pre>
+<h3><a name="label-10" id="label-10">using FASTA from a remote internet site</a></h3><!-- RDLabel: "using FASTA from a remote internet site" -->
+<ul>
+<li>Note: Currently, only GenomeNet (fasta.genome.jp) is</li>
+</ul>
+<p>supported. check the class documentation for updates.</p>
+<p>For accessing a remote site the Bio::Fasta.remote method is used
+instead of Bio::Fasta.local.  When using a remote method, the
+databases available may be limited, but, otherwise, you can do the
+same things as with a local method.</p>
+<p>Available databases in GenomeNet:</p>
+<ul>
+<li>Protein database
+<ul>
+<li>nr-aa, genes, vgenes.pep, swissprot, swissprot-upd, pir, prf, pdbstr</li>
+</ul></li>
+<li>Nucleic acid database
+<ul>
+<li>nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss, htgs, dbsts,
+      embl-nonst, embnonst-upd, genes-nt, genome, vgenes.nuc</li>
+</ul></li>
+</ul>
+<p>Select the databases you require.  Next, give the search program from
+the type of query sequence and database.</p>
+<ul>
+<li>When query is a amino acid sequence
+<ul>
+<li>When protein database, program is "fasta".</li>
+<li>When nucleic database, program is "tfasta".</li>
+</ul></li>
+<li>When query is a nucleic acid sequence
+<ul>
+<li>When nucleic database, program is "fasta".</li>
+<li>(When protein database, you would fail to search.)</li>
+</ul></li>
+</ul>
+<p>For example:</p>
+<pre>program = 'fasta'
+database = 'genes'
+factory = Bio::Fasta.remote(program, database)</pre>
+<p>and try out the same commands as with the local search shown earlier.</p>
+<h2><a name="label-11" id="label-11">Homology search by using BLAST (Bio::Blast class)</a></h2><!-- RDLabel: "Homology search by using BLAST (Bio::Blast class)" -->
+<p>The BLAST interface is very similar to that of FASTA and
+both local and remote execution are supported. Basically
+replace above examples Bio::Fasta with Bio::Blast!</p>
+<p>For example the BLAST version of f_search.rb is:</p>
+<pre># create BLAST factory object
+factory = Bio::Blast.local('blastp', ARGV.pop)</pre>
+<p>For remote execution of BLAST in GenomeNet, Bio::Blast.remote is used.
+The parameter "program" is different from FASTA - as you can expect:</p>
+<ul>
+<li>When query is a amino acid sequence
+<ul>
+<li>When protein database, program is "blastp".</li>
+<li>When nucleic database, program is "tblastn".</li>
+</ul></li>
+<li>When query is a nucleic acid sequence
+<ul>
+<li>When protein database, program is "blastx"</li>
+<li>When nucleic database, program is "blastn".</li>
+<li>("tblastx" for six-frame search.)</li>
+</ul></li>
+</ul>
+<p>Bio::BLAST uses "-m 7" XML output of BLAST by default when either
+XMLParser or REXML (both of them are XML parser libraries for Ruby -
+of the two XMLParser is the fastest) is installed on your computer. In
+Ruby version 1.8.0, or later, REXML is bundled with Ruby's
+distribution.</p>
+<p>When no XML parser library is present, Bio::BLAST uses "-m 8" tabular
+deliminated format. Available information is limited with the
+"-m 8" format so installing an XML parser is recommended.</p>
+<p>Again, the methods in Bio::Fasta::Report and Bio::Blast::Report (and
+Bio::Fasta::Report::Hit and Bio::Blast::Report::Hit) are similar.
+There are some additional BLAST methods, for example, bit_score and
+midline.</p>
+<pre>report.each do |hit|
+  puts hit.bit_score
+  puts hit.query_seq
+  puts hit.midline
+  puts hit.target_seq
+  puts hit.evalue
+  puts hit.identity
+  puts hit.overlap
+  puts hit.query_id
+  puts hit.query_def
+  puts hit.query_len
+  puts hit.target_id
+  puts hit.target_def
+  puts hit.target_len
+  puts hit.query_start
+  puts hit.query_end
+  puts hit.target_start
+  puts hit.target_end
+  puts hit.lap_at
+end</pre>
+<p>For simplicity and API compatibility, some information such as score
+are extracted from the first Hsp (High-scoring Segment Pair).</p>
+<p>Check the documentation for Bio::Blast::Report to see what can be
+retrieved. For now suffice to state that Bio::Blast::Report has a
+hierarchical structure mirroring the general BLAST output stream:</p>
+<ul>
+<li>In a Bio::Blast::Report object, @iteratinos is an array of
+    Bio::Blast::Report::Iteration objects.
+<ul>
+<li>In a Bio::Blast::Report::Iteration object, @hits is an array of
+      Bio::Blast::Report::Hits objects.
+<ul>
+<li>In a Bio::Blast::Report::Hits object, @hsps is an array of
+        Bio::Blast::Report::Hsp objects.</li>
+</ul></li>
+</ul></li>
+</ul>
+<p>See bio/appl/blast.rb and bio/appl/blast/*.rb for more information.</p>
+<h3><a name="label-12" id="label-12">Parsing existing BLAST output files</a></h3><!-- RDLabel: "Parsing existing BLAST output files" -->
+<p>When you already have BLAST output files and you want to parse them,
+you can directly create Bio::Blast::Report objects without the
+Bio::Blast factory object. For this purpose use Bio::Blast.reports,
+which supports the "-m 0" default and "-m 7" XML type output format.</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+# Iterates over each XML result.
+# The variable "report" is a Bio::Blast::Report object.
+Bio::Blast.reports(ARGF) do |report|
+  puts "Hits for " + report.query_def + " against " + report.db
+  report.each do |hit|
+    print hit.target_id, "\t", hit.evalue, "\n" if hit.evalue &lt; 0.001
+  end
+end</pre>
+<p>Save the script as hits_under_0.001.rb and to process BLAST output
+files *.xml, you can</p>
+<pre>% ruby hits_under_0.001.rb *.xml</pre>
+<p>Sometimes BLAST XML output may be wrong and can not be parsed. We
+recommended to install BLAST 2.2.5 or later, and try combinations of
+the -D and -m options when you encounter problems.</p>
+<h3><a name="label-13" id="label-13">Add remote BLAST search sites</a></h3><!-- RDLabel: "Add remote BLAST search sites" -->
+<pre>Note: this section is an advanced topic</pre>
+<p>Here a more advanced application for using BLAST sequence homology
+search services. BioRuby currently only supports GenomeNet. If you
+want to add other sites, you must write the following:</p>
+<ul>
+<li>the calling CGI (command-line options must be processed for the site).</li>
+<li>make sure you get BLAST output text as supported format by BioRuby
+    (e.g. "-m 8", "-m 7" or default("-m 0")).</li>
+</ul>
+<p>In addition, you must write a private class method in Bio::Blast
+named "exec_MYSITE" to get query sequence and to pass the result to
+Bio::Blast::Report.new(or Bio::Blast::Default::Report.new):</p>
+<pre>factory = Bio::Blast.remote(program, db, option, 'MYSITE')</pre>
+<p>When you write above routines, please send to the BioRuby project and
+they may be included.</p>
+<h2><a name="label-14" id="label-14">Generate a reference list using PubMed (Bio::PubMed)</a></h2><!-- RDLabel: "Generate a reference list using PubMed (Bio::PubMed)" -->
+<p>Below script is an example which seaches PubMed and creates a reference list.</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+ARGV.each do |id|
+  entry = Bio::PubMed.query(id)     # searches PubMed and get entry
+  medline = Bio::MEDLINE.new(entry) # creates Bio::MEDLINE object from entry text
+  reference = medline.reference     # converts into Bio::Reference object
+  puts reference.bibtex             # shows BibTeX formatted text
+end</pre>
+<p>We named the script pmfetch.rb.</p>
+<pre>% ./pmfetch.rb 11024183 10592278 10592173</pre>
+<p>To give some PubMed ID (PMID) in arguments, the script retrieves informations
+from NCBI, parses MEDLINE format text, converts into BibTeX format and
+shows them.</p>
+<p>A keyword search is also available.</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+# Concatinates argument keyword list to a string
+keywords = ARGV.join(' ')
+# PubMed keyword search
+entries = Bio::PubMed.search(keywords)
+entries.each do |entry|
+  medline = Bio::MEDLINE.new(entry) # creates Bio::MEDLINE object from text
+  reference = medline.reference     # converts into Bio::Reference object
+  puts reference.bibtex             # shows BibTeX format text
+end</pre>
+<p>We named the script pmsearch.rb.</p>
+<pre>% ./pmsearch.rb genome bioinformatics</pre>
+<p>To give keywords in arguments, the script searches PubMed by given
+keywords and shows bibliography informations in a BibTex format. Other
+output formats are also avaialble like the bibitem method described
+below. Some journal formats like nature and nar can be used, but lack
+bold and italic font output.</p>
+<p>(EDITORs NOTE: do we have some simple object that can be queried for
+author, title etc.?)</p>
+<p>Nowadays using NCBI E-Utils is recommended. Use Bio::PubMed.esearch
+and Bio::PubMed.efetch instead of above methods.</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+keywords = ARGV.join(' ')
+options = {
+  'maxdate' =&gt; '2003/05/31',
+  'retmax' =&gt; 1000,
+}
+entries = Bio::PubMed.esearch(keywords, options)
+Bio::PubMed.efetch(entries).each do |entry|
+  medline = Bio::MEDLINE.new(entry)
+  reference = medline.reference
+  puts reference.bibtex
+end</pre>
+<p>The script works same as pmsearch.rb. But, by using NCBI E-Utils, more
+options are available. For example published dates to search and
+maximum number of hits to show results can be specified.</p>
+<p>See the <a href="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html">help page of
+E-Utils</a>
+for more details.</p>
+<h3><a name="label-15" id="label-15">More about BibTeX</a></h3><!-- RDLabel: "More about BibTeX" -->
+<p>In this section, we explain the simple usage of TeX for the BibTeX format
+bibliography list collected by above scripts. For example, to save
+BibTeX format bibliography data to a file named genoinfo.bib.</p>
+<pre>% ./pmfetch.rb 10592173 &gt;&gt; genoinfo.bib
+% ./pmsearch.rb genome bioinformatics &gt;&gt; genoinfo.bib</pre>
+<p>The BibTeX can be used with Tex or LaTeX to form bibliography
+information with your journal article. For more information
+on BibTex see (EDITORS NOTE: insert URL). A quick example:</p>
+<p>Save this to hoge.tex:</p>
+<pre>\documentclass{jarticle}
+\begin{document}
+\bibliographystyle{plain}
+foo bar KEGG database~\cite{PMID:10592173} baz hoge fuga.
+\bibliography{genoinfo}
+\end{document}</pre>
+<p>Then,</p>
+<pre>% latex hoge
+% bibtex hoge # processes genoinfo.bib
+% latex hoge  # creates bibliography list
+% latex hoge  # inserts correct bibliography reference</pre>
+<p>Now, you get hoge.dvi and hoge.ps - the latter you can view any
+Postscript viewer.</p>
+<h3><a name="label-16" id="label-16">Bio::Reference#bibitem</a></h3><!-- RDLabel: "Bio::Reference#bibitem" -->
+<p>When you don't want to create a bib file, you can use
+Bio::Reference#bibitem method instead of Bio::Reference#bibtex.
+In above pmfetch.rb and pmsearch.rb scripts, change</p>
+<pre>puts reference.bibtex</pre>
+<p>to</p>
+<pre>puts reference.bibitem</pre>
+<p>Output documents should be bundled in \begin{thebibliography}
+and \end{thebibliography}. Save the following to hoge.tex</p>
+<pre>\documentclass{jarticle}
+\begin{document}
+foo bar KEGG database~\cite{PMID:10592173} baz hoge fuga.
+\begin{thebibliography}{00}
+\bibitem{PMID:10592173}
+Kanehisa, M., Goto, S.
+KEGG: kyoto encyclopedia of genes and genomes.,
+{\em Nucleic Acids Res}, 28(1):27--30, 2000.
+\end{thebibliography}
+\end{document}</pre>
+<p>and run</p>
+<pre>% latex hoge   # creates bibliography list
+% latex hoge   # inserts corrent bibliography reference</pre>
+<h1><a name="label-17" id="label-17">OBDA</a></h1><!-- RDLabel: "OBDA" -->
+<p>OBDA (Open Bio Database Access) is a standardized method of sequence
+database access developed by the Open Bioinformatics Foundation.  It
+was created during the BioHackathon by BioPerl, BioJava, BioPython,
+BioRuby and other projects' members (2002).</p>
+<ul>
+<li>BioRegistry (Directory)
+<ul>
+<li>Mechanism to specify how and where to retrieve sequence data for each database.</li>
+</ul></li>
+<li>BioFlat
+<ul>
+<li>Flatfile indexing by using binary tree or BDB(Berkeley DB).</li>
+</ul></li>
+<li>BioFetch
+<ul>
+<li>Server-client model for getting entry from database via http.</li>
+</ul></li>
+<li>BioSQL
+<ul>
+<li>Schemas to store sequence data to relational database such as
+    MySQL and PostgreSQL, and methods to retrieve entries from the database.</li>
+</ul></li>
+</ul>
+<p>Here we give a quick overview. Check out
+<a href="http://obda.open-bio.org/">&lt;URL:http://obda.open-bio.org/&gt;</a> for more extensive details.</p>
+<p>The specification is stored on CVS repository at cvs.open-bio.org,
+also available via http from:
+<a href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/obda-specs/?cvsroot=obf-common">&lt;URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/obda-specs/?cvsroot=obf-common&gt;</a></p>
+<h2><a name="label-18" id="label-18">BioRegistry</a></h2><!-- RDLabel: "BioRegistry" -->
+<p>BioRegistry allows for locating retrieval methods and database
+locations through configuration files.  The priorities are</p>
+<ul>
+<li>The file specified with method's parameter</li>
+<li>~/.bioinformatics/seqdatabase.ini</li>
+<li>/etc/bioinformatics/seqdatabase.ini</li>
+<li>http://www.open-bio.org/registry/seqdatabase.ini</li>
+</ul>
+<p>Note that the last locaation refers to www.open-bio.org and is only used
+when all local configulation files are not available.</p>
+<p>In the current BioRuby implementation all local configulation files
+are read. For databases with the same name settings encountered first
+are used. This means that if you don't like some settings of a
+database in system global configuration file
+(/etc/bioinformatics/seqdatabase.ini), you can easily override it by
+writing settings to ~/.bioinformatics/seqdatabase.ini.</p>
+<p>The syntax of the configuration file is called a stanza format. For example</p>
+<pre>[DatabaseName]
+protocol=ProtocolName
+location=ServeName</pre>
+<p>You can write a description like above entry for every database.</p>
+<p>The database name is a local label for yourself, so you can name it
+freely and it can differ from the name of the actual databases. In the
+actual specification of BioRegistry where there are two or more
+settings for a database of the same name, it is proposed that
+connection to the database is tried sequentially with the order
+written in configuration files. However, this has not (yet) been
+implemented in BioRuby.</p>
+<p>In addition, for some protocol, you must set additional options
+other than locations (e.g. user name of MySQL). In the BioRegistory
+specification, current available protocols are:</p>
+<ul>
+<li>index-flat</li>
+<li>index-berkeleydb</li>
+<li>biofetch</li>
+<li>biosql</li>
+<li>bsane-corba</li>
+<li>xembl</li>
+</ul>
+<p>In BioRuby, you can use index-flat, index-berkleydb, biofetch and biosql.
+Note that the BioRegistry specification sometimes gets updated and BioRuby
+does not always follow quickly.</p>
+<p>Here an example. Create a Bio::Registry object. It reads the configuration
+files:</p>
+<pre>reg = Bio::Registry.new
+# connects to the database "genbank"
+serv = reg.get_database('genbank')
+# gets entry of the ID
+entry = serv.get_by_id('AA2CG')</pre>
+<p>The variable "serv" is a server object corresponding to the setting
+written in configuration files. The class of the object is one of
+Bio::SQL, Bio::Fetch, and so on. Note that Bio::Registry#get_database("name")
+returns nil if no database is found.</p>
+<p>After that, you can use get_by_id method and some specific methods.
+Please refer to below documents.</p>
+<h2><a name="label-19" id="label-19">BioFlat</a></h2><!-- RDLabel: "BioFlat" -->
+<p>BioFlat is a mechanism to create index files of flat files and to retrieve
+these entries fast. There are two index types. index-flat is a simple index
+performing binary search without using an external library of Ruby. index-berkeleydb
+uses Berkeley DB for indexing - but requires installing bdb on your computer,
+as well as the BDB Ruby package. For creating the index itself, you can use
+br_bioflat.rb command bundled with BioRuby.</p>
+<pre>% br_bioflat.rb --makeindex database_name [--format data_format] filename...</pre>
+<p>The format can be omitted because BioRuby has autodetection.  If that
+does not work you can try specifying data format as a name of BioRuby
+database class.</p>
+<p>Search and retrieve data from database:</p>
+<pre>% br_bioflat.rb database_name identifier</pre>
+<p>For example, to create index of GenBank files gbbct*.seq and get entry
+from the database:</p>
+<pre>% br_bioflat.rb --makeindex my_bctdb --format GenBank gbbct*.seq
+% br_bioflat.rb my_bctdb A16STM262</pre>
+<p>If you have Berkeley DB on your system and installed the bdb extension
+module of Ruby (see http://raa.ruby-lang.org/project/bdb/), you can
+create and search indexes with Berkeley DB - a very fast alternative
+that uses little computer memory. When creating the index, use the
+"--makeindex-bdb" option instead of "--makeindex".</p>
+<pre>% br_bioflat.rb --makeindex-bdb database_name [--format data_format] filename...</pre>
+<h2><a name="label-20" id="label-20">BioFetch</a></h2><!-- RDLabel: "BioFetch" -->
+<pre>Note: this section is an advanced topic</pre>
+<p>BioFetch is a database retrieval mechanism via CGI.  CGI Parameters,
+options and error codes are standardized.  There client access via
+http is possible giving the database name, identifiers and format to
+retrieve entries.</p>
+<p>The BioRuby project has a BioFetch server in bioruby.org. It uses
+GenomeNet's DBGET system as a backend. The source code of the
+server is in sample/ directory. Currently, there are only two
+BioFetch servers in the world: bioruby.org and EBI.</p>
+<p>Here are some methods to retrieve entries from our BioFetch server.</p>
+<ol>
+<li><p>Using a web browser</p>
+<pre>http://bioruby.org/cgi-bin/biofetch.rb</pre></li>
+<li><p>Using the br_biofetch.rb command</p>
+<pre>% br_biofetch.rb db_name entry_id</pre></li>
+<li><p>Directly using Bio::Fetch in a script</p>
+<pre>serv = Bio::Fetch.new(server_url)
+entry = serv.fetch(db_name, entry_id)</pre></li>
+<li><p>Indirectly using Bio::Fetch via BioRegistry in script</p>
+<pre>reg = Bio::Registry.new
+serv = reg.get_database('genbank')
+entry = serv.get_by_id('AA2CG')</pre></li>
+</ol>
+<p>If you want to use (4), you, obviously, have to include some settings
+in seqdatabase.ini. E.g.</p>
+<pre>[genbank]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+biodbname=genbank</pre>
+<h3><a name="label-21" id="label-21">The combination of BioFetch, Bio::KEGG::GENES and Bio::AAindex1</a></h3><!-- RDLabel: "The combination of BioFetch, Bio::KEGG::GENES and Bio::AAindex1" -->
+<p>Bioinformatics is often about glueing things together. Here we give an
+example to get the bacteriorhodopsin gene (VNG1467G) of the archaea
+Halobacterium from KEGG GENES database and to get alpha-helix index
+data (BURA740101) from the AAindex (Amino acid indices and similarity
+matrices) database, and show the helix score for each 15-aa length
+overlapping window.</p>
+<pre>#!/usr/bin/env ruby
+require 'bio'
+entry = Bio::Fetch.query('hal', 'VNG1467G')
+aaseq = Bio::KEGG::GENES.new(entry).aaseq
+entry = Bio::Fetch.query('aax1', 'BURA740101')
+helix = Bio::AAindex1.new(entry).index
+position = 1
+win_size = 15
+aaseq.window_search(win_size) do |subseq|
+  score = subseq.total(helix)
+  puts [ position, score ].join("\t")
+  position += 1
+end</pre>
+<p>The special method Bio::Fetch.query uses preset BioFetch server
+in bioruby.org. (The server internally get data from GenomeNet.
+Because the KEGG/GENES database and AAindex database are not available
+from other BioFetch servers, we used bioruby.org server with
+Bio::Fetch.query method.)</p>
+<h2><a name="label-22" id="label-22">BioSQL</a></h2><!-- RDLabel: "BioSQL" -->
+<p>to be written...</p>
+<h2><a name="label-23" id="label-23">The BioRuby example programs</a></h2><!-- RDLabel: "The BioRuby example programs" -->
+<p>Some sample programs are stored in ./samples/ directory. Run for example:</p>
+<pre>./sample/na2aa.rb test/data/fasta/example1.txt </pre>
+<h2><a name="label-24" id="label-24">Unit testing and doctests</a></h2><!-- RDLabel: "Unit testing and doctests" -->
+<p>BioRuby comes with an extensive testing framework with over 1300 tests and 2700
+assertions. To run the unit tests:</p>
+<pre>cd test
+ruby runner.rb</pre>
+<p>We have also started with doctest for Ruby. We are porting the examples
+in this tutorial to doctest - more info upcoming.</p>
+<h2><a name="label-25" id="label-25">Further reading</a></h2><!-- RDLabel: "Further reading" -->
+<p>See the BioRuby in anger Wiki.  A lot of BioRuby's documentation exists in the
+source code and unit tests. To really dive in you will need the latest source
+code tree. The embedded rdoc documentation can be viewed online at
+<a href="http://bioruby.org/rdoc/">&lt;URL:http://bioruby.org/rdoc/&gt;</a>.</p>
+<h2><a name="label-26" id="label-26">BioRuby Shell</a></h2><!-- RDLabel: "BioRuby Shell" -->
+<p>The BioRuby shell implementation you find in ./lib/bio/shell. It is very interesting
+as it uses IRB (the Ruby intepreter) which is a powerful environment described in
+<a href="http://ruby-doc.org/docs/ProgrammingRuby/html/irb.html">Programming Ruby's irb chapter</a>. IRB commands can directly be typed in the shell, e.g.</p>
+<pre>bioruby!&gt; IRB.conf[:PROMPT_MODE]
+==!&gt; :PROMPT_C</pre>
+<p>optionally you also may want to install the optional Ruby readline support -
+with Debian libreadline-ruby. To edit a previous line you may have to press
+line down (arrow down) first.</p>
+<h1><a name="label-27" id="label-27">Helpful tools</a></h1><!-- RDLabel: "Helpful tools" -->
+<p>Apart from rdoc you may also want to use rtags - which allows jumping around
+source code by clicking on class and method names. </p>
+<pre>cd bioruby/lib
+rtags -R --vi</pre>
+<p>For a tutorial see <a href="http://rtags.rubyforge.org/">&lt;URL:http://rtags.rubyforge.org/&gt;</a></p>
+<h1><a name="label-28" id="label-28">APPENDIX</a></h1><!-- RDLabel: "APPENDIX" -->
+<h2><a name="label-29" id="label-29">KEGG API</a></h2><!-- RDLabel: "KEGG API" -->
+<p>Please refer to KEGG_API.rd.ja (English version: <a href="http://www.genome.jp/kegg/soap/doc/keggapi_manual.html">&lt;URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html&gt;</a> ) and</p>
+<ul>
+<li><a href="http://www.genome.jp/kegg/soap/">&lt;URL:http://www.genome.jp/kegg/soap/&gt;</a></li>
+</ul>
+<h2><a name="label-30" id="label-30">Comparing BioProjects</a></h2><!-- RDLabel: "Comparing BioProjects" -->
+<p>For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see <a href="http://sciruby.codeforpeople.com/sr.cgi/BioProjects">&lt;URL:http://sciruby.codeforpeople.com/sr.cgi/BioProjects&gt;</a></p>
+<h2><a name="label-31" id="label-31">Using BioRuby with R</a></h2><!-- RDLabel: "Using BioRuby with R" -->
+<p>Using Ruby with R Pjotr wrote a section on SciRuby. See <a href="http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang">&lt;URL:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang&gt;</a></p>
+<h2><a name="label-32" id="label-32">Using BioPerl or BioPython from Ruby</a></h2><!-- RDLabel: "Using BioPerl or BioPython from Ruby" -->
+<p>At the moment there is no easy way of accessing BioPerl from Ruby. The best way, perhaps, is to create a Perl server that gets accessed through XML/RPC or SOAP.</p>
+<h2><a name="label-33" id="label-33">Installing required external library</a></h2><!-- RDLabel: "Installing required external library" -->
+<p>At this point for using BioRuby no additional libraries are needed.
+This may change, so keep an eye on the Bioruby website. Also when
+a package is missing BioRuby should show an informative message.</p>
+<p>At this point installing third party Ruby packages can be a bit
+painful, as the gem standard for packages evolved late and some still
+force you to copy things by hand. Therefore read the README's
+carefully that come with each package.</p>
+<h2><a name="label-34" id="label-34">Trouble shooting</a></h2><!-- RDLabel: "Trouble shooting" -->
+<ul>
+<li>Error: in `require': no such file to load -- bio (LoadError)</li>
+</ul>
+<p>Ruby fails to find the BioRuby libraries - add it to the RUBYLIB path, or pass
+it to the interpeter. For example:</p>
+<pre>ruby -I~/cvs/bioruby/lib yourprogram.rb</pre>
+<h2><a name="label-35" id="label-35">Modifying this page</a></h2><!-- RDLabel: "Modifying this page" -->
+<p>IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
+repository. Please edit the file there otherwise changes may get
+lost. See <!-- Reference, RDLabel "BioRuby Developer Information" doesn't exist --><em class="label-not-found">BioRuby Developer Information</em><!-- Reference end --> for CVS and mailing list
+access.</p>
+</body>
+</html>