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xml2html.rb
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xml2html.rb
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#!/usr/bin/env ruby
require_relative 'citation'
require 'date'
def expand_macro(text)
["Gene","Species","Program"].each do |w|
text = text.gsub(/\\#{w}\{([^\}]*)\}/,"<i>\\1</i>")
end
return text
end
def expand_author(author)
return author.gsub(/(et\. al)\.$/,"<i>\\1</i>.")
end
journalnames = [
"Nature Genetics",
"Nature",
"Nature Biotechnology",
"Nature Communications",
"Science",
"Genome Research",
"Genome Biology",
"Nucl. Acids Res.",
"Bioinformatics",
"PLOS one",
"Gene",
"Genetics",
"Plant Biology",
"Plant Molecular Biology",
"Journal of Plant Physiology",
"Molecular Plant Pathology",
"Rice",
"The Plant Cell",
"The Plant Journal",
"Front Plant Sci.",
"Genomics",
"BMC Genomics",
"BMC Genetics",
"BMC Plant Biology",
"BMC Bioinformatics",
"Animal Genetics",
"Current Bioinformatics",
"Database--the journal of biological databases and curation",
"Microbial Cell Factories",
"Molecular Genetics and Genomics",
"Philos Trans A Math Phys Eng Sci.",
"International Journal of Genomics"]
journalrank = Hash.new()
journalnames.each_with_index do |name,idx|
journalrank[name] = idx
end
def compare_rank(a,b,journalrank)
if not journalrank.has_key?(a.journal)
STDERR.puts "rank of \"#{a.journal}\" not defined"
exit 1
end
if not journalrank.has_key?(b.journal)
STDERR.puts "rank of \"#{b.journal}\" not defined"
exit 1
end
ra = journalrank[a.journal]
rb = journalrank[b.journal]
if ra < rb
return -1
elsif ra > rb
return 1
elsif a.year < b.year
return 1
elsif a.year > b.year
return -1
else
return 0
end
end
puts <<'HEADER'
<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!--http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd-->
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>GenomeThreader Gene Prediction Software</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="description" content="The GenomeThreader gene prediction software computes gene structure predictions using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments." />
<meta name="keywords" content="gene structure prediction, gene prediction, cDNA alignment, EST alignment, protein alignment, cDNA mapping, EST mapping, protein mapping, spliced alignment, consensus spliced alignment, genome annotation, bioinformatics, computational biology" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body>
<h1><i>GenomeThreader</i> Gene Prediction Software</h1>
<div id="trialbox">
<ul>
<li><a href="download.html">Download <i>GenomeThreader</i>!</a></li>
</ul>
</div>
<p>
<i>GenomeThreader</i> is a software tool to compute gene structure predictions.
The gene structure predictions are calculated using a similarity-based approach
where additional cDNA/EST and/or protein sequences are used to predict gene
structures via spliced alignments.
<i>GenomeThreader</i> was motivated by disabling limitations in
<a href="http://bioinformatics.iastate.edu/cgi-bin/gs.cgi">
<i>GeneSeqer</i></a>, a popular gene prediction program which is widely used
for plant genome annotation.
</p>
<h2>Features</h2>
<ul>
<li>
Intron Cutout Technique: <br/>
The intron cutout technique allows to overcome the time and space
limitations of the dynamic programming (DP) algorithms used in
<a href="http://bioinformatics.iastate.edu/cgi-bin/gs.cgi"><i>GeneSeqer</i></a>,
in particular, when applied to organisms containing long introns.
</li>
<li>
Baysian Splice Site Models (BSSMs): <br/>
With BSSMs it is possible to assign probabilities to GT donor, GC donor,
and AG acceptor sites. This information is used in the DP to get the exact
exon/intron boundaries right.
</li>
<li>
Combination of cDNA/EST Based Spliced Alignments with Protein Based Spliced
Alignments: <br/>
After (spliced) aligning the supplied cDNAs/ESTs and protein sequences onto
the genomic template, <i>GenomeThreader</i> computes consensus spliced
alignments. Consensus spliced alignments combine several spliced alignments
to resolve the complete gene structure and to uncover alternative splicing.
</li>
<li>
Incremental Updates: <br/>
When the used cDNA/EST or protein database is updated, a common approach
was to redo the complete mapping. With <i>GenomeThreader</i>, you can combine
newly computed spliced alignments with precomputed spliced alignments to
quickly recompute consensus spliced alignments.
</li>
<li>
XML: <br/>
The additional <i>GenomeThreader</i> XML output conforms to our gthXML
standard <a href="GenomeThreader.rng.txt">GenomeThreader.rng.txt</a>. With
the included script XML2GFF.py, it is possible to convert gthXML output to the
<a href="http://www.sanger.ac.uk/software/GFF">GFF</a> format.
A variety of gthXML-specific tools can be found
<a href="http://brendelgroup.org/mespar1/gthxml/">here</a>.
</li>
<li>
gthDB: <br/>
We also <a href="http://brendelgroup.org/mespar1/gthxml/">provide</a>
a schema and load script for gthDB, which permits storage
and query of <i>GenomeThreader</i> output in a relational format.
</li>
</ul>
<p>
References have been omitted for brevity; you can find them and more details on
the implementation in the <i>GenomeThreader</i>
<a href="doc/GreBreSpaKur2005.pdf">paper</a>.
How to take advantage of these features and many more is described in depth in
the <i>GenomeThreader</i> <a href="doc/gthmanual.pdf">manual</a>.
Please consult the <a href="faq.html">FAQ</a> page for frequently asked
questions.
All mentioned files and scripts are also part of the <i>GenomeThreader</i>
distribution (see below).
</p>
<h2>Availability</h2>
<p>
<i>GenomeThreader</i> is available free of charge.
You can <a href="download.html">download</a> a copy.
</p>
<h2>Examples</h2>
<ul>
<li>
Evaluation <a href="gthcases/softeng.html">cases</a> described in Gremme et
al. 2005 (see below)
</li>
<li>
A 16.6Kb rice gene structure tractable with <i>GenomeThreader</i> (using
both an <a href="gthcases/biggene.gth.cut.txt">intron cutout</a> technique
and <a href="gthcases/biggene.gth.nocut.txt">without</a>), but beyond
<a href="gthcases/biggene.gsq.txt"><i>GeneSeqer</i></a>'s limitations.
</li>
<li>
A 125Kb intron-containing human
<a href="gthcases/bigintron.gth.txt">gene structure</a>.
</li>
<li>
Small samples of gzip'ed
<a href="gthcases/small_demo.gth.out.gz">plain text</a> and
<a href="gthcases/small_demo.gthxml.out.gz">XML</a>
GenomeThreader output.
</li>
</ul>
<h2>Users</h2>
<p>
The following sites use <i>GenomeThreader</i>. This list is not intended to be
comprehensive.
</p>
<ul>
<li>
MIPS (Munich Information Center for Protein Sequences),
<a href="http://www.helmholtz-muenchen.de/en/ibis">Institute of Bioinformatics and
Systems Biology</a>
(for plant genome annotation)
</li>
<li>
<a href="http://www.cosmoss.org/">University of Freiburg,
Plant Biotechnology</a> (to annotate <i>Physcomitrella patens</i>)
</li>
<li>
<a href="http://www.plantgdb.org/">PlantGDB</a>
</li>
<li>
<a href="http://waksman.rutgers.edu/">Waksman Institute</a>, Rutgers
University
</li>
<li>
<a href="http://sgn.cornell.edu/">SOL Genomics Network (SGN)</a>, Cornell
University
</li>
<li>
<a href="http://bioinformatics.psb.ugent.be/">Bioinformatics and
evolutionary genomics division, VIB</a>, Gent University
</li>
</ul>
<h2>Citations</h2>
<p>
<a name="citations"></a>
Here are the most important publications citing <i>GenomeThreader</i> (sorted by Journal)
</p>
<ol>
HEADER
citation_list = Array.new()
citation_iterator("index.xml") do |citation|
citation_list.push(citation)
end
cite_stat = Hash.new() {0}
citation_list.sort {|a,b| compare_rank(a,b,journalrank)}.each do |citation|
puts "<li>"
puts " #{expand_author(citation.author)}"
puts " <a href=\"#{citation.url}\">"
puts " #{expand_macro(citation.title)}</a>,"
puts " <i>#{citation.journal}</i>"
print " <b>#{citation.volume}</b>"
if not citation.number.nil?
if citation.number.match(/^[0-9]*$/)
print "(#{citation.number})"
else
print " #{citation.number}"
end
end
if not citation.pages.nil?
print ":#{citation.pages}"
end
puts ", #{citation.year}."
puts "</li>"
cite_stat[citation.year] += 1
end
puts <<'FOOTER'
</ol>
<p>
If I missed a publication which cites <i>GenomeThreader</i>, please contact
<a href="mailto:gordon@gremme.org">me</a>.
</p>
<h2>Developers</h2>
<p>
<i>GenomeThreader</i> is being actively developed by the following individuals:
</p>
<ul>
<li>
<a href="http://gremme.org/">Gordon Gremme</a> (primary developer)
</li>
<li>
<a href="http://www.zbh.uni-hamburg.de/en/prof-dr-stefan-kurtz.html">Stefan Kurtz</a> (<a href="http://www.vmatch.de"><i>Vmatch</i></a>,
<a href="http://www.vmatch.de"><i>Mkvtree</i></a>, libkurtz)
</li>
<li>
<a href="http://brendelgroup.org/group/volker.php">Volker Brendel</a> (BSSMs, conceptual ideas)
</li>
<li>
<a href="http://brendelgroup.org/mespar1/">Michael E Sparks</a>
(BSSMs, gthXML, gthDB)
</li>
</ul>
<h2>Publications</h2>
<p>
Please cite the following article in publications about research using
<i>GenomeThreader</i>:
</p>
<ul>
<li>
G. Gremme, V. Brendel, M.E. Sparks, and S. Kurtz.
<a href="doc/GreBreSpaKur2005.pdf">Engineering a software tool for gene
structure prediction in higher organisms.</a> <i>Information and Software
Technology</i>, <b>47</b>(15):965-978, 2005
</li>
</ul>
<p>
For in-depth information about <i>GenomeThreader</i> please refer to the
following dissertation:
</p>
<ul>
<li>
G. Gremme. <a href="http://ediss.sub.uni-hamburg.de/volltexte/2013/6237/pdf/Dissertation.pdf">Computational Gene Structure Prediction.</a> Ph.D. thesis, University of Hamburg, 2012
</li>
</ul>
FOOTER
today = Date.today
puts <<FOOTER
<div id="footer">
Copyright © 2003-#{today.year} <a href="mailto:gordon@gremme.org">
Gordon Gremme</a>. Last update: #{today}
</div>
FOOTER
totalcitations = 0
cite_stat.sort.each do |k,v|
totalcitations += v
STDERR.puts "#{k}\t#{v}\t#{totalcitations}"
end