Mercurial > repos > jankanis > blast2html

changeset 22:efce16c98650

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rename blast2html
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 15 May 2014 10:48:09 +0200
parents 9596fea636bb
children 6995a6f34f3f
files blast2html.html.jinja blast2html.py blast_html.html.jinja blast_html.py
diffstat 4 files changed, 904 insertions(+), 904 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2html.html.jinja	Thu May 15 10:48:09 2014 +0200
@@ -0,0 +1,600 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="UTF-8">
+    <meta name=generator content="blast2html; see ...">
+    
+    <title>Blast output</title>
+    
+    <style>
+      body {
+      color: #333333;
+      font-family: Arial,Sans-Serif;
+      }
+
+      :link {
+      color: #336699;
+      }
+
+      .right {
+      float: right;
+      }
+
+      #content {
+      margin: 0 2em;
+      padding: 0.5em;
+      border: 1px solid #888888;
+      background-color: #d3dff5;
+      }
+
+      h1, h2, h3, h4, h5, h6 {
+      color: #2A6979;
+      font-family: arial,verdana,sans-serif;
+      letter-spacing: -1px;
+      margin: 1.2em 0 0.3em;
+      }
+
+      h1 {
+      border-bottom: 1px solid #CCCCCC;
+      font-size: 150%;
+      padding-bottom: 0.1em;
+      }
+
+      h2 {
+      font-size: 120%;
+      font-weight: bold;
+      }
+
+      h4.darkHeader {
+      color: #4D4D4D;
+      letter-spacing: 0;
+      font-weight: bold;
+      }
+
+      #nodata {
+      font-weight: bold;
+      }
+
+      .index {
+      margin-bottom: 3em;
+      }
+      .index div.indexentry {
+      margin: 1.2em 1.6em;
+      font-weight: bold;
+      font-size: 100%;
+      }
+      
+      .headerdata {
+      font-size: 90%;
+      }
+      .headerdata .param {
+      font-weight: bold;
+      text-align: right;
+      padding: 0 1em;
+      }
+
+      .grey {
+      background-color: #eeeeee;
+      border: 1px solid #cccccc;
+      padding: 1em;
+      }
+
+      .white {
+      background-color: white;
+      border: 1px solid #cccccc;
+      padding: 1.5em 2%;
+      }
+
+      .graphicrow {
+      clear: left;
+      width: 100%;
+      }
+
+      .graphicitem {
+      float: left;
+      }
+
+
+      
+      .graphics .grey {
+      text-align: center;
+      }
+
+      .graphic {
+      background-color: white;
+      border: 2px solid black;
+      padding: 1.5em;
+      margin: auto;
+      }
+
+      .centered, .defline, div.legend, div.tablewrapper {
+      margin-left: auto;
+      margin-right: auto;
+      }
+
+      .defline {
+      background-color: white;
+      border: 1px solid black;
+      margin: .5em auto;
+      padding-left: .2em;
+      padding-right: .2em;
+      max-width: 50em;
+      text-align: left;
+      height: 2.8em;
+      overflow-y: hidden;
+      }
+
+      div.legend {
+      max-width: 40em;
+      }
+      div.legend div {
+      width: 100%;
+      color: white;
+      font-weight: bold;
+      border-spacing: 0;
+      }
+      div.legend div .graphicitem {
+      width: 20%;
+      padding: 0;
+      margin: 0;
+      border: none;
+      }
+
+      div.tablewrapper {
+      width: 50%;
+      min-width: 60em;
+      }
+
+      /* For small widths we give the graphic 100% */
+      @media (max-width: 72.5em) {
+      div.tablewrapper {
+      width: 100%;
+      min-width: 0px;
+      }
+      }
+
+      .scale {
+      width: 100%;
+      margin: .5em 0;
+      font-weight: bold;
+      }
+      .scale div {
+      color: red;
+      text-align: left;
+      }
+      .scale .graphicrow {
+      margin: .5em 0 .5em 0;
+      color: white;
+      }
+      .scale .graphicitem {
+      position: relative;
+      }
+      .scale .graphicitem div {
+      margin: 0 1px;
+      padding: 0 2px;
+      text-align: right;
+      background-color: red;
+      color: white;
+      }
+      .scale .graphicitem:first-child div {
+      margin-left: 0px;
+      }
+      .scale .graphicitem:last-child div {
+      margin-right: 0px;
+      }
+      .scale .graphicitem .lastlabel {
+      position: absolute;
+      top: 0px;
+      left: 100%;
+      background-color: transparent;
+      color: red;
+      }
+
+      a.matchresult {
+      display: block;
+      margin: 0;
+      padding: 0;
+      }
+      div.matchrow {
+      margin-top: 4px;
+      }
+      div.matchrow, div.matchitem {
+      height: 4px;
+      }
+
+      
+      table.descriptiontable {
+      font-size: 85%;
+      border: 1px solid #97b0c8;
+      border-spacing: 0;
+      color: #222222;
+      line-height: 1.3em;
+      background-color: white;
+      }
+      table.descriptiontable col:first-child {
+      width: 100%;
+      }
+      table.descriptiontable tr:hover {
+      background-color: #D5DEE3;
+      }
+      table.descriptiontable th {
+      color: #14376C;
+      font-weight: normal;
+      background-color: #F0F0F0;
+      background: linear-gradient(#FFFFFF, #F0F0F0);
+      border-bottom: 1px solid #D4DFE9;
+      border-right: 1px solid #CFCFCF;
+      border-left: 0px solid black;
+      border-top: 0px solid black;
+      }
+      table.descriptiontable td {
+      overflow: hidden;
+      text-align: center;
+      padding: .4em .8em;
+      }
+      table.descriptiontable td div {
+      width: 1em;
+      overflow: visible;
+      white-space: nowrap;
+      text-align: left;
+      }
+
+
+      
+      .alignments .white {
+      padding: 1.5em 1em;
+      }
+      
+      .alignment {
+      border-top: 1px solid black;
+      padding-left: 1em;
+      padding-right: 1em;
+      }
+      
+      div.linkheader {
+      padding-top: .2em;
+      font-size: 85%;
+      color: #14376C;
+      }
+      div.linkheader a.linkheader {
+      margin-right: 1em;
+      }
+      div.linkheader .right a {
+      text-decoration: none;
+      }
+
+      .title .hittitle {
+      color: #222222;
+      margin-bottom: .3em;
+      }
+      .title .titleinfo {
+      font-size: 80%;
+      margin-top: 0;
+      margin-bottom: .3em;
+      }
+      .title .titleinfo .b {
+      color: #606060;
+      font-weight: bold;
+      font-size: 90%;
+      }
+
+      .moretitles {
+      margin: 1.2em;
+      }
+      .moretitles .titleinfo {
+      margin: 0;
+      padding: 0;
+      }
+      .moretitles .hittitle {
+      margin: .4em 0 .2em 0;
+      padding: 0;
+      }
+      
+      a.showmoretitles {
+      font-size: 75%;
+      color: #336699;
+      font-weight: bold;
+      margin-top: 0;
+      }
+      a.showmoretitles:hover {
+      }
+
+      .hotspot {
+      color: #606060;
+      font-family: verdana, arial, sans-serif;
+      margin-bottom: 2.5em;
+      }
+
+      .hotspot p.range {
+      font-size: 70%;
+      margin-top: 0;
+      margin-top: 1em;
+      margin-bottom: .2em;
+      }
+      .hotspot p.range span.range {
+      font-weight: bold;
+      }
+      .hotspot p.range a.range {
+      margin-left: .5em;
+      }
+
+      table.hotspotstable {
+      border-top: 1px solid;
+      border-bottom: 1px solid;
+      text-align: left;
+      border-collapse: collapse;
+      }
+      table.hotspotstable th, table.hotspotstable td {
+      padding: .1em 1em;
+      }
+      table.hotspotstable th {
+      font-size: 70%;
+      }
+      table.hotspotstable td {
+      min-width: 7em;
+      color: #222222;
+      font-size: 80%;
+      }
+
+      pre.alignmentgraphic {
+      color: #222222;
+      }
+
+      
+    </style>
+
+    <script type="text/javascript">
+      function toggle_visibility(id) {
+          var e = document.getElementById(id);
+          if(e.style.display != 'block')
+              e.style.display = 'block';
+          else
+              e.style.display = 'none';
+      }
+    </script>
+
+  </head>
+
+  
+  <body>
+    <div id=content>
+
+      {% if not blast.BlastOutput_iterations.findall('Iteration') %}
+      <section class=nodata>
+        <h1>No data</h1>
+        <div class=grey>
+          No matches
+        </div>
+      </section>
+
+      {% else %}
+
+      {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %}
+      <section class=index>
+        <h1>Queries</h1>
+
+        {% for result in blast.BlastOutput_iterations.Iteration %}
+        <div class=indexentry><a href="#match{{result['Iteration_iter-num']}}">
+            {% set hits = result|hits %}
+            {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}}
+            ({{result|len}} letters, {{hits|length}} hits)
+        </a></div>
+        {% endfor %}
+
+      </section>
+      {% endif %}
+
+      {% for result in blast.BlastOutput_iterations.Iteration %}
+      
+      <section class=match id=match{{result['Iteration_iter-num']}}>
+      
+        <h1>Nucleotide Sequence ({{result|len}} letters)</h1>
+
+        <section class=header>
+
+          <table class=headerdata>
+            {% for param, value in params %}
+              <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
+            {% endfor %}
+          </table>
+
+        </section>
+
+        {% set hits = result|hits %}
+        {% if not hits %}
+        <section>
+          <h2>No Hits</h2>
+          <div class=grey>
+            This query did not match anywhere
+          </div>
+        </section>
+        {% else %}
+
+        <section class=graphics>
+          <h2>Graphic Summary</h2>
+
+          <div class=grey>
+            <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3>
+
+            <div class=defline id=defline{{result['Iteration_iter-num']}}>
+              Mouse-over to show defline and scores, click to show alignments
+            </div>
+
+            <div class=graphic>
+              <h4 class=darkHeader>Color key for alignment scores</h4>
+              <div class=legend><div class=graphicrow>
+                  <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
+                  <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
+                  <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
+                  <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
+                  <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
+              </div></div>
+              <div style="clear: left"></div>
+
+              <div class=tablewrapper>
+
+                <div class=scale>
+                  <div>query:</div>
+                  <div class=graphicrow>
+                    <div>
+                      {% for s in result|queryscale %}
+                      <div class=graphicitem style="width: {{s.width}}%">
+                        {% if s.width > 3.0 %}
+                        <div>{{s.label}}</div>
+                        {% else %}
+                        <div>&nbsp;</div>
+                        <div class=lastlabel>{{s.label}}</div>
+                        {% endif %}
+                      </div>
+                      {% endfor %}
+                    </div>
+                  </div>
+                  <div style="clear: left"></div>
+                </div>
+
+                {% for line in result|match_colors %}
+                <a class=matchresult
+                   href="{{line.link}}"
+                   onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"'
+                   onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
+                   title="{{line.defline}}">
+                  <div class="matchrow graphicrow">
+                    {% for hit in line.colors %}
+                    <div class="matchitem graphicitem"
+                         style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div>
+                    {% endfor %}
+                  </div>
+                </a>
+
+                {% endfor %}
+              </div>
+            </div>
+          </div>
+        </section>
+
+
+
+        <section class=descriptions>
+          <h2>Descriptions</h2>
+
+          <div class=grey><div class=white>
+              <h4 class=darkHeader>Sequences producing significant alignments:</h4>
+
+              <table class=descriptiontable>
+                <col/><col/><col/><col/><col/><col/><col/>
+                <tr>
+                  <th>Description</th>
+                  <th>Max score</th>
+                  <th>Total score</th>
+                  <th>Query cover</th>
+                  <th>E value</th>
+                  <th>Ident</th>
+                  <th>Accession</th>
+                </tr>
+                {% for hit in result|hit_info %}
+                <tr>
+                  <td><div><a href="#hit{{hit.link_id}}"
+                              title="{{hit.title}}"
+                              id="description{{hit.link_id}}">
+                        {{hit.title}}
+                  </a></div></td>
+                  <td>{{hit.maxscore}}</td>
+                  <td>{{hit.totalscore}}</td>
+                  <td>{{hit.cover}}</td>
+                  <td>{{hit.e_value}}</td>
+                  <td>{{hit.ident}}</td>
+                  <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
+                </tr>
+                {% endfor %}
+              </table>
+
+          </div></div>
+        </section>
+
+
+
+        <section class=alignments>
+          <h2>Alignments</h2>
+
+          <div class=grey><div class=white>
+              {% for hit in hits %}
+              <div class=alignment id=hit{{hit.Hit_num}}>
+
+                <div class=linkheader>
+                  <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
+                  <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
+                  <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
+                </div>
+
+                <div class=title>
+                  <p class=hittitle>{{hit|firsttitle}}</p>
+                  <p class=titleinfo>
+                    <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
+                    <span class=b>Length:</span> {{hit.Hit_len}}
+                    <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
+                  </p>
+                </div>
+
+                {% if hit|othertitles|length %}
+                <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
+                  See {{hit|othertitles|length}} more title(s)
+                </a>
+
+                <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
+                  {% for title in hit|othertitles %}
+                  <div class=title>
+                    <p class=hittitle>{{title.title}}</p>
+                    <p class=titleinfo>
+                      <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
+                    </p>
+                  </div>
+                  {% endfor %}
+                </div>
+                {% endif %}
+
+                {% for hsp in hit.Hit_hsps.Hsp %}
+                <div class=hotspot>
+                  <p class=range>
+                    <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
+                    <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
+                    <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
+                  </p>
+
+                  <table class=hotspotstable>
+                    <tr>
+                      <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
+                    </tr>
+                    <tr>
+                      <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
+                      <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
+                      <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
+                        (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
+                      <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
+                        }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
+                      <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
+                    </tr>
+                  </table>
+
+                  <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
+                </div>
+                {% endfor %}
+
+              </div>
+
+              {% endfor %}
+          </div></div>
+        </section>
+        {% endif %}
+
+        {% endfor %}
+        {% endif %}
+    </div>
+  </body>
+</html>
+
+{#
+Local Variables:
+tab-width: 2
+indent-tabs-mode: nil
+End:
+#}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2html.py	Thu May 15 10:48:09 2014 +0200
@@ -0,0 +1,304 @@
+#!/usr/bin/env python3
+
+# Copyright The Hyve B.V. 2014
+# License: GPL version 3 or higher
+
+import sys
+import math
+import warnings
+from os import path
+from itertools import repeat
+import argparse
+from lxml import objectify
+import jinja2
+
+
+
+_filters = {}
+def filter(func_or_name):
+    "Decorator to register a function as filter in the current jinja environment"
+    if isinstance(func_or_name, str):
+        def inner(func):
+            _filters[func_or_name] = func.__name__
+            return func
+        return inner
+    else:
+        _filters[func_or_name.__name__] = func_or_name.__name__
+        return func_or_name
+
+
+def color_idx(length):
+    if length < 40:
+        return 0
+    elif length < 50:
+        return 1
+    elif length < 80:
+        return 2
+    elif length < 200:
+        return 3
+    return 4
+
+@filter
+def fmt(val, fmt):
+    return format(float(val), fmt)
+
+@filter
+def firsttitle(hit):
+    return hit.Hit_def.text.split('>')[0]
+
+@filter
+def othertitles(hit):
+    """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
+    id_titles = hit.Hit_def.text.split('>')
+
+    titles = []
+    for t in id_titles[1:]:
+        fullid, title = t.split(' ', 1)
+        hitid, id = fullid.split('|', 2)[1:3]
+        titles.append(dict(id = id,
+                           hitid = hitid,
+                           fullid = fullid,
+                           title = title))
+    return titles
+
+@filter
+def hitid(hit):
+    return hit.Hit_id.text.split('|', 2)[1]
+
+@filter
+def seqid(hit):
+    return hit.Hit_id.text.split('|', 2)[2]
+
+@filter
+def alignment_pre(hsp):
+    return (
+        "Query  {:>7s}  {}  {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) +
+        "       {:7s}  {}\n".format('', hsp.Hsp_midline) +
+        "Subject{:>7s}  {}  {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to'])
+    )
+
+@filter('len')
+def blastxml_len(node):
+    if node.tag == 'Hsp':
+        return int(node['Hsp_align-len'])
+    elif node.tag == 'Iteration':
+        return int(node['Iteration_query-len'])
+    raise Exception("Unknown XML node type: "+node.tag)
+        
+
+@filter
+def asframe(frame):
+    if frame == 1:
+        return 'Plus'
+    elif frame == -1:
+        return 'Minus'
+    raise Exception("frame should be either +1 or -1")
+
+def genelink(hit, type='genbank', hsp=None):
+    if not isinstance(hit, str):
+        hit = hitid(hit)
+    link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
+    if hsp != None:
+        link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
+    return link
+
+
+# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
+# I've removed the html escapes, since html escaping is already being performed by the template engine.
+
+_base_js_escapes = (
+    ('\\', r'\u005C'),
+    ('\'', r'\u0027'),
+    ('"', r'\u0022'),
+    # ('>', r'\u003E'),
+    # ('<', r'\u003C'),
+    # ('&', r'\u0026'),
+    # ('=', r'\u003D'),
+    # ('-', r'\u002D'),
+    # (';', r'\u003B'),
+    # (u'\u2028', r'\u2028'),
+    # (u'\u2029', r'\u2029')
+)
+
+# Escape every ASCII character with a value less than 32. This is
+# needed a.o. to prevent html parsers from jumping out of javascript
+# parsing mode.
+_js_escapes = (_base_js_escapes +
+               tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))
+
+@filter
+def js_string_escape(value):
+    """Escape javascript string literal escapes. Note that this only works
+    within javascript string literals, not in general javascript
+    snippets."""
+
+    value = str(value)
+
+    for bad, good in _js_escapes:
+        value = value.replace(bad, good)
+
+    return value
+
+@filter
+def hits(result):
+    # sort hits by longest hotspot first
+    return sorted(result.Iteration_hits.findall('Hit'),
+                  key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
+                  reverse=True)
+
+
+
+class BlastVisualize:
+
+    colors = ('black', 'blue', 'green', 'magenta', 'red')
+
+    max_scale_labels = 10
+
+    def __init__(self, input, templatedir, templatename):
+        self.input = input
+        self.templatename = templatename
+
+        self.blast = objectify.parse(self.input).getroot()
+        self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
+        self.environment = jinja2.Environment(loader=self.loader,
+                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)
+
+        self._addfilters(self.environment)
+
+
+    def _addfilters(self, environment):
+        for filtername, funcname in _filters.items():
+            try:
+                environment.filters[filtername] = getattr(self, funcname)
+            except AttributeError:
+                environment.filters[filtername] = globals()[funcname]
+
+    def render(self, output):
+        template = self.environment.get_template(self.templatename)
+
+        params = (('Query ID', self.blast["BlastOutput_query-ID"]),
+                  ('Query definition', self.blast["BlastOutput_query-def"]),
+                  ('Query length', self.blast["BlastOutput_query-len"]),
+                  ('Program', self.blast.BlastOutput_version),
+                  ('Database', self.blast.BlastOutput_db),
+        )
+
+        output.write(template.render(blast=self.blast,
+                                     iterations=self.blast.BlastOutput_iterations.Iteration,
+                                     colors=self.colors,
+                                     # match_colors=self.match_colors(),
+                                     # hit_info=self.hit_info(),
+                                     genelink=genelink,
+                                     params=params))
+
+    @filter
+    def match_colors(self, result):
+        """
+        An iterator that yields lists of length-color pairs. 
+        """
+
+        query_length = blastxml_len(result)
+        
+        percent_multiplier = 100 / query_length
+
+        for hit in hits(result):
+            # sort hotspots from short to long, so we can overwrite index colors of
+            # short matches with those of long ones.
+            hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp))
+            table = bytearray([255]) * query_length
+            for hsp in hotspots:
+                frm = hsp['Hsp_query-from'] - 1
+                to = int(hsp['Hsp_query-to'])
+                table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm)
+
+            matches = []
+            last = table[0]
+            count = 0
+            for i in range(query_length):
+                if table[i] == last:
+                    count += 1
+                    continue
+                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
+                last = table[i]
+                count = 1
+            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
+
+            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
+
+    @filter
+    def queryscale(self, result):
+        query_length = blastxml_len(result)
+        skip = math.ceil(query_length / self.max_scale_labels)
+        percent_multiplier = 100 / query_length
+        for i in range(1, query_length+1):
+            if i % skip == 0:
+                yield dict(label = i, width = skip * percent_multiplier, shorter = False\)
+        if query_length % skip != 0:
+            yield dict(label = query_length,
+                       width = (query_length % skip) * percent_multiplier,
+                       shorter = True)
+
+    @filter
+    def hit_info(self, result):
+
+        query_length = blastxml_len(result)
+
+        for hit in hits(result):
+            hsps = hit.Hit_hsps.Hsp
+
+            cover = [False] * query_length
+            for hsp in hsps:
+                cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
+            cover_count = cover.count(True)
+
+            def hsp_val(path):
+                return (float(hsp[path]) for hsp in hsps)
+
+            yield dict(hit = hit,
+                       title = firsttitle(hit),
+                       link_id = hit.Hit_num,
+                       maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))),
+                       totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
+                       cover = "{:.0%}".format(cover_count / query_length),
+                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
+                       # FIXME: is this the correct formula vv?
+                       ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),
+                       accession = hit.Hit_accession)
+
+def main():
+
+    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
+                                     usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
+    input_group = parser.add_mutually_exclusive_group(required=True)
+    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
+                             help='The input Blast XML file, same as -i/--input')
+    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
+                             help='The input Blast XML file')
+    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
+                        help='The output html file')
+    # We just want the file name here, so jinja can open the file
+    # itself. But it is easier to just use a FileType so argparse can
+    # handle the errors. This introduces a small race condition when
+    # jinja later tries to re-open the template file, but we don't
+    # care too much.
+    parser.add_argument('--template', type=argparse.FileType(mode='r'), default='blast2html.html.jinja',
+                        help='The template file to use. Defaults to blast_html.html.jinja')
+
+    args = parser.parse_args()
+    if args.input == None:
+        args.input = args.positional_arg
+    if args.input == None:
+        parser.error('no input specified')
+
+    templatedir, templatename = path.split(args.template.name)
+    args.template.close()
+    if not templatedir:
+        templatedir = '.'
+
+    b = BlastVisualize(args.input, templatedir, templatename)
+    b.render(args.output)
+
+
+if __name__ == '__main__':
+    main()
+
--- a/blast_html.html.jinja	Thu May 15 10:45:34 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,600 +0,0 @@
-<!DOCTYPE html>
-<html>
-  <head>
-    <meta charset="UTF-8">
-    <meta name=generator content="blast_html; see ...">
-    
-    <title>Blast output</title>
-    
-    <style>
-      body {
-      color: #333333;
-      font-family: Arial,Sans-Serif;
-      }
-
-      :link {
-      color: #336699;
-      }
-
-      .right {
-      float: right;
-      }
-
-      #content {
-      margin: 0 2em;
-      padding: 0.5em;
-      border: 1px solid #888888;
-      background-color: #d3dff5;
-      }
-
-      h1, h2, h3, h4, h5, h6 {
-      color: #2A6979;
-      font-family: arial,verdana,sans-serif;
-      letter-spacing: -1px;
-      margin: 1.2em 0 0.3em;
-      }
-
-      h1 {
-      border-bottom: 1px solid #CCCCCC;
-      font-size: 150%;
-      padding-bottom: 0.1em;
-      }
-
-      h2 {
-      font-size: 120%;
-      font-weight: bold;
-      }
-
-      h4.darkHeader {
-      color: #4D4D4D;
-      letter-spacing: 0;
-      font-weight: bold;
-      }
-
-      #nodata {
-      font-weight: bold;
-      }
-
-      .index {
-      margin-bottom: 3em;
-      }
-      .index div.indexentry {
-      margin: 1.2em 1.6em;
-      font-weight: bold;
-      font-size: 100%;
-      }
-      
-      .headerdata {
-      font-size: 90%;
-      }
-      .headerdata .param {
-      font-weight: bold;
-      text-align: right;
-      padding: 0 1em;
-      }
-
-      .grey {
-      background-color: #eeeeee;
-      border: 1px solid #cccccc;
-      padding: 1em;
-      }
-
-      .white {
-      background-color: white;
-      border: 1px solid #cccccc;
-      padding: 1.5em 2%;
-      }
-
-      .graphicrow {
-      clear: left;
-      width: 100%;
-      }
-
-      .graphicitem {
-      float: left;
-      }
-
-
-      
-      .graphics .grey {
-      text-align: center;
-      }
-
-      .graphic {
-      background-color: white;
-      border: 2px solid black;
-      padding: 1.5em;
-      margin: auto;
-      }
-
-      .centered, .defline, div.legend, div.tablewrapper {
-      margin-left: auto;
-      margin-right: auto;
-      }
-
-      .defline {
-      background-color: white;
-      border: 1px solid black;
-      margin: .5em auto;
-      padding-left: .2em;
-      padding-right: .2em;
-      max-width: 50em;
-      text-align: left;
-      height: 2.8em;
-      overflow-y: hidden;
-      }
-
-      div.legend {
-      max-width: 40em;
-      }
-      div.legend div {
-      width: 100%;
-      color: white;
-      font-weight: bold;
-      border-spacing: 0;
-      }
-      div.legend div .graphicitem {
-      width: 20%;
-      padding: 0;
-      margin: 0;
-      border: none;
-      }
-
-      div.tablewrapper {
-      width: 50%;
-      min-width: 60em;
-      }
-
-      /* For small widths we give the graphic 100% */
-      @media (max-width: 72.5em) {
-      div.tablewrapper {
-      width: 100%;
-      min-width: 0px;
-      }
-      }
-
-      .scale {
-      width: 100%;
-      margin: .5em 0;
-      font-weight: bold;
-      }
-      .scale div {
-      color: red;
-      text-align: left;
-      }
-      .scale .graphicrow {
-      margin: .5em 0 .5em 0;
-      color: white;
-      }
-      .scale .graphicitem {
-      position: relative;
-      }
-      .scale .graphicitem div {
-      margin: 0 1px;
-      padding: 0 2px;
-      text-align: right;
-      background-color: red;
-      color: white;
-      }
-      .scale .graphicitem:first-child div {
-      margin-left: 0px;
-      }
-      .scale .graphicitem:last-child div {
-      margin-right: 0px;
-      }
-      .scale .graphicitem .lastlabel {
-      position: absolute;
-      top: 0px;
-      left: 100%;
-      background-color: transparent;
-      color: red;
-      }
-
-      a.matchresult {
-      display: block;
-      margin: 0;
-      padding: 0;
-      }
-      div.matchrow {
-      margin-top: 4px;
-      }
-      div.matchrow, div.matchitem {
-      height: 4px;
-      }
-
-      
-      table.descriptiontable {
-      font-size: 85%;
-      border: 1px solid #97b0c8;
-      border-spacing: 0;
-      color: #222222;
-      line-height: 1.3em;
-      background-color: white;
-      }
-      table.descriptiontable col:first-child {
-      width: 100%;
-      }
-      table.descriptiontable tr:hover {
-      background-color: #D5DEE3;
-      }
-      table.descriptiontable th {
-      color: #14376C;
-      font-weight: normal;
-      background-color: #F0F0F0;
-      background: linear-gradient(#FFFFFF, #F0F0F0);
-      border-bottom: 1px solid #D4DFE9;
-      border-right: 1px solid #CFCFCF;
-      border-left: 0px solid black;
-      border-top: 0px solid black;
-      }
-      table.descriptiontable td {
-      overflow: hidden;
-      text-align: center;
-      padding: .4em .8em;
-      }
-      table.descriptiontable td div {
-      width: 1em;
-      overflow: visible;
-      white-space: nowrap;
-      text-align: left;
-      }
-
-
-      
-      .alignments .white {
-      padding: 1.5em 1em;
-      }
-      
-      .alignment {
-      border-top: 1px solid black;
-      padding-left: 1em;
-      padding-right: 1em;
-      }
-      
-      div.linkheader {
-      padding-top: .2em;
-      font-size: 85%;
-      color: #14376C;
-      }
-      div.linkheader a.linkheader {
-      margin-right: 1em;
-      }
-      div.linkheader .right a {
-      text-decoration: none;
-      }
-
-      .title .hittitle {
-      color: #222222;
-      margin-bottom: .3em;
-      }
-      .title .titleinfo {
-      font-size: 80%;
-      margin-top: 0;
-      margin-bottom: .3em;
-      }
-      .title .titleinfo .b {
-      color: #606060;
-      font-weight: bold;
-      font-size: 90%;
-      }
-
-      .moretitles {
-      margin: 1.2em;
-      }
-      .moretitles .titleinfo {
-      margin: 0;
-      padding: 0;
-      }
-      .moretitles .hittitle {
-      margin: .4em 0 .2em 0;
-      padding: 0;
-      }
-      
-      a.showmoretitles {
-      font-size: 75%;
-      color: #336699;
-      font-weight: bold;
-      margin-top: 0;
-      }
-      a.showmoretitles:hover {
-      }
-
-      .hotspot {
-      color: #606060;
-      font-family: verdana, arial, sans-serif;
-      margin-bottom: 2.5em;
-      }
-
-      .hotspot p.range {
-      font-size: 70%;
-      margin-top: 0;
-      margin-top: 1em;
-      margin-bottom: .2em;
-      }
-      .hotspot p.range span.range {
-      font-weight: bold;
-      }
-      .hotspot p.range a.range {
-      margin-left: .5em;
-      }
-
-      table.hotspotstable {
-      border-top: 1px solid;
-      border-bottom: 1px solid;
-      text-align: left;
-      border-collapse: collapse;
-      }
-      table.hotspotstable th, table.hotspotstable td {
-      padding: .1em 1em;
-      }
-      table.hotspotstable th {
-      font-size: 70%;
-      }
-      table.hotspotstable td {
-      min-width: 7em;
-      color: #222222;
-      font-size: 80%;
-      }
-
-      pre.alignmentgraphic {
-      color: #222222;
-      }
-
-      
-    </style>
-
-    <script type="text/javascript">
-      function toggle_visibility(id) {
-          var e = document.getElementById(id);
-          if(e.style.display != 'block')
-              e.style.display = 'block';
-          else
-              e.style.display = 'none';
-      }
-    </script>
-
-  </head>
-
-  
-  <body>
-    <div id=content>
-
-      {% if not blast.BlastOutput_iterations.findall('Iteration') %}
-      <section class=nodata>
-        <h1>No data</h1>
-        <div class=grey>
-          No matches
-        </div>
-      </section>
-
-      {% else %}
-
-      {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %}
-      <section class=index>
-        <h1>Queries</h1>
-
-        {% for result in blast.BlastOutput_iterations.Iteration %}
-        <div class=indexentry><a href="#match{{result['Iteration_iter-num']}}">
-            {% set hits = result|hits %}
-            {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}}
-            ({{result|len}} letters, {{hits|length}} hits)
-        </a></div>
-        {% endfor %}
-
-      </section>
-      {% endif %}
-
-      {% for result in blast.BlastOutput_iterations.Iteration %}
-      
-      <section class=match id=match{{result['Iteration_iter-num']}}>
-      
-        <h1>Nucleotide Sequence ({{result|len}} letters)</h1>
-
-        <section class=header>
-
-          <table class=headerdata>
-            {% for param, value in params %}
-              <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
-            {% endfor %}
-          </table>
-
-        </section>
-
-        {% set hits = result|hits %}
-        {% if not hits %}
-        <section>
-          <h2>No Hits</h2>
-          <div class=grey>
-            This query did not match anywhere
-          </div>
-        </section>
-        {% else %}
-
-        <section class=graphics>
-          <h2>Graphic Summary</h2>
-
-          <div class=grey>
-            <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3>
-
-            <div class=defline id=defline{{result['Iteration_iter-num']}}>
-              Mouse-over to show defline and scores, click to show alignments
-            </div>
-
-            <div class=graphic>
-              <h4 class=darkHeader>Color key for alignment scores</h4>
-              <div class=legend><div class=graphicrow>
-                  <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
-                  <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
-                  <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
-                  <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
-                  <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
-              </div></div>
-              <div style="clear: left"></div>
-
-              <div class=tablewrapper>
-
-                <div class=scale>
-                  <div>query:</div>
-                  <div class=graphicrow>
-                    <div>
-                      {% for s in result|queryscale %}
-                      <div class=graphicitem style="width: {{s.width}}%">
-                        {% if s.width > 3.0 %}
-                        <div>{{s.label}}</div>
-                        {% else %}
-                        <div>&nbsp;</div>
-                        <div class=lastlabel>{{s.label}}</div>
-                        {% endif %}
-                      </div>
-                      {% endfor %}
-                    </div>
-                  </div>
-                  <div style="clear: left"></div>
-                </div>
-
-                {% for line in result|match_colors %}
-                <a class=matchresult
-                   href="{{line.link}}"
-                   onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"'
-                   onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
-                   title="{{line.defline}}">
-                  <div class="matchrow graphicrow">
-                    {% for hit in line.colors %}
-                    <div class="matchitem graphicitem"
-                         style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div>
-                    {% endfor %}
-                  </div>
-                </a>
-
-                {% endfor %}
-              </div>
-            </div>
-          </div>
-        </section>
-
-
-
-        <section class=descriptions>
-          <h2>Descriptions</h2>
-
-          <div class=grey><div class=white>
-              <h4 class=darkHeader>Sequences producing significant alignments:</h4>
-
-              <table class=descriptiontable>
-                <col/><col/><col/><col/><col/><col/><col/>
-                <tr>
-                  <th>Description</th>
-                  <th>Max score</th>
-                  <th>Total score</th>
-                  <th>Query cover</th>
-                  <th>E value</th>
-                  <th>Ident</th>
-                  <th>Accession</th>
-                </tr>
-                {% for hit in result|hit_info %}
-                <tr>
-                  <td><div><a href="#hit{{hit.link_id}}"
-                              title="{{hit.title}}"
-                              id="description{{hit.link_id}}">
-                        {{hit.title}}
-                  </a></div></td>
-                  <td>{{hit.maxscore}}</td>
-                  <td>{{hit.totalscore}}</td>
-                  <td>{{hit.cover}}</td>
-                  <td>{{hit.e_value}}</td>
-                  <td>{{hit.ident}}</td>
-                  <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
-                </tr>
-                {% endfor %}
-              </table>
-
-          </div></div>
-        </section>
-
-
-
-        <section class=alignments>
-          <h2>Alignments</h2>
-
-          <div class=grey><div class=white>
-              {% for hit in hits %}
-              <div class=alignment id=hit{{hit.Hit_num}}>
-
-                <div class=linkheader>
-                  <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
-                  <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
-                  <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
-                </div>
-
-                <div class=title>
-                  <p class=hittitle>{{hit|firsttitle}}</p>
-                  <p class=titleinfo>
-                    <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
-                    <span class=b>Length:</span> {{hit.Hit_len}}
-                    <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
-                  </p>
-                </div>
-
-                {% if hit|othertitles|length %}
-                <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
-                  See {{hit|othertitles|length}} more title(s)
-                </a>
-
-                <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
-                  {% for title in hit|othertitles %}
-                  <div class=title>
-                    <p class=hittitle>{{title.title}}</p>
-                    <p class=titleinfo>
-                      <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
-                    </p>
-                  </div>
-                  {% endfor %}
-                </div>
-                {% endif %}
-
-                {% for hsp in hit.Hit_hsps.Hsp %}
-                <div class=hotspot>
-                  <p class=range>
-                    <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
-                    <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
-                    <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
-                  </p>
-
-                  <table class=hotspotstable>
-                    <tr>
-                      <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
-                    </tr>
-                    <tr>
-                      <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
-                      <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
-                      <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
-                        (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
-                      <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
-                        }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
-                      <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
-                    </tr>
-                  </table>
-
-                  <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
-                </div>
-                {% endfor %}
-
-              </div>
-
-              {% endfor %}
-          </div></div>
-        </section>
-        {% endif %}
-
-        {% endfor %}
-        {% endif %}
-    </div>
-  </body>
-</html>
-
-{#
-Local Variables:
-tab-width: 2
-indent-tabs-mode: nil
-End:
-#}
--- a/blast_html.py	Thu May 15 10:45:34 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,304 +0,0 @@
-#!/usr/bin/env python3
-
-# Copyright The Hyve B.V. 2014
-# License: GPL version 3 or higher
-
-import sys
-import math
-import warnings
-from os import path
-from itertools import repeat
-import argparse
-from lxml import objectify
-import jinja2
-
-
-
-_filters = {}
-def filter(func_or_name):
-    "Decorator to register a function as filter in the current jinja environment"
-    if isinstance(func_or_name, str):
-        def inner(func):
-            _filters[func_or_name] = func.__name__
-            return func
-        return inner
-    else:
-        _filters[func_or_name.__name__] = func_or_name.__name__
-        return func_or_name
-
-
-def color_idx(length):
-    if length < 40:
-        return 0
-    elif length < 50:
-        return 1
-    elif length < 80:
-        return 2
-    elif length < 200:
-        return 3
-    return 4
-
-@filter
-def fmt(val, fmt):
-    return format(float(val), fmt)
-
-@filter
-def firsttitle(hit):
-    return hit.Hit_def.text.split('>')[0]
-
-@filter
-def othertitles(hit):
-    """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
-    id_titles = hit.Hit_def.text.split('>')
-
-    titles = []
-    for t in id_titles[1:]:
-        fullid, title = t.split(' ', 1)
-        hitid, id = fullid.split('|', 2)[1:3]
-        titles.append(dict(id = id,
-                           hitid = hitid,
-                           fullid = fullid,
-                           title = title))
-    return titles
-
-@filter
-def hitid(hit):
-    return hit.Hit_id.text.split('|', 2)[1]
-
-@filter
-def seqid(hit):
-    return hit.Hit_id.text.split('|', 2)[2]
-
-@filter
-def alignment_pre(hsp):
-    return (
-        "Query  {:>7s}  {}  {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) +
-        "       {:7s}  {}\n".format('', hsp.Hsp_midline) +
-        "Subject{:>7s}  {}  {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to'])
-    )
-
-@filter('len')
-def blastxml_len(node):
-    if node.tag == 'Hsp':
-        return int(node['Hsp_align-len'])
-    elif node.tag == 'Iteration':
-        return int(node['Iteration_query-len'])
-    raise Exception("Unknown XML node type: "+node.tag)
-        
-
-@filter
-def asframe(frame):
-    if frame == 1:
-        return 'Plus'
-    elif frame == -1:
-        return 'Minus'
-    raise Exception("frame should be either +1 or -1")
-
-def genelink(hit, type='genbank', hsp=None):
-    if not isinstance(hit, str):
-        hit = hitid(hit)
-    link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
-    if hsp != None:
-        link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
-    return link
-
-
-# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
-# I've removed the html escapes, since html escaping is already being performed by the template engine.
-
-_base_js_escapes = (
-    ('\\', r'\u005C'),
-    ('\'', r'\u0027'),
-    ('"', r'\u0022'),
-    # ('>', r'\u003E'),
-    # ('<', r'\u003C'),
-    # ('&', r'\u0026'),
-    # ('=', r'\u003D'),
-    # ('-', r'\u002D'),
-    # (';', r'\u003B'),
-    # (u'\u2028', r'\u2028'),
-    # (u'\u2029', r'\u2029')
-)
-
-# Escape every ASCII character with a value less than 32. This is
-# needed a.o. to prevent html parsers from jumping out of javascript
-# parsing mode.
-_js_escapes = (_base_js_escapes +
-               tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))
-
-@filter
-def js_string_escape(value):
-    """Escape javascript string literal escapes. Note that this only works
-    within javascript string literals, not in general javascript
-    snippets."""
-
-    value = str(value)
-
-    for bad, good in _js_escapes:
-        value = value.replace(bad, good)
-
-    return value
-
-@filter
-def hits(result):
-    # sort hits by longest hotspot first
-    return sorted(result.Iteration_hits.findall('Hit'),
-                  key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
-                  reverse=True)
-
-
-
-class BlastVisualize:
-
-    colors = ('black', 'blue', 'green', 'magenta', 'red')
-
-    max_scale_labels = 10
-
-    def __init__(self, input, templatedir, templatename):
-        self.input = input
-        self.templatename = templatename
-
-        self.blast = objectify.parse(self.input).getroot()
-        self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
-        self.environment = jinja2.Environment(loader=self.loader,
-                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)
-
-        self._addfilters(self.environment)
-
-
-    def _addfilters(self, environment):
-        for filtername, funcname in _filters.items():
-            try:
-                environment.filters[filtername] = getattr(self, funcname)
-            except AttributeError:
-                environment.filters[filtername] = globals()[funcname]
-
-    def render(self, output):
-        template = self.environment.get_template(self.templatename)
-
-        params = (('Query ID', self.blast["BlastOutput_query-ID"]),
-                  ('Query definition', self.blast["BlastOutput_query-def"]),
-                  ('Query length', self.blast["BlastOutput_query-len"]),
-                  ('Program', self.blast.BlastOutput_version),
-                  ('Database', self.blast.BlastOutput_db),
-        )
-
-        output.write(template.render(blast=self.blast,
-                                     iterations=self.blast.BlastOutput_iterations.Iteration,
-                                     colors=self.colors,
-                                     # match_colors=self.match_colors(),
-                                     # hit_info=self.hit_info(),
-                                     genelink=genelink,
-                                     params=params))
-
-    @filter
-    def match_colors(self, result):
-        """
-        An iterator that yields lists of length-color pairs. 
-        """
-
-        query_length = blastxml_len(result)
-        
-        percent_multiplier = 100 / query_length
-
-        for hit in hits(result):
-            # sort hotspots from short to long, so we can overwrite index colors of
-            # short matches with those of long ones.
-            hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp))
-            table = bytearray([255]) * query_length
-            for hsp in hotspots:
-                frm = hsp['Hsp_query-from'] - 1
-                to = int(hsp['Hsp_query-to'])
-                table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm)
-
-            matches = []
-            last = table[0]
-            count = 0
-            for i in range(query_length):
-                if table[i] == last:
-                    count += 1
-                    continue
-                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
-                last = table[i]
-                count = 1
-            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
-
-            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
-
-    @filter
-    def queryscale(self, result):
-        query_length = blastxml_len(result)
-        skip = math.ceil(query_length / self.max_scale_labels)
-        percent_multiplier = 100 / query_length
-        for i in range(1, query_length+1):
-            if i % skip == 0:
-                yield dict(label = i, width = skip * percent_multiplier, shorter = False)
-        if query_length % skip != 0:
-            yield dict(label = query_length,
-                       width = (query_length % skip) * percent_multiplier,
-                       shorter = True)
-
-    @filter
-    def hit_info(self, result):
-
-        query_length = blastxml_len(result)
-
-        for hit in hits(result):
-            hsps = hit.Hit_hsps.Hsp
-
-            cover = [False] * query_length
-            for hsp in hsps:
-                cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
-            cover_count = cover.count(True)
-
-            def hsp_val(path):
-                return (float(hsp[path]) for hsp in hsps)
-
-            yield dict(hit = hit,
-                       title = firsttitle(hit),
-                       link_id = hit.Hit_num,
-                       maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))),
-                       totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
-                       cover = "{:.0%}".format(cover_count / query_length),
-                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
-                       # FIXME: is this the correct formula vv?
-                       ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),
-                       accession = hit.Hit_accession)
-
-def main():
-
-    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
-                                     usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
-    input_group = parser.add_mutually_exclusive_group(required=True)
-    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
-                             help='The input Blast XML file, same as -i/--input')
-    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
-                             help='The input Blast XML file')
-    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
-                        help='The output html file')
-    # We just want the file name here, so jinja can open the file
-    # itself. But it is easier to just use a FileType so argparse can
-    # handle the errors. This introduces a small race condition when
-    # jinja later tries to re-open the template file, but we don't
-    # care too much.
-    parser.add_argument('--template', type=argparse.FileType(mode='r'), default='blast_html.html.jinja',
-                        help='The template file to use. Defaults to blast_html.html.jinja')
-
-    args = parser.parse_args()
-    if args.input == None:
-        args.input = args.positional_arg
-    if args.input == None:
-        parser.error('no input specified')
-
-    templatedir, templatename = path.split(args.template.name)
-    args.template.close()
-    if not templatedir:
-        templatedir = '.'
-
-    b = BlastVisualize(args.input, templatedir, templatename)
-    b.render(args.output)
-
-
-if __name__ == '__main__':
-    main()
-