Mercurial > repos > jankanis > blast2html

changeset 13:c2d63adb83db

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renamed files
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 17:13:49 +0200
parents a459c754cdb5
children 0b33898bba45
files blast_html.html.jinja blast_html.py visualise.html.jinja visualise.py
diffstat 4 files changed, 787 insertions(+), 787 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_html.html.jinja	Mon May 12 17:13:49 2014 +0200
@@ -0,0 +1,542 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="UTF-8">
+    
+    <title>Blast output</title>
+
+    <style>
+      body {
+      color: #33333;
+      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;
+      }
+      
+      .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;
+      }
+
+
+      
+      .graphic {
+      background-color: white;
+      border: 2px solid black;
+      padding: .5em 1.5em;
+      align: center;
+      margin: auto;
+      }
+
+      #graphics .grey {
+      text-align: center;
+      }
+
+      .centered, #defline, div.legend, div.tablewrapper {
+      align: center;
+      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 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;
+      }
+
+      a.matchresult {
+      display: block;
+      margin: 0;
+      padding: 0;
+      }
+      div.matchrow {
+      margin-top: 4px;
+      }
+      div.matchrow, div.matchitem {
+      height: 4px;
+      }
+
+
+      
+      div#descriptions {
+      }
+      
+      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: #22222;
+      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>
+      <h1>Nucleotide Sequence ({{length}} letters)</h1>
+
+      <div id=header>
+
+        <table class=headerdata>
+          {% for param, value in params %}
+            <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
+          {% endfor %}
+        </table>
+          
+      </div>
+      
+      {% if not (blast.BlastOutput_iterations.findall('Iteration') and
+                 blast.BlastOutput_iterations.Iteration.Iteration_hits.findall('Hit')) %}
+      <div id=nodata>
+	<h2>No Results</h2>
+	<div class=grey>
+	  No Matches
+	</div>
+      </div>
+      {% else %}
+
+
+      
+      <div id=graphics>
+        <h2>Graphic Summary</h2>
+
+        <div class=grey>
+          <h3 class=centered>Distribution of {{hits|length}} Blast Hits on the Query Sequence</h3>
+          
+          <div id=defline>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>
+                    {% for s in queryscale %}
+                    <div class=graphicitem
+			 style="width: {{s.width|safe}}%">
+		      <div>{{s.label|safe}}</div>
+		    </div>
+                    {% endfor %}
+		</div>
+		<div style="clear: left"></div>
+              </div>
+              
+              {% for line in match_colors %}
+              <a class=matchresult
+		 href="{{line.link}}"
+                 onmouseover='document.getElementById("defline").innerHTML="{{line.defline}}"'
+                 onmouseout='document.getElementById("defline").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
+                 title="{{line.defline}}">
+                <div class="matchrow graphicrow">
+                    {% for match in line.colors %}
+                    <div class="matchitem graphicitem"
+			 style="background-color: {{match[1]}}; width: {{match[0]}}%"></div>
+                    {% endfor %}
+                </div>
+              </a>
+              
+              {% endfor %}
+            </div>
+          </div>
+        </div>
+      </div>
+
+
+      
+      <div id=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 hit_info %}
+              <tr>
+                <td><div><a href="#hit{{hit.link_id}}"
+			    title="{{hit.title}}"
+			    name=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>
+      </div>
+
+      
+
+      <div id=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}}'); 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>
+      </div>
+
+      {% endif %}
+    </div>
+  </body>
+</html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_html.py	Mon May 12 17:13:49 2014 +0200
@@ -0,0 +1,245 @@
+#!/usr/bin/env python3
+
+# Copyright The Hyve B.V. 2014
+# License: GPL version 3 or higher
+
+import sys
+import math
+import warnings
+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
+            return func
+        return inner
+    else:
+        _filters[func_or_name.__name__] = func_or_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'], hsp.Hsp_qseq, hsp['Hsp_query-to']) +
+        "       {:7s}  {}\n".format('', hsp.Hsp_midline) +
+        "Subject{:>7s}  {}  {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to'])
+    )
+
+@filter('len')
+def hsplen(node):
+    return int(node['Hsp_align-len'])
+
+@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 jinja2.Markup(link)
+
+
+
+
+class BlastVisualize:
+
+    colors = ('black', 'blue', 'green', 'magenta', 'red')
+
+    max_scale_labels = 10
+
+    templatename = 'visualise.html.jinja'
+
+    def __init__(self, input):
+        self.input = input
+
+        self.blast = objectify.parse(self.input).getroot()
+        self.loader = jinja2.FileSystemLoader(searchpath='.')
+        self.environment = jinja2.Environment(loader=self.loader,
+                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)
+
+        self.environment.filters['color'] = lambda length: match_colors[color_idx(length)]
+
+        for name, filter in _filters.items():
+            self.environment.filters[name] = filter
+
+        self.query_length = int(self.blast["BlastOutput_query-len"])
+        self.hits = self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
+        # sort hits by longest hotspot first
+        self.ordered_hits = sorted(self.hits,
+                                   key=lambda h: max(hsplen(hsp) for hsp in h.Hit_hsps.Hsp),
+                                   reverse=True)
+
+    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),
+        )
+
+        if len(self.blast.BlastOutput_iterations.Iteration) > 1:
+            warnings.warn("Multiple 'Iteration' elements found, showing only the first")
+
+        output.write(template.render(blast=self.blast,
+                                          length=self.query_length,
+                                          hits=self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
+                                          colors=self.colors,
+                                          match_colors=self.match_colors(),
+                                          queryscale=self.queryscale(),
+                                          hit_info=self.hit_info(),
+                                          genelink=genelink,
+                                          params=params))
+            
+
+    def match_colors(self):
+        """
+        An iterator that yields lists of length-color pairs. 
+        """
+
+        percent_multiplier = 100 / self.query_length
+
+        for hit in self.hits:
+            # 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: hsplen(hsp))
+            table = bytearray([255]) * self.query_length
+            for hsp in hotspots:
+                frm = hsp['Hsp_query-from'] - 1
+                to = int(hsp['Hsp_query-to'])
+                table[frm:to] = repeat(color_idx(hsplen(hsp)), to - frm)
+
+            matches = []
+            last = table[0]
+            count = 0
+            for i in range(self.query_length):
+                if table[i] == last:
+                    count += 1
+                    continue
+                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none'))
+                last = table[i]
+                count = 1
+            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none'))
+
+            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
+
+
+    def queryscale(self):
+        skip = math.ceil(self.query_length / self.max_scale_labels)
+        percent_multiplier = 100 / self.query_length
+        for i in range(1, self.query_length+1):
+            if i % skip == 0:
+                yield dict(label = i, width = skip * percent_multiplier)
+        if self.query_length % skip != 0:
+            yield dict(label = self.query_length, width = (self.query_length % skip) * percent_multiplier)
+
+
+    def hit_info(self):
+
+        for hit in self.ordered_hits:
+            hsps = hit.Hit_hsps.Hsp
+
+            cover = [False] * self.query_length
+            for hsp in hsps:
+                cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, hsplen(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 / self.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 / hsplen(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')
+
+    args = parser.parse_args()
+    if args.input == None:
+        args.input = args.positional_arg
+    if args.input == None:
+        parser.error('no input specified')
+
+    b = BlastVisualize(args.input)
+    b.render(args.output)
+
+
+if __name__ == '__main__':
+    main()
+
--- a/visualise.html.jinja	Mon May 12 17:12:24 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,542 +0,0 @@
-<!DOCTYPE html>
-<html>
-  <head>
-    <meta charset="UTF-8">
-    
-    <title>Blast output</title>
-
-    <style>
-      body {
-      color: #33333;
-      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;
-      }
-      
-      .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;
-      }
-
-
-      
-      .graphic {
-      background-color: white;
-      border: 2px solid black;
-      padding: .5em 1.5em;
-      align: center;
-      margin: auto;
-      }
-
-      #graphics .grey {
-      text-align: center;
-      }
-
-      .centered, #defline, div.legend, div.tablewrapper {
-      align: center;
-      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 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;
-      }
-
-      a.matchresult {
-      display: block;
-      margin: 0;
-      padding: 0;
-      }
-      div.matchrow {
-      margin-top: 4px;
-      }
-      div.matchrow, div.matchitem {
-      height: 4px;
-      }
-
-
-      
-      div#descriptions {
-      }
-      
-      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: #22222;
-      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>
-      <h1>Nucleotide Sequence ({{length}} letters)</h1>
-
-      <div id=header>
-
-        <table class=headerdata>
-          {% for param, value in params %}
-            <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
-          {% endfor %}
-        </table>
-          
-      </div>
-      
-      {% if not (blast.BlastOutput_iterations.findall('Iteration') and
-                 blast.BlastOutput_iterations.Iteration.Iteration_hits.findall('Hit')) %}
-      <div id=nodata>
-	<h2>No Results</h2>
-	<div class=grey>
-	  No Matches
-	</div>
-      </div>
-      {% else %}
-
-
-      
-      <div id=graphics>
-        <h2>Graphic Summary</h2>
-
-        <div class=grey>
-          <h3 class=centered>Distribution of {{hits|length}} Blast Hits on the Query Sequence</h3>
-          
-          <div id=defline>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>
-                    {% for s in queryscale %}
-                    <div class=graphicitem
-			 style="width: {{s.width|safe}}%">
-		      <div>{{s.label|safe}}</div>
-		    </div>
-                    {% endfor %}
-		</div>
-		<div style="clear: left"></div>
-              </div>
-              
-              {% for line in match_colors %}
-              <a class=matchresult
-		 href="{{line.link}}"
-                 onmouseover='document.getElementById("defline").innerHTML="{{line.defline}}"'
-                 onmouseout='document.getElementById("defline").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
-                 title="{{line.defline}}">
-                <div class="matchrow graphicrow">
-                    {% for match in line.colors %}
-                    <div class="matchitem graphicitem"
-			 style="background-color: {{match[1]}}; width: {{match[0]}}%"></div>
-                    {% endfor %}
-                </div>
-              </a>
-              
-              {% endfor %}
-            </div>
-          </div>
-        </div>
-      </div>
-
-
-      
-      <div id=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 hit_info %}
-              <tr>
-                <td><div><a href="#hit{{hit.link_id}}"
-			    title="{{hit.title}}"
-			    name=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>
-      </div>
-
-      
-
-      <div id=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}}'); 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>
-      </div>
-
-      {% endif %}
-    </div>
-  </body>
-</html>
-
--- a/visualise.py	Mon May 12 17:12:24 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,245 +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 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
-            return func
-        return inner
-    else:
-        _filters[func_or_name.__name__] = func_or_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'], hsp.Hsp_qseq, hsp['Hsp_query-to']) +
-        "       {:7s}  {}\n".format('', hsp.Hsp_midline) +
-        "Subject{:>7s}  {}  {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to'])
-    )
-
-@filter('len')
-def hsplen(node):
-    return int(node['Hsp_align-len'])
-
-@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 jinja2.Markup(link)
-
-
-
-
-class BlastVisualize:
-
-    colors = ('black', 'blue', 'green', 'magenta', 'red')
-
-    max_scale_labels = 10
-
-    templatename = 'visualise.html.jinja'
-
-    def __init__(self, input):
-        self.input = input
-
-        self.blast = objectify.parse(self.input).getroot()
-        self.loader = jinja2.FileSystemLoader(searchpath='.')
-        self.environment = jinja2.Environment(loader=self.loader,
-                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)
-
-        self.environment.filters['color'] = lambda length: match_colors[color_idx(length)]
-
-        for name, filter in _filters.items():
-            self.environment.filters[name] = filter
-
-        self.query_length = int(self.blast["BlastOutput_query-len"])
-        self.hits = self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
-        # sort hits by longest hotspot first
-        self.ordered_hits = sorted(self.hits,
-                                   key=lambda h: max(hsplen(hsp) for hsp in h.Hit_hsps.Hsp),
-                                   reverse=True)
-
-    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),
-        )
-
-        if len(self.blast.BlastOutput_iterations.Iteration) > 1:
-            warnings.warn("Multiple 'Iteration' elements found, showing only the first")
-
-        output.write(template.render(blast=self.blast,
-                                          length=self.query_length,
-                                          hits=self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
-                                          colors=self.colors,
-                                          match_colors=self.match_colors(),
-                                          queryscale=self.queryscale(),
-                                          hit_info=self.hit_info(),
-                                          genelink=genelink,
-                                          params=params))
-            
-
-    def match_colors(self):
-        """
-        An iterator that yields lists of length-color pairs. 
-        """
-
-        percent_multiplier = 100 / self.query_length
-
-        for hit in self.hits:
-            # 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: hsplen(hsp))
-            table = bytearray([255]) * self.query_length
-            for hsp in hotspots:
-                frm = hsp['Hsp_query-from'] - 1
-                to = int(hsp['Hsp_query-to'])
-                table[frm:to] = repeat(color_idx(hsplen(hsp)), to - frm)
-
-            matches = []
-            last = table[0]
-            count = 0
-            for i in range(self.query_length):
-                if table[i] == last:
-                    count += 1
-                    continue
-                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none'))
-                last = table[i]
-                count = 1
-            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none'))
-
-            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
-
-
-    def queryscale(self):
-        skip = math.ceil(self.query_length / self.max_scale_labels)
-        percent_multiplier = 100 / self.query_length
-        for i in range(1, self.query_length+1):
-            if i % skip == 0:
-                yield dict(label = i, width = skip * percent_multiplier)
-        if self.query_length % skip != 0:
-            yield dict(label = self.query_length, width = (self.query_length % skip) * percent_multiplier)
-
-
-    def hit_info(self):
-
-        for hit in self.ordered_hits:
-            hsps = hit.Hit_hsps.Hsp
-
-            cover = [False] * self.query_length
-            for hsp in hsps:
-                cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, hsplen(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 / self.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 / hsplen(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')
-
-    args = parser.parse_args()
-    if args.input == None:
-        args.input = args.positional_arg
-    if args.input == None:
-        parser.error('no input specified')
-
-    b = BlastVisualize(args.input)
-    b.render(args.output)
-
-
-if __name__ == '__main__':
-    main()
-