--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualise.py	Wed May 07 18:49:54 2014 +0200
@@ -0,0 +1,86 @@
+#!/usr/bin/env python3
+
+# Copyright The Hyve B.V. 2014
+# License: GPL version 3 or higher
+
+import sys
+import warnings
+from itertools import repeat
+from lxml import objectify
+import jinja2
+
+
+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
+
+
+colors = ['black', 'blue', 'green', 'magenta', 'red']
+
+blast = objectify.parse('blast xml example1.xml').getroot()
+loader = jinja2.FileSystemLoader(searchpath='.')
+environment = jinja2.Environment(loader=loader)
+environment.filters['color'] = lambda length: match_colors[color_idx(length)]
+
+def match_colors():
+    """
+    An iterator that yields lists of length-color pairs. 
+    """
+    
+    hits = blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
+    query_length = blast["BlastOutput_query-len"]
+    # sort hits by longest hotspot first
+    hits = sorted(hits, key=lambda h: max(hsp['Hsp_align-len'] for hsp in h.Hit_hsps.Hsp), reverse=True)
+
+    for hit in 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: hsp['Hsp_align-len'])
+        table = bytearray([255]) * query_length
+        for hsp in hotspots:
+            frm = hsp['Hsp_query-from'] - 1
+            to = hsp['Hsp_query-to'] - 1
+            table[frm:to] = repeat(color_idx(hsp['Hsp_align-len']), to - frm)
+
+        matches = []
+        last = table[0]
+        count = 0
+        for i in range(int(query_length)):
+            if table[i] == last:
+                count += 1
+                continue
+            matches.append((count, colors[last] if last != 255 else 'none'))
+            last = table[i]
+            count = 1
+        matches.append((count, colors[last] if last != 255 else 'none'))
+
+        yield dict(colors=matches, link="#hit"+hit.Hit_num.text)
+
+
+def main():
+    template = environment.get_template('visualise.html.jinja')
+
+    params = (('Query ID', blast["BlastOutput_query-ID"]),
+              ('Query definition', blast["BlastOutput_query-def"]),
+              ('Query length', blast["BlastOutput_query-len"]),
+              ('Program', blast.BlastOutput_version),
+              ('Database', blast.BlastOutput_db),
+            )
+
+    if len(blast.BlastOutput_iterations.Iteration) > 1:
+        warnings.warn("Multiple 'Iteration' elements found, showing only the first")
+
+    sys.stdout.write(template.render(blast=blast,
+                                     hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
+                                     colors=colors,
+                                     match_colors=match_colors(),
+                                     params=params))
+
+main()