--- /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()
+