| Previous changeset 18:4434ffab721a (2014-05-13) Next changeset 20:53cd304c5f26 (2014-05-14) |
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Commit message:
make it work with multiple queries |
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modified:
blast_html.html.jinja blast_html.py |
| b |
| diff -r 4434ffab721a -r 67ddcb807b7d blast_html.html.jinja --- a/blast_html.html.jinja Tue May 13 15:26:20 2014 +0200 +++ b/blast_html.html.jinja Tue May 13 18:06:36 2014 +0200 |
| [ |
| b'@@ -2,6 +2,7 @@\n <html>\n <head>\n <meta charset="UTF-8">\n+ <meta name=generator content="blast_html; see ...">\n \n <title>Blast output</title>\n \n@@ -97,12 +98,12 @@\n margin: auto;\n }\n \n- .centered, #defline, div.legend, div.tablewrapper {\n+ .centered, .defline, div.legend, div.tablewrapper {\n margin-left: auto;\n margin-right: auto;\n }\n \n- #defline {\n+ .defline {\n background-color: white;\n border: 1px solid black;\n margin: .5em auto;\n@@ -338,197 +339,213 @@\n \n <body>\n <div id=content>\n- <h1>Nucleotide Sequence ({{length}} letters)</h1>\n \n- <section class=header>\n-\n- <table class=headerdata>\n- {% for param, value in params %}\n- <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>\n- {% endfor %}\n- </table>\n- \n- </section>\n- \n- {% if not (blast.BlastOutput_iterations.findall(\'Iteration\') and\n- blast.BlastOutput_iterations.Iteration.Iteration_hits.findall(\'Hit\')) %}\n+ {% if not blast.BlastOutput_iterations.findall(\'Iteration\') %}\n <section class=nodata>\n- <h2>No Results</h2>\n- <div class=grey>\n- No Matches\n- </div>\n- </section>\n- {% else %}\n-\n-\n- \n- <section class=graphics>\n- <h2>Graphic Summary</h2>\n-\n+ <h1>No data</h1>\n <div class=grey>\n- <h3 class=centered>Distribution of {{hits|length}} Blast Hits on the Query Sequence</h3>\n- \n- <div id=defline>Mouse-over to show defline and scores, click to show alignments</div>\n-\n- <div class=graphic>\n- <h4 class=darkHeader>Color key for alignment scores</h4>\n- <div class=legend><div class=graphicrow>\n- <div class=graphicitem style="background-color: {{colors[0]}}"><40</div>\n- <div class=graphicitem style="background-color: {{colors[1]}}">40\xe2\x80\x9350</div>\n- <div class=graphicitem style="background-color: {{colors[2]}}">50\xe2\x80\x9380</div>\n- <div class=graphicitem style="background-color: {{colors[3]}}">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: {{colors[4]}}">200\xe2\x89\xa4</div>\n- </div></div>\n- <div style="clear: left"></div>\n-\n- <div class=tablewrapper>\n-\n- <div class=scale>\n- <div>query:</div>\n- <div class=graphicrow>\n- {% for s in queryscale %}\n- <div class=graphicitem style="width: {{s.width}}%">\n- <div>{{s.label}}</div>\n- </div>\n- {% endfor %}\n- </div>\n- <div style="clear: left"></div>\n- </div>\n- \n- {% for line in match_colors %}\n- <a class=matchresult\n- href="{{line.link}}"\n- onmouseover=\'document.getElementById("defline").innerHTML="{{line.defline|js_string_escape}}"\'\n- onmouseout=\'document.getElementById("defline").innerHTML="Mouse-over to show defline and scores, click to show alignments"\'\n- title="{{line.defline}}">\n- <div class="matchrow graphicrow">\n- {% for match in line.colors %}\n- <div class="matchitem graphicitem"\n- style="background-color: {{match[1]}}; width: {{match[0]}}%"></div>\n- {% endfor %}\n- </div>\n- </a>\n- \n- {% endfor %}\n- </div>\n- </div>\n+ No matches\n </div>\n </section>\n \n-\n+ {% else %}\n+ {% for result in blast.BlastOutput_iterations.Iteration %}\n+ \n+ <section class=match>\n \n- <section class=descriptions>\n- <h2>Descriptions</h2>\n+ <h1>Nucleotide Sequence ({{result|len}} letters)</h1>\n+\n+ <section class=header>\n+\n+ '..b' class=b>Length:</span> {{hit.Hit_len}}\n- <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}\n- </p>\n+ {% for hsp in hit.Hit_hsps.Hsp %}\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range {{hsp.Hsp_num}}: {{hsp[\'Hsp_hit-from\']}} to {{hsp[\'Hsp_hit-to\']}}</span>\n+ <a class=range href="{{genelink(hit|hitid, \'genbank\', hsp)}}">GenBank</a>\n+ <a class=range href="{{genelink(hit|hitid, \'graph\', hsp)}}">Graphics</a>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>{{hsp[\'Hsp_bit-score\']|fmt(\'.1f\')}} bits({{hsp.Hsp_score}})</td>\n+ <td>{{hsp.Hsp_evalue|fmt(\'.1f\')}}</td>\n+ <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{\n+ (hsp.Hsp_identity/hsp|len) |fmt(\'.0%\') }})</td>\n+ <td>{{ hsp.Hsp_gaps }}/{{ hsp|len\n+ }}({{ (hsp.Hsp_gaps / hsp|len) | fmt(\'.0%\') }})</td>\n+ <td>{{ hsp[\'Hsp_query-frame\']|asframe }}/{{ hsp[\'Hsp_hit-frame\']|asframe }}</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>\n+ </div>\n+ {% endfor %}\n+\n </div>\n \n- {% if hit|othertitles|length %}\n- <a class=showmoretitles onclick="toggle_visibility(\'moretitles{{hit.Hit_num|js_string_escape}}\'); return false;" href=\'\'>\n- See {{hit|othertitles|length}} more title(s)\n- </a>\n-\n- <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">\n- {% for title in hit|othertitles %}\n- <div class=title>\n- <p class=hittitle>{{title.title}}</p>\n- <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>\n- </p>\n- </div>\n- {% endfor %}\n- </div>\n- {% endif %}\n-\n- {% for hsp in hit.Hit_hsps.Hsp %}\n- <div class=hotspot>\n- <p class=range>\n- <span class=range>Range {{hsp.Hsp_num}}: {{hsp[\'Hsp_hit-from\']}} to {{hsp[\'Hsp_hit-to\']}}</span>\n- <a class=range href="{{genelink(hit|hitid, \'genbank\', hsp)}}">GenBank</a>\n- <a class=range href="{{genelink(hit|hitid, \'graph\', hsp)}}">Graphics</a>\n- </p>\n+ {% endfor %}\n+ </div></div>\n+ </section>\n+ {% endif %}\n \n- <table class=hotspotstable>\n- <tr>\n- <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n- </tr>\n- <tr>\n- <td>{{hsp[\'Hsp_bit-score\']|fmt(\'.1f\')}} bits({{hsp.Hsp_score}})</td>\n- <td>{{hsp.Hsp_evalue|fmt(\'.1f\')}}</td>\n- <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{\n- (hsp.Hsp_identity/hsp|len) |fmt(\'.0%\') }})</td>\n- <td>{{ hsp.Hsp_gaps }}/{{ hsp|len\n- }}({{ (hsp.Hsp_gaps / hsp|len) | fmt(\'.0%\') }})</td>\n- <td>{{ hsp[\'Hsp_query-frame\']|asframe }}/{{ hsp[\'Hsp_hit-frame\']|asframe }}</td>\n- </tr>\n- </table>\n-\n- <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>\n- </div>\n- {% endfor %}\n- \n- </div>\n-\n- {% endfor %}\n- </div></div>\n- </section>\n-\n- {% endif %}\n+ {% endfor %}\n+ {% endif %}\n </div>\n </body>\n </html>\n' |
| b |
| diff -r 4434ffab721a -r 67ddcb807b7d blast_html.py --- a/blast_html.py Tue May 13 15:26:20 2014 +0200 +++ b/blast_html.py Tue May 13 18:06:36 2014 +0200 |
| [ |
| @@ -19,11 +19,11 @@ "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 + _filters[func_or_name] = func.__name__ return func return inner else: - _filters[func_or_name.__name__] = func_or_name + _filters[func_or_name.__name__] = func_or_name.__name__ return func_or_name @@ -78,8 +78,13 @@ ) @filter('len') -def hsplen(node): - return int(node['Hsp_align-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): @@ -134,6 +139,13 @@ 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: @@ -151,15 +163,15 @@ self.environment = jinja2.Environment(loader=self.loader, lstrip_blocks=True, trim_blocks=True, autoescape=True) - self.environment.filters.update(_filters) - self.environment.filters['color'] = lambda length: match_colors[color_idx(length)] + self._addfilters(self.environment) + - 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 _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) @@ -171,41 +183,38 @@ ('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, + iterations=self.blast.BlastOutput_iterations.Iteration, colors=self.colors, - match_colors=self.match_colors(), - queryscale=self.queryscale(), - hit_info=self.hit_info(), + # match_colors=self.match_colors(), + # hit_info=self.hit_info(), genelink=genelink, params=params)) - - def match_colors(self): + @filter + def match_colors(self, result): """ An iterator that yields lists of length-color pairs. """ - percent_multiplier = 100 / self.query_length + query_length = blastxml_len(result) + + percent_multiplier = 100 / query_length - for hit in self.hits: + 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: hsplen(hsp)) - table = bytearray([255]) * self.query_length + 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(hsplen(hsp)), to - frm) + table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm) matches = [] last = table[0] count = 0 - for i in range(self.query_length): + for i in range(query_length): if table[i] == last: count += 1 continue @@ -216,25 +225,28 @@ 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): + @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) - if self.query_length % skip != 0: - yield dict(label = self.query_length, width = (self.query_length % skip) * percent_multiplier) - + if query_length % skip != 0: + yield dict(label = query_length, width = (query_length % skip) * percent_multiplier) - def hit_info(self): + @filter + def hit_info(self, result): - for hit in self.ordered_hits: + query_length = blastxml_len(result) + + for hit in hits(result): hsps = hit.Hit_hsps.Hsp - cover = [False] * self.query_length + cover = [False] * query_length for hsp in hsps: - cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, hsplen(hsp)) + 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): @@ -245,10 +257,10 @@ 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), + 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 / hsplen(hsp) for hsp in hsps))), + ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))), accession = hit.Hit_accession) def main(): |