# HG changeset patch # User Jan Kanis # Date 1399997196 -7200 # Node ID 67ddcb807b7dfedcabbb1f9fd92fa5ef4ef954c4 # Parent 4434ffab721aea648731e1125062ac1a09059c18 make it work with multiple queries 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 @@ -2,6 +2,7 @@ + Blast output @@ -97,12 +98,12 @@ margin: auto; } - .centered, #defline, div.legend, div.tablewrapper { + .centered, .defline, div.legend, div.tablewrapper { margin-left: auto; margin-right: auto; } - #defline { + .defline { background-color: white; border: 1px solid black; margin: .5em auto; @@ -338,197 +339,213 @@
-

Nucleotide Sequence ({{length}} letters)

-
- - - {% for param, value in params %} - - {% endfor %} -
{{param}}:{{value}}
- -
- - {% if not (blast.BlastOutput_iterations.findall('Iteration') and - blast.BlastOutput_iterations.Iteration.Iteration_hits.findall('Hit')) %} + {% if not blast.BlastOutput_iterations.findall('Iteration') %}
-

No Results

-
- No Matches -
-
- {% else %} - - - -
-

Graphic Summary

- +

No data

-

Distribution of {{hits|length}} Blast Hits on the Query Sequence

- -
Mouse-over to show defline and scores, click to show alignments
- -
-

Color key for alignment scores

-
-
<40
-
40–50
-
50–80
-
80–200
-
200≤
-
-
- -
- -
-
query:
-
- {% for s in queryscale %} -
-
{{s.label}}
-
- {% endfor %} -
-
-
- - {% for line in match_colors %} - -
- {% for match in line.colors %} -
- {% endfor %} -
- - - {% endfor %} -
-
+ No matches
- + {% else %} + {% for result in blast.BlastOutput_iterations.Iteration %} + +
-
-

Descriptions

+

Nucleotide Sequence ({{result|len}} letters)

+ +
+ + + {% for param, value in params %} + + {% endfor %} +
{{param}}:{{value}}
+ +
+ + {% set hits = result|hits %} + {% if not hits %} +
+

No Hits

+
+ This query did not match anywhere +
+
+ {% else %} + +
+

Graphic Summary

+ +
+

Distribution of {{result|length}} Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
-
-

Sequences producing significant alignments:

+
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+ {% for s in result|queryscale %} +
+
{{s.label}}
+
+ {% endfor %} +
+
+
+ + {% for line in result|match_colors %} + +
+ {% for hit in line.colors %} +
+ {% endfor %} +
+ + + {% endfor %} +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

- - - - - - - - - - - - {% for hit in hit_info %} - - - - - - - - - - {% endfor %} -
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
{{hit.maxscore}}{{hit.totalscore}}{{hit.cover}}{{hit.e_value}}{{hit.ident}}{{hit.accession}}
- -
-
+ + + + + + + + + + + + {% for hit in result|hit_info %} + + + + + + + + + + {% endfor %} +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
{{hit.maxscore}}{{hit.totalscore}}{{hit.cover}}{{hit.e_value}}{{hit.ident}}{{hit.accession}}
+ +
+ + + + +
+

Alignments

+ +
+ {% for hit in hits %} +
+ +
+
Descriptions
+ GenBank + Graphics +
- +
+

{{hit|firsttitle}}

+

+ Sequence ID: {{hit|seqid}} + Length: {{hit.Hit_len}} + Number of Matches: {{hit.Hit_hsps.Hsp|length}} +

+
+ + {% if hit|othertitles|length %} + + See {{hit|othertitles|length}} more title(s) + + + + {% endif %} -
-

Alignments

- -
- {% for hit in hits %} -
- -
-
Descriptions
- GenBank - Graphics -
- -
-

{{hit|firsttitle}}

-

- Sequence ID: {{hit|seqid}} - Length: {{hit.Hit_len}} - Number of Matches: {{hit.Hit_hsps.Hsp|length}} -

+ {% for hsp in hit.Hit_hsps.Hsp %} +
+

+ Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}} + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}}){{hsp.Hsp_evalue|fmt('.1f')}}{{ hsp.Hsp_identity }}/{{ hsp|len }}({{ + (hsp.Hsp_identity/hsp|len) |fmt('.0%') }}){{ hsp.Hsp_gaps }}/{{ hsp|len + }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }}){{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}
+ + 
{{hsp|alignment_pre}}
+
+ {% endfor %} +
- {% if hit|othertitles|length %} - - See {{hit|othertitles|length}} more title(s) - - - - {% endif %} - - {% for hsp in hit.Hit_hsps.Hsp %} -
-

- Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}} - GenBank - Graphics -

+ {% endfor %} +
+
+ {% endif %} - - - - - - - - - - - -
ScoreExpectIdentitiesGapsStrand
{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}}){{hsp.Hsp_evalue|fmt('.1f')}}{{ hsp.Hsp_identity }}/{{ hsp|len }}({{ - (hsp.Hsp_identity/hsp|len) |fmt('.0%') }}){{ hsp.Hsp_gaps }}/{{ hsp|len - }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }}){{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}
- - 
{{hsp|alignment_pre}}
-
- {% endfor %} - -
- - {% endfor %} -
-
- - {% endif %} + {% endfor %} + {% endif %} 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():