Nucleotide Sequence ({{blast["BlastOutput_query-len"]}} letters)

Nucleotide Sequence ({{length}} letters)

{{param}}	{{value}}

{{param}}	{{value}}

Graphic Summary

+ +

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

+ +

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

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

Color key for alignment scores

- - - - - - -

<40

40-50

50-80

80-200

>=200

Color key for alignment scores

+ + + + + +

<40

40-50

50-80

80-200

200≤

+ +

- {% for line in match_colors %} - - - {% for match in line.colors %} -

- {% endfor %} -

- - {% endfor %} - -

hoi

query:

+ + {% for s in queryscale %} + + {% endfor %} +

+ + {% for line in match_colors %} + + + {% for match in line.colors %} +

+ {% endfor %} +

+ + + {% endfor %} +

Descriptions

Sequences producing significant alignments:

+ + + + + + + + + + + {% for hit in hit_info %} + + + + + + + + + + {% endfor %} +

Description	Max score	Total score	Query cover	E value	Ident	Accession
{{hit.description}}	{{hit.maxscore}}	{{hit.totalscore}}	{{hit.cover}}	{{hit.e_value}}	{{hit.ident}}	{{hit.accession}}

+ +

diff -r d20ce91e1297 -r 9e7927673089 visualise.py --- a/visualise.py Wed May 07 19:02:20 2014 +0200 +++ b/visualise.py Thu May 08 16:51:52 2014 +0200 @@ -4,6 +4,7 @@ # License: GPL version 3 or higher import sys +import math import warnings from itertools import repeat from lxml import objectify @@ -26,19 +27,24 @@ blast = objectify.parse('blast xml example1.xml').getroot() loader = jinja2.FileSystemLoader(searchpath='.') -environment = jinja2.Environment(loader=loader) +environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True) environment.filters['color'] = lambda length: match_colors[color_idx(length)] +query_length = int(blast["BlastOutput_query-len"]) + +hits = blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit +# sort hits by longest hotspot first +ordered_hits = sorted(hits, + key=lambda h: max(hsp['Hsp_align-len'] for hsp in h.Hit_hsps.Hsp), + reverse=True) + def match_colors(): """ An iterator that yields lists of length-color pairs. """ + + percent_multiplier = 100 / query_length - 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. @@ -46,24 +52,58 @@ table = bytearray([255]) * query_length for hsp in hotspots: frm = hsp['Hsp_query-from'] - 1 - to = hsp['Hsp_query-to'] - 1 + to = int(hsp['Hsp_query-to']) 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)): + for i in range(query_length): if table[i] == last: count += 1 continue - matches.append((count, colors[last] if last != 255 else 'none')) + matches.append((count * percent_multiplier, colors[last] if last != 255 else 'none')) last = table[i] count = 1 - matches.append((count, colors[last] if last != 255 else 'none')) + matches.append((count * percent_multiplier, colors[last] if last != 255 else 'none')) + + yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=hit.Hit_def) + - yield dict(colors=matches, link="#hit"+hit.Hit_num.text) +def queryscale(): + max_labels = 10 + skip = math.ceil(query_length / max_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 query_length % skip != 0: + yield dict(label = query_length, width = (query_length % skip) * percent_multiplier) +def hit_info(): + + for hit in ordered_hits: + 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, int(hsp['Hsp_align-len'])) + cover_count = cover.count(True) + + def hsp_val(path): + return (hsp[path] for hsp in hsps) + + yield dict(description = hit.Hit_def, + maxscore = max(hsp_val('Hsp_bit-score')), + totalscore = sum(hsp_val('Hsp_bit-score')), + cover = "{:.0%}".format(cover_count / query_length), + e_value = min(hsp_val('Hsp_evalue')), + # FIXME: is this the correct formula vv? + ident = "{:.0%}".format(min(hsp.Hsp_identity / hsp['Hsp_align-len'] for hsp in hsps)), + accession = hit.Hit_accession) + + def main(): template = environment.get_template('visualise.html.jinja') @@ -78,9 +118,12 @@ 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, + length=query_length, + #hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit, colors=colors, match_colors=match_colors(), + queryscale=queryscale(), + hit_info=hit_info(), params=params)) main()