| Previous changeset 9:bbdc8fb0de2b (2014-05-08) Next changeset 11:7660519f2dc9 (2014-05-12) |
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Commit message:
All data is displayed now, still some formatting to do |
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modified:
visualise.html.jinja visualise.py |
| b |
| diff -r bbdc8fb0de2b -r 2fbdf2eb27b4 visualise.html.jinja --- a/visualise.html.jinja Thu May 08 18:59:32 2014 +0200 +++ b/visualise.html.jinja Fri May 09 18:16:48 2014 +0200 |
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| @@ -60,7 +60,7 @@ .white { background-color: white; border: 1px solid #cccccc; - padding: 1em; + padding: 1.5em 2%; } .graphicrow { @@ -98,7 +98,7 @@ padding-right: .2em; max-width: 50em; text-align: left; - height: 4em; + height: 2.8em; overflow-y: hidden; } @@ -151,6 +151,12 @@ background-color: red; color: white; } + .scale .graphicitem:first-child div { + margin-left: 0px; + } + .scale .graphicitem:last-child div { + margin-right: 0px; + } a.matchresult { display: block; @@ -164,22 +170,55 @@ height: 4px; } + div#descriptions { + } + table.descriptiontable { + font-size: 85%; + border: 1px solid #97b0c8; + border-spacing: 0; + color: #222222; + line-height: 1.3em; + background-color: white; + } + table.descriptiontable col:first-child { width: 100%; } + table.descriptiontable tr:hover { + background-color: #D5DEE3; + } + table.descriptiontable th { + background-color: #F0F0F0; + background: linear-gradient(#FFFFFF, #F0F0F0); + border-bottom: 1px solid #D4DFE9; + border-right: 1px solid #CFCFCF; + border-left: 0px solid black; + border-top: 0px solid black; + } table.descriptiontable td { overflow: hidden; - white-space: nowrap; + text-align: center; + padding: .4em .8em; } table.descriptiontable td div { width: 1em; overflow: visible; white-space: nowrap; + text-align: left; } </style> - + <script type="text/javascript"> + function toggle_visibility(id) { + var e = document.getElementById(id); + if(e.style.display == 'none') + e.style.display = 'block'; + else + e.style.display = 'none'; + } + </script> + </head> <body> @@ -223,7 +262,7 @@ {% for s in queryscale %} <div class=graphicitem style="width: {{s.width|safe}}%"> - <div style="{{'margin-left: 0px' if loop.first else 'margin-right: 0px' if loop.last}}">{{s.label|safe}}</div> + <div>{{s.label|safe}}</div> </div> {% endfor %} </div> @@ -250,11 +289,14 @@ </div> </div> + + <div id=descriptions> <h2>Descriptions</h2> <div class=grey><div class=white> <h4 class=blackHeader>Sequences producing significant alignments:</h4> + <table class=descriptiontable> <col/><col/><col/><col/><col/><col/><col/> <tr> @@ -268,7 +310,11 @@ </tr> {% for hit in hit_info %} <tr> - <td style="width: 100%"><div>{{hit.description}}</div></td> + <td><div><a href="#hit{{hit.link_id}}" + title="{{hit.title}}" + name=description{{hit.link_id}}> + {{hit.title}} + </a></div></td> <td>{{hit.maxscore}}</td> <td>{{hit.totalscore}}</td> <td>{{hit.cover}}</td> @@ -280,7 +326,78 @@ </table> </div></div> + </div> + + + <div id=alignments> + <h2>Alignments</h2> + + <div class=grey><div class=white> + {% for hit in hits %} + <div class=alignment id=hit{{hit.Hit_num}}> + + <div class=linkheader> + <a href="#description{{hit.Hit_num}}">Descriptions</a> + </div> + + <div class=title> + <p class=hittitle>{{hit|firsttitle}}</p> + <p class=titleinfo> + <span class=b>Sequence ID:</span> {{hit|seqid}} + <span class=b>Length:</span> {{hit.Hit_len}} + <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}} + </p> + </div> + + <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num}}'); return false;" href=''> + Show {{hit|othertitles|length}} more title(s) + </a> + + <div class=moretitles id=moretitles{{hit.Hit_num}}> + {% for title in hit|othertitles %} + <div class=title> + <p class=hittitle>{{title.title}}</p> + <p class=titleinfo> + <span class=b>Sequence ID:</span> {{title.id}} + </p> + </div> + {% endfor %} + </div> + + {% for hsp in hit.Hit_hsps.Hsp %} + <div class=hotspots> + <p>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</p> + + <table class=hotspotstable> + <tr> + <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> + </tr> + <tr> + <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td> + <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td> + <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{ + (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td> + <td>{{ hsp.Hsp_gaps }}/{{ hsp|len + }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td> + <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td> + + </tr> + </table> + + <pre>{{hsp|alignment_pre}}</pre> + + </div> + {% endfor %} + + <p> + {{hit.Hit_id}} + + Hit {{hit.Hit_num}} + </p> + </div> + {% endfor %} + </div></div> </div> </div> |
| b |
| diff -r bbdc8fb0de2b -r 2fbdf2eb27b4 visualise.py --- a/visualise.py Thu May 08 18:59:32 2014 +0200 +++ b/visualise.py Fri May 09 18:16:48 2014 +0200 |
| [ |
| @@ -11,6 +11,21 @@ import jinja2 +blast = objectify.parse('blast xml example1.xml').getroot() +loader = jinja2.FileSystemLoader(searchpath='.') +environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True) + +def filter(func_or_name): + if isinstance(func_or_name, str): + def inner(func): + environment.filters[func_or_name] = func + return func + return inner + else: + environment.filters[func_or_name.__name__] = func_or_name + return func_or_name + + def color_idx(length): if length < 40: return 0 @@ -22,20 +37,66 @@ 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, lstrip_blocks=True, trim_blocks=True, autoescape=True) environment.filters['color'] = lambda length: match_colors[color_idx(length)] +@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) + id = fullid.split('|', 2)[2] + titles.append(dict(id = id, + 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'], hsp.Hsp_qseq, hsp['Hsp_query-to']) + + " {:7s} {}\n".format('', hsp.Hsp_midline) + + "Subject {:>7s} {} {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to'])) + +@filter('len') +def hsplen(node): + return int(node['Hsp_align-len']) + +@filter +def asframe(frame): + if frame == 1: + return 'Plus' + elif frame == -1: + return 'Minus' + raise Exception("frame should be either +1 or -1") + + 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), + key=lambda h: max(hsplen(hsp) for hsp in h.Hit_hsps.Hsp), reverse=True) def match_colors(): @@ -48,12 +109,12 @@ 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']) + hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: hsplen(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(hsp['Hsp_align-len']), to - frm) + table[frm:to] = repeat(color_idx(hsplen(hsp)), to - frm) matches = [] last = table[0] @@ -67,7 +128,7 @@ count = 1 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, defline=firsttitle(hit)) def queryscale(): @@ -88,22 +149,23 @@ 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[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, hsplen(hsp)) 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')), + yield dict(title = firsttitle(hit), + link_id = hit.Hit_num, + maxscore = "{:.1f}".format(float(max(hsp_val('Hsp_bit-score')))), + totalscore = "{:.1f}".format(float(sum(hsp_val('Hsp_bit-score')))), cover = "{:.0%}".format(cover_count / query_length), - e_value = min(hsp_val('Hsp_evalue')), + e_value = "{:.4g}".format(float(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)), + ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))), accession = hit.Hit_accession) - - + + def main(): template = environment.get_template('visualise.html.jinja') @@ -119,7 +181,7 @@ sys.stdout.write(template.render(blast=blast, length=query_length, - #hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit, + hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit, colors=colors, match_colors=match_colors(), queryscale=queryscale(), |