| Previous changeset 11:7660519f2dc9 (2014-05-12) Next changeset 13:c2d63adb83db (2014-05-12) |
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Commit message:
add links, refactor, proper commandline arguments |
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modified:
visualise.html.jinja visualise.py |
| b |
| diff -r 7660519f2dc9 -r a459c754cdb5 visualise.html.jinja --- a/visualise.html.jinja Mon May 12 13:55:04 2014 +0200 +++ b/visualise.html.jinja Mon May 12 17:12:24 2014 +0200 |
| [ |
| @@ -11,6 +11,14 @@ font-family: Arial,Sans-Serif; } + :link { + color: #336699; + } + + .right { + float: right; + } + #content { margin: 0 2em; padding: 0.5em; @@ -76,10 +84,12 @@ float: left; } + + .graphic { background-color: white; border: 2px solid black; - padding: .5em; + padding: .5em 1.5em; align: center; margin: auto; } @@ -128,7 +138,7 @@ } /* For small widths we give the graphic 100% */ - @media (max-width: 70em) { + @media (max-width: 72.5em) { div.tablewrapper { width: 100%; min-width: 0px; @@ -174,6 +184,8 @@ height: 4px; } + + div#descriptions { } @@ -212,10 +224,9 @@ white-space: nowrap; text-align: left; } - table.descriptiontable a:link { - color: #336699; - } + + #alignments .white { padding: 1.5em 1em; } @@ -228,12 +239,13 @@ div.linkheader { padding-top: .2em; - text-align: right; font-size: 85%; color: #14376C; } - div.linkheader a { - color: #14376C; + div.linkheader a.linkheader { + margin-right: 1em; + } + div.linkheader .right a { text-decoration: none; } @@ -244,6 +256,7 @@ .title .titleinfo { font-size: 80%; margin-top: 0; + margin-bottom: .3em; } .title .titleinfo .b { color: #606060; @@ -259,13 +272,15 @@ padding: 0; } .moretitles .hittitle { - margin: .2em 0; + margin: .4em 0 .2em 0; padding: 0; } a.showmoretitles { - font-size: 85%; + font-size: 75%; color: #336699; + font-weight: bold; + margin-top: 0; } a.showmoretitles:hover { } @@ -276,13 +291,18 @@ margin-bottom: 2.5em; } - .hotspot .range { + .hotspot p.range { font-size: 70%; margin-top: 0; - font-weight: bold; margin-top: 1em; margin-bottom: .2em; } + .hotspot p.range span.range { + font-weight: bold; + } + .hotspot p.range a.range { + margin-left: .5em; + } table.hotspotstable { border-top: 1px solid; @@ -330,14 +350,14 @@ <table class=headerdata> {% for param, value in params %} - <tr><td class=param>{{param}}</td><td>{{value}}</td></tr> + <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr> {% endfor %} </table> </div> - - {% if not (blast.BlastOutput_iterations.find('Iteration') and - blast.BlastOutput_iterations.Iteration.Iteration_hits.find('Hit')) %} + + {% if not (blast.BlastOutput_iterations.findall('Iteration') and + blast.BlastOutput_iterations.Iteration.Iteration_hits.findall('Hit')) %} <div id=nodata> <h2>No Results</h2> <div class=grey> @@ -360,9 +380,9 @@ <h4 class=darkHeader>Color key for alignment scores</h4> <div class=legend><div class=graphicrow> <div class=graphicitem style="background-color: {{colors[0]}}"><40</div> - <div class=graphicitem style="background-color: {{colors[1]}}">40&endash;50</div> - <div class=graphicitem style="background-color: {{colors[2]}}">50-80</div> - <div class=graphicitem style="background-color: {{colors[3]}}">80-200</div> + <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div> + <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div> + <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div> <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div> </div></div> <div style="clear: left"></div> @@ -433,7 +453,7 @@ <td>{{hit.cover}}</td> <td>{{hit.e_value}}</td> <td>{{hit.ident}}</td> - <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/{{hit.hit|hitid}}?report=genbank&log$=nucltop&blast_rank=1">{{hit.accession}}</a></td> + <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td> </tr> {% endfor %} </table> @@ -451,13 +471,15 @@ <div class=alignment id=hit{{hit.Hit_num}}> <div class=linkheader> - <a href="#description{{hit.Hit_num}}">Descriptions</a> + <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div> + <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a> + <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a> </div> - + <div class=title> <p class=hittitle>{{hit|firsttitle}}</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/{{hit|hitid}}?report=genbank&log$=nuclalign&blast_rank=1">{{hit|seqid}}</a> + <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a> <span class=b>Length:</span> {{hit.Hit_len}} <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}} </p> @@ -473,7 +495,7 @@ <div class=title> <p class=hittitle>{{title.title}}</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> {{title.id}} + <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a> </p> </div> {% endfor %} @@ -482,7 +504,11 @@ {% for hsp in hit.Hit_hsps.Hsp %} <div class=hotspot> - <p class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}} <a href="http://www.ncbi.nlm.nih.gov/nucleotide/{{hit|hitid}}?report=genbank&log$=nuclalign&blast_rank=1&from={{hsp['Hsp_hit-from']}}&to={{hsp['Hsp_hit-to']}}">GenBank</a></p> + <p class=range> + <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span> + <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a> + <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a> + </p> <table class=hotspotstable> <tr> |
| b |
| diff -r 7660519f2dc9 -r a459c754cdb5 visualise.py --- a/visualise.py Mon May 12 13:55:04 2014 +0200 +++ b/visualise.py Mon May 12 17:12:24 2014 +0200 |
| [ |
| b'@@ -7,23 +7,22 @@\n import math\n import warnings\n from itertools import repeat\n+import argparse\n from lxml import objectify\n import jinja2\n \n \n-blast = objectify.parse(\'blast xml example1.xml\').getroot()\n-loader = jinja2.FileSystemLoader(searchpath=\'.\')\n-environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True)\n \n+_filters = {}\n def filter(func_or_name):\n "Decorator to register a function as filter in the current jinja environment"\n if isinstance(func_or_name, str):\n def inner(func):\n- environment.filters[func_or_name] = func\n+ _filters[func_or_name] = func\n return func\n return inner\n else:\n- environment.filters[func_or_name.__name__] = func_or_name\n+ _filters[func_or_name.__name__] = func_or_name\n return func_or_name\n \n \n@@ -38,10 +37,6 @@\n return 3\n return 4\n \n-colors = [\'black\', \'blue\', \'green\', \'magenta\', \'red\']\n-\n-environment.filters[\'color\'] = lambda length: match_colors[color_idx(length)]\n-\n @filter\n def fmt(val, fmt):\n return format(float(val), fmt)\n@@ -58,8 +53,9 @@\n titles = []\n for t in id_titles[1:]:\n fullid, title = t.split(\' \', 1)\n- id = fullid.split(\'|\', 2)[2]\n+ hitid, id = fullid.split(\'|\', 2)[1:3]\n titles.append(dict(id = id,\n+ hitid = hitid,\n fullid = fullid,\n title = title))\n return titles\n@@ -92,108 +88,158 @@\n return \'Minus\'\n raise Exception("frame should be either +1 or -1")\n \n-\n-query_length = int(blast["BlastOutput_query-len"])\n-\n-hits = blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit\n-# sort hits by longest hotspot first\n-ordered_hits = sorted(hits,\n- key=lambda h: max(hsplen(hsp) for hsp in h.Hit_hsps.Hsp),\n- reverse=True)\n-\n-def match_colors():\n- """\n- An iterator that yields lists of length-color pairs. \n- """\n+def genelink(hit, type=\'genbank\', hsp=None):\n+ if not isinstance(hit, str):\n+ hit = hitid(hit)\n+ link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)\n+ if hsp != None:\n+ link += "&from={}&to={}".format(hsp[\'Hsp_hit-from\'], hsp[\'Hsp_hit-to\'])\n+ return jinja2.Markup(link)\n \n- percent_multiplier = 100 / query_length\n- \n- for hit in hits:\n- # sort hotspots from short to long, so we can overwrite index colors of\n- # short matches with those of long ones.\n- hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: hsplen(hsp))\n- table = bytearray([255]) * query_length\n- for hsp in hotspots:\n- frm = hsp[\'Hsp_query-from\'] - 1\n- to = int(hsp[\'Hsp_query-to\'])\n- table[frm:to] = repeat(color_idx(hsplen(hsp)), to - frm)\n \n- matches = []\n- last = table[0]\n- count = 0\n- for i in range(query_length):\n- if table[i] == last:\n- count += 1\n- continue\n- matches.append((count * percent_multiplier, colors[last] if last != 255 else \'none\'))\n- last = table[i]\n- count = 1\n- matches.append((count * percent_multiplier, colors[last] if last != 255 else \'none\'))\n-\n- yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))\n \n \n-def queryscale():\n- max_labels = 10\n- skip = math.ceil(query_length / max_labels)\n- percent_multiplier = 100 / query_length\n- for i in range(1, query_length+1):\n- if i % skip == 0:\n- yield dict(label = i, width = skip * percent_multiplier)\n- if query_length % skip != 0:\n- yield dict(label = query_length, width = (query_length % skip) * percent_multiplier)\n+class BlastVisualize:\n+\n+ colors = (\'black\', \'blue\', \'green\', \'magenta\', \'red\')\n+\n+ max_scale_labels = 10\n+\n+ templatename = \'visualise.html.jinja\'\n+\n+ def __init__(self, input):\n+ '..b')),\n- # FIXME: is this the correct formula vv?\n- ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))),\n- accession = hit.Hit_accession)\n+ cover = [False] * self.query_length\n+ for hsp in hsps:\n+ cover[hsp[\'Hsp_query-from\']-1 : int(hsp[\'Hsp_query-to\'])] = repeat(True, hsplen(hsp))\n+ cover_count = cover.count(True)\n+\n+ def hsp_val(path):\n+ return (float(hsp[path]) for hsp in hsps)\n+\n+ yield dict(hit = hit,\n+ title = firsttitle(hit),\n+ link_id = hit.Hit_num,\n+ maxscore = "{:.1f}".format(max(hsp_val(\'Hsp_bit-score\'))),\n+ totalscore = "{:.1f}".format(sum(hsp_val(\'Hsp_bit-score\'))),\n+ cover = "{:.0%}".format(cover_count / self.query_length),\n+ e_value = "{:.4g}".format(min(hsp_val(\'Hsp_evalue\'))),\n+ # FIXME: is this the correct formula vv?\n+ ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))),\n+ accession = hit.Hit_accession)\n \n \n def main():\n- template = environment.get_template(\'visualise.html.jinja\')\n \n- params = ((\'Query ID\', blast["BlastOutput_query-ID"]),\n- (\'Query definition\', blast["BlastOutput_query-def"]),\n- (\'Query length\', blast["BlastOutput_query-len"]),\n- (\'Program\', blast.BlastOutput_version),\n- (\'Database\', blast.BlastOutput_db),\n- )\n-\n- if len(blast.BlastOutput_iterations.Iteration) > 1:\n- warnings.warn("Multiple \'Iteration\' elements found, showing only the first")\n+ parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",\n+ usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))\n+ input_group = parser.add_mutually_exclusive_group(required=True)\n+ input_group.add_argument(\'positional_arg\', metavar=\'INPUT\', nargs=\'?\', type=argparse.FileType(mode=\'r\'),\n+ help=\'The input Blast XML file, same as -i/--input\')\n+ input_group.add_argument(\'-i\', \'--input\', type=argparse.FileType(mode=\'r\'), \n+ help=\'The input Blast XML file\')\n+ parser.add_argument(\'-o\', \'--output\', type=argparse.FileType(mode=\'w\'), default=sys.stdout,\n+ help=\'The output html file\')\n \n- sys.stdout.write(template.render(blast=blast,\n- length=query_length,\n- hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,\n- colors=colors,\n- match_colors=match_colors(),\n- queryscale=queryscale(),\n- hit_info=hit_info(),\n- params=params))\n+ args = parser.parse_args()\n+ if args.input == None:\n+ args.input = args.positional_arg\n+ if args.input == None:\n+ parser.error(\'no input specified\')\n \n-main()\n+ b = BlastVisualize(args.input)\n+ b.render(args.output)\n+\n \n-# http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014\n-# http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj\n+if __name__ == \'__main__\':\n+ main()\n \n-# http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nucltop&blast_rank=1&RID=PHWP1JNZ014\n' |