| Previous changeset 114:4f0ed3b5ae46 (2014-07-09) Next changeset 116:f5066973029a (2014-07-14) |
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Commit message:
make external gene bank name configurable |
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modified:
blast2html.html.jinja blast2html.py blast2html.xml test-data/blast xml example4b.html test-data/blastdb.loc |
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| diff -r 4f0ed3b5ae46 -r 0c2a03f9740b blast2html.html.jinja --- a/blast2html.html.jinja Wed Jul 09 15:20:38 2014 +0200 +++ b/blast2html.html.jinja Mon Jul 14 15:01:32 2014 +0200 |
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| @@ -571,7 +571,7 @@ <div class=linkheader> <div class=right><a href="#description{{hit|nodeid}}">Descriptions</a></div> - {{ hit|genelink('Gene Bank', clas='linkheader', display_nolink=False) }} + {{ hit|genelink(text_from='dbname', cssclass='linkheader', display_nolink=False) }} </div> <div class=title> |
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| diff -r 4f0ed3b5ae46 -r 0c2a03f9740b blast2html.py --- a/blast2html.py Wed Jul 09 15:20:38 2014 +0200 +++ b/blast2html.py Mon Jul 14 15:01:32 2014 +0200 |
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| @@ -15,7 +15,7 @@ from six.moves import builtins from os import path from itertools import repeat -from collections import defaultdict +from collections import defaultdict, namedtuple import glob import argparse from lxml import objectify @@ -238,9 +238,10 @@ max_scale_labels = 10 - def __init__(self, input, templatedir, templatename, genelinks={}): + def __init__(self, input, templatedir, templatename, dbname, genelinks={}): self.input = input self.templatename = templatename + self.dbname = dbname self.genelinks = genelinks self.blast = objectify.parse(self.input).getroot() @@ -348,24 +349,32 @@ ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps)))) @filter - def genelink(self, hit, text=None, clas=None, display_nolink=True): + def genelink(self, hit, text=None, text_from='hitid', cssclass=None, display_nolink=True): """Create a html link from a hit node to a configured gene bank webpage. - text: The text of the link, defaults to the hit_id - clas: extra css classes that will be added to the <a> element + text: The text of the link. If not set applies text_from. + text_from: string, if text is not specified, take it from specified source. Either 'hitid' (default) or 'dbname'. + cssclass: extra css classes that will be added to the <a> element display_nolink: boolean, if false don't display anything if no link can be created. Default True. """ - if text is None: - text = hitid(hit) - db = hit.getroottree().getroot().BlastOutput_db if isinstance(self.genelinks, six.string_types): template = self.genelinks else: - template = self.genelinks.get(db) + template = self.genelinks[db].template + + if text is None: + if text_from == 'hitid': + text = hitid(hit) + elif text_from == 'dbname': + text = self.dbname or self.genelinks[db].dbname or 'Gene Bank' + else: + raise ValueError("Unknown value for text_from: '{0}'. Use 'hitid' or 'dbname'.".format(text_from)) + if template is None: return text if display_nolink else '' + args = dict(id=hitid(hit).split('|'), fullid=hitid(hit), defline=str(hit.Hit_def).split(' ', 1)[0].split('|'), @@ -377,12 +386,13 @@ warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e)) return text if display_nolink else '' - classattr = 'class="{0}" '.format(jinja2.escape(clas)) if clas is not None else '' + classattr = 'class="{0}" '.format(jinja2.escape(cssclass)) if cssclass is not None else '' return jinja2.Markup("<a {0}href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text))) +genelinks_entry = namedtuple('genelinks_entry', 'dbname template') def read_genelinks(dir): - links = {} + links = defaultdict(lambda: genelinks_entry(None, None)) # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc. files = sorted(glob.glob(path.join(dir, 'blastdb*.loc'))) # reversed, so blastdb.loc will take precedence @@ -394,7 +404,7 @@ continue line = l.rstrip('\n').split('\t') try: - links[line[2]] = line[3] + links[line[2]] = genelinks_entry(dbname=line[3], template=line[4]) except IndexError: continue f.close() @@ -427,7 +437,9 @@ # care too much. parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template, help='The template file to use. Defaults to blast_html.html.jinja') - + + parser.add_argument('--dbname', type=str, default=None, + help="The link text to use for external links to a gene bank database. Defaults to 'Gene Bank'") dblink_group = parser.add_mutually_exclusive_group() dblink_group.add_argument('--genelink-template', metavar='URL_TEMPLATE', default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign', @@ -438,7 +450,7 @@ The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign', which is a link to the NCBI nucleotide database.""") - + dblink_group.add_argument('--db-config-dir', help="""The directory where databases are configured in blastdb*.loc files. These files are consulted for creating a gene bank link. The files should be tab-separated tables (with lines @@ -473,20 +485,20 @@ args.output.close() args.output = io.open(args.output.name, 'w', encoding='utf-8') - + templatedir, templatename = path.split(args.template.name) args.template.close() if not templatedir: templatedir = '.' if args.db_config_dir is None: - genelinks = args.genelink_template + genelinks = defaultdict(lambda: genelinks_entry(template=args.genelink_template, dbname=None)) elif not path.isdir(args.db_config_dir): parser.error('db-config-dir does not exist or is not a directory') else: genelinks = read_genelinks(args.db_config_dir) - b = BlastVisualize(args.input, templatedir, templatename, genelinks) + b = BlastVisualize(args.input, templatedir, templatename, dbname=args.dbname, genelinks=genelinks) b.render(args.output) args.output.close() |
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| diff -r 4f0ed3b5ae46 -r 0c2a03f9740b blast2html.xml --- a/blast2html.xml Wed Jul 09 15:20:38 2014 +0200 +++ b/blast2html.xml Mon Jul 14 15:01:32 2014 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="blast2html" name="blast2html" version="0.0.12"> +<tool id="blast2html" name="blast2html" version="0.0.13"> <description>Convert BLAST XML to HTML</description> |
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| diff -r 4f0ed3b5ae46 -r 0c2a03f9740b test-data/blast xml example4b.html --- a/test-data/blast xml example4b.html Wed Jul 09 15:20:38 2014 +0200 +++ b/test-data/blast xml example4b.html Mon Jul 14 15:01:32 2014 +0200 |
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| @@ -605,7 +605,7 @@ <div class=linkheader> <div class=right><a href="#description1-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Example Gene Bank</a> </div> <div class=title> @@ -647,7 +647,7 @@ <div class=linkheader> <div class=right><a href="#description1-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Example Gene Bank</a> </div> <div class=title> @@ -905,7 +905,7 @@ <div class=linkheader> <div class=right><a href="#description3-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Example Gene Bank</a> </div> <div class=title> @@ -947,7 +947,7 @@ <div class=linkheader> <div class=right><a href="#description3-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Example Gene Bank</a> </div> <div class=title> @@ -989,7 +989,7 @@ <div class=linkheader> <div class=right><a href="#description3-3">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AJ308515.1/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/AJ308515.1/">Example Gene Bank</a> </div> <div class=title> @@ -1247,7 +1247,7 @@ <div class=linkheader> <div class=right><a href="#description6-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/EUG/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/EUG/">Example Gene Bank</a> </div> <div class=title> @@ -1289,7 +1289,7 @@ <div class=linkheader> <div class=right><a href="#description6-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Example Gene Bank</a> </div> <div class=title> @@ -1497,7 +1497,7 @@ <div class=linkheader> <div class=right><a href="#description7-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/EUG/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/EUG/">Example Gene Bank</a> </div> <div class=title> @@ -1542,7 +1542,7 @@ <div class=linkheader> <div class=right><a href="#description7-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Gene Bank</a> + <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Example Gene Bank</a> </div> <div class=title> |
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| diff -r 4f0ed3b5ae46 -r 0c2a03f9740b test-data/blastdb.loc --- a/test-data/blastdb.loc Wed Jul 09 15:20:38 2014 +0200 +++ b/test-data/blastdb.loc Mon Jul 14 15:01:32 2014 +0200 |
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| @@ -36,4 +36,4 @@ #See also blastdb_p.loc which is for any protein BLAST database, and #blastdb_d.loc which is for any protein domains databases (like CDD). -EUginius_plasmid Euginius plasmid insert /opt/galaxy/blastdbs/EUginius_plasmid_insert http://example.com/example-genebank/{defline[0]}/ +EUginius_plasmid Euginius plasmid insert /opt/galaxy/blastdbs/EUginius_plasmid_insert Example Gene Bank http://example.com/example-genebank/{defline[0]}/ |