blast2html: blast2html.py comparison

comparison blast2html.py @ 115:0c2a03f9740b

make external gene bank name configurable

author	Jan Kanis <jan.code@jankanis.nl>
date	Mon, 14 Jul 2014 15:01:32 +0200
parents	e17aae23cc1c
children	f5066973029a

comparison

equal deleted inserted replaced

-:4f0ed3b5ae46
+:0c2a03f9740b
 import warnings
 import six, codecs, io
 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
 import jinja2
 colors = ('black', 'blue', 'green', 'magenta', 'red')
 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()
 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
 self.environment = jinja2.Environment(loader=self.loader,
 # FIXME: is this the correct formula vv?
 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
 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
+text: The text of the link. If not set applies text_from.
-clas: extra css classes that will be added to the <a> element
+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('|'),
 fulldefline=str(hit.Hit_def).split(' ', 1)[0],
 accession=str(hit.Hit_accession))
 link = template.format(**args)
 except Exception as e:
 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
 for f in reversed(files):
 try:
 for l in f.readlines():
 if l.strip().startswith('#'):
 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()
 except OSError:
 continue
 # handle the errors. This introduces a small race condition when
 # jinja later tries to re-open the template file, but we don't
 # 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$=nuclalign',
 help="""A link template to link hits to a gene bank webpage. The template string is a
 Python format string. It can contain the following replacement elements: {id[N]}, {fullid},
 {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be
 replaced by the Nth element of the id or defline, where '|' is the field separator.
 The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=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
 starting with '#' ignored), where the third field of a line should be a database path and the fourth
 a genebank link template conforming to the --genelink-template option syntax.
 #         self.write(i)
 # args.output.writelines = fixed_writelines
 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()
 if __name__ == '__main__':

Mercurial > repos > jankanis > blast2html

comparison blast2html.py @ 115:0c2a03f9740b