1.1 --- a/allpy/fileio/markup.py	Thu Jun 14 20:24:26 2012 +0400
     1.2 +++ b/allpy/fileio/markup.py	Tue Jun 19 16:55:44 2012 +0400
     1.3 @@ -101,7 +101,7 @@
     1.4              if sequence.name == record['sequence_name']:
     1.5                  description = record.get('sequence_description')
     1.6                  if description:
     1.7 -                    assert sequence.description == description
     1.8 +                    assert sequence.description == description, "Descriptions don't match: {0} != {1} for {2}".format(sequence.description, description, sequence.name)
     1.9                  cls = get_markups_class(record['class'])
    1.10                  cls.from_record(sequence, record, name=record.get('name'))
    1.11                  return

     2.1 --- a/utils/markup_to_html.py	Thu Jun 14 20:24:26 2012 +0400
     2.2 +++ b/utils/markup_to_html.py	Tue Jun 19 16:55:44 2012 +0400
     2.3 @@ -13,10 +13,14 @@
     2.4  template_file = join(template_prefix, "markup_to_html.html")
     2.5  
     2.6  parser = optparse.OptionParser(description=__doc__, usage="%prog [options] [infile]")
     2.7 +parser.add_option("-t", "--template-file", default=template_file,
     2.8 +	help="HTML template file")
     2.9  parser.add_option("-o", "--outfile",
    2.10  	help="Output file name, default: stdout")
    2.11 +parser.add_option("-p", "--import-path", default=".",
    2.12 +	help="Path to imported module")
    2.13  parser.add_option("-m", "--import-module",
    2.14 -	help="Import this module before anything, useful for custom markup classes")
    2.15 +	help="import this module before anything, useful for custom markup classes")
    2.16  options, args = parser.parse_args()
    2.17  
    2.18  outfile = options.outfile and open(options.outfile, "w") or sys.stdout
    2.19 @@ -24,9 +28,11 @@
    2.20  if len(args) > 1:
    2.21  	parser.error("Too many arguments on the command line")
    2.22  
    2.23 +module = None
    2.24 +
    2.25  if options.import_module:
    2.26 -	sys.path.append(".")
    2.27 -	__import__(options.import_module)
    2.28 +	sys.path.insert(0, options.import_path)
    2.29 +	module = __import__(options.import_module)
    2.30  
    2.31  aln = protein.Alignment().append_file(infile, format="markup")
    2.32  
    2.33 @@ -43,6 +49,9 @@
    2.34  		items += repr_items([('sequence ' + k, v) for k, v in vars(sequence).items() if k != 'markups'])
    2.35  		monomer.description = "\n".join(items)
    2.36  
    2.37 +if hasattr(module, 'init'):
    2.38 +	module.init(aln)
    2.39 +
    2.40  rows = aln.rows_as_lists()
    2.41 -template = Template(open(template_file).read())
    2.42 +template = Template(open(options.template_file).read())
    2.43  outfile.write(template.render(vars()))