allpy
changeset 1110:e0eb2d0f0822
markup_to_html. Html template files and path to imported module can be passed on the command line. In the imported module can be function "init" which takes an alignment for adding some attributes after alignment is loaded.
| author | Mmmasha! |
|---|---|
| date | Tue, 19 Jun 2012 16:55:37 +0400 |
| parents | f0d2f37d05b9 |
| children | 7bc44212ca15 |
| files | utils/markup_to_html.py |
| diffstat | 1 files changed, 13 insertions(+), 4 deletions(-) [+] |
line diff
1.1 --- a/utils/markup_to_html.py Tue Jun 19 15:51:12 2012 +0400 1.2 +++ b/utils/markup_to_html.py Tue Jun 19 16:55:37 2012 +0400 1.3 @@ -13,10 +13,14 @@ 1.4 template_file = join(template_prefix, "markup_to_html.html") 1.5 1.6 parser = optparse.OptionParser(description=__doc__, usage="%prog [options] [infile]") 1.7 +parser.add_option("-t", "--template-file", default=template_file, 1.8 + help="HTML template file") 1.9 parser.add_option("-o", "--outfile", 1.10 help="Output file name, default: stdout") 1.11 +parser.add_option("-p", "--import-path", default=".", 1.12 + help="Path to imported module") 1.13 parser.add_option("-m", "--import-module", 1.14 - help="Import this module before anything, useful for custom markup classes") 1.15 + help="import this module before anything, useful for custom markup classes") 1.16 options, args = parser.parse_args() 1.17 1.18 outfile = options.outfile and open(options.outfile, "w") or sys.stdout 1.19 @@ -24,9 +28,11 @@ 1.20 if len(args) > 1: 1.21 parser.error("Too many arguments on the command line") 1.22 1.23 +module = None 1.24 + 1.25 if options.import_module: 1.26 - sys.path.append(".") 1.27 - __import__(options.import_module) 1.28 + sys.path.insert(0, options.import_path) 1.29 + module = __import__(options.import_module) 1.30 1.31 aln = protein.Alignment().append_file(infile, format="markup") 1.32 1.33 @@ -43,6 +49,9 @@ 1.34 items += repr_items([('sequence ' + k, v) for k, v in vars(sequence).items() if k != 'markups']) 1.35 monomer.description = "\n".join(items) 1.36 1.37 +if hasattr(module, 'init'): 1.38 + module.init(aln) 1.39 + 1.40 rows = aln.rows_as_lists() 1.41 -template = Template(open(template_file).read()) 1.42 +template = Template(open(options.template_file).read()) 1.43 outfile.write(template.render(vars()))