Mercurial > repos > jankanis > blast2html
diff blast2html.py @ 27:4e6ac737ba17
improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Thu, 15 May 2014 16:46:09 +0200 |
| parents | c8347745bbad |
| children | bfc82a8aa3c9 |
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--- a/blast2html.py Thu May 15 12:44:44 2014 +0200 +++ b/blast2html.py Thu May 15 16:46:09 2014 +0200 @@ -1,4 +1,5 @@ #!/usr/bin/env python3 +# Actually runs under either python 2 or 3 # Copyright The Hyve B.V. 2014 # License: GPL version 3 or higher @@ -273,8 +274,10 @@ ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))), accession = hit.Hit_accession) + def main(): - + default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') + parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) input_group = parser.add_mutually_exclusive_group(required=True) @@ -289,7 +292,7 @@ # 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='blast2html.html.jinja', + parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template, help='The template file to use. Defaults to blast_html.html.jinja') args = parser.parse_args()