comparison blast2html.py @ 27:4e6ac737ba17

improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy

26:eee23a36c582

#!/usr/bin/env python3

# Copyright The Hyve B.V. 2014
# License: GPL version 3 or higher

import sys

                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?
                       ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),
                       accession = hit.Hit_accession)

def main():

    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)
    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
                             help='The input Blast XML file, same as -i/--input')

    # We just want the file name here, so jinja can open the file
    # itself. But it is easier to just use a FileType so argparse can
    # 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',
                        help='The template file to use. Defaults to blast_html.html.jinja')

    args = parser.parse_args()
    if args.input == None:
        args.input = args.positional_arg

27:4e6ac737ba17

#!/usr/bin/env python3
# Actually runs under either python 2 or 3

# Copyright The Hyve B.V. 2014
# License: GPL version 3 or higher

import sys

                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?
                       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)
    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
                             help='The input Blast XML file, same as -i/--input')

    # We just want the file name here, so jinja can open the file
    # itself. But it is easier to just use a FileType so argparse can
    # 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')

    args = parser.parse_args()
    if args.input == None:
        args.input = args.positional_arg