comparison blast2html.py @ 50:bfc82a8aa3c9

unicodify python sources

49:85f757f4fcd5

#!/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
import math
import warnings
from os import path

    def __init__(self, input, templatedir, templatename):
        self.input = input
        self.templatename = templatename

        self.blast = objectify.parse(self.input).getroot()
        self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
        self.environment = jinja2.Environment(loader=self.loader,
                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)

        self._addfilters(self.environment)

    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')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
                             help='The input Blast XML file')
    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
                        help='The output html file')
    # 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

50:bfc82a8aa3c9

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Actually runs under either python 2 or 3

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

from __future__ import unicode_literals

import sys
import math
import warnings
from os import path

    def __init__(self, input, templatedir, templatename):
        self.input = input
        self.templatename = templatename

        self.blast = objectify.parse(self.input).getroot()
        self.loader = jinja2.FileSystemLoader(searchpath=templatedir, encoding='utf-8')
        self.environment = jinja2.Environment(loader=self.loader,
                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)

        self._addfilters(self.environment)

    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')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r', encoding='utf-8'), 
                             help='The input Blast XML file')
    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w', encoding='utf-8'), default=sys.stdout,
                        help='The output html file')
    # 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', encoding='utf-8'), 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