Mercurial > repos > jankanis > blast2html

comparison blast2html.py @ 50:bfc82a8aa3c9

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unicodify python sources
author Jan Kanis <jan.code@jankanis.nl>
date Wed, 21 May 2014 18:17:03 +0200
parents 4e6ac737ba17
children b15a20c2372a
comparison
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49:85f757f4fcd5 50:bfc82a8aa3c9
1 #!/usr/bin/env python3 1 #!/usr/bin/env python3
2 # -*- coding: utf-8 -*-
3 #
2 # Actually runs under either python 2 or 3 4 # Actually runs under either python 2 or 3
3 5
4 # Copyright The Hyve B.V. 2014 6 # Copyright The Hyve B.V. 2014
5 # License: GPL version 3 or higher 7 # License: GPL version 3 or higher
8
9 from __future__ import unicode_literals
6 10
7 import sys 11 import sys
8 import math 12 import math
9 import warnings 13 import warnings
10 from os import path 14 from os import path
167 def __init__(self, input, templatedir, templatename): 171 def __init__(self, input, templatedir, templatename):
168 self.input = input 172 self.input = input
169 self.templatename = templatename 173 self.templatename = templatename
170 174
171 self.blast = objectify.parse(self.input).getroot() 175 self.blast = objectify.parse(self.input).getroot()
172 self.loader = jinja2.FileSystemLoader(searchpath=templatedir) 176 self.loader = jinja2.FileSystemLoader(searchpath=templatedir, encoding='utf-8')
173 self.environment = jinja2.Environment(loader=self.loader, 177 self.environment = jinja2.Environment(loader=self.loader,
174 lstrip_blocks=True, trim_blocks=True, autoescape=True) 178 lstrip_blocks=True, trim_blocks=True, autoescape=True)
175 179
176 self._addfilters(self.environment) 180 self._addfilters(self.environment)
177 181
281 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", 285 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
282 usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) 286 usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
283 input_group = parser.add_mutually_exclusive_group(required=True) 287 input_group = parser.add_mutually_exclusive_group(required=True)
284 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), 288 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
285 help='The input Blast XML file, same as -i/--input') 289 help='The input Blast XML file, same as -i/--input')
286 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 290 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r', encoding='utf-8'),
287 help='The input Blast XML file') 291 help='The input Blast XML file')
288 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout, 292 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w', encoding='utf-8'), default=sys.stdout,
289 help='The output html file') 293 help='The output html file')
290 # We just want the file name here, so jinja can open the file 294 # We just want the file name here, so jinja can open the file
291 # itself. But it is easier to just use a FileType so argparse can 295 # itself. But it is easier to just use a FileType so argparse can
292 # handle the errors. This introduces a small race condition when 296 # handle the errors. This introduces a small race condition when
293 # jinja later tries to re-open the template file, but we don't 297 # jinja later tries to re-open the template file, but we don't
294 # care too much. 298 # care too much.
295 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template, 299 parser.add_argument('--template', type=argparse.FileType(mode='r', encoding='utf-8'), default=default_template,
296 help='The template file to use. Defaults to blast_html.html.jinja') 300 help='The template file to use. Defaults to blast_html.html.jinja')
297 301
298 args = parser.parse_args() 302 args = parser.parse_args()
299 if args.input == None: 303 if args.input == None:
300 args.input = args.positional_arg 304 args.input = args.positional_arg