comparison blast2html.py @ 99:8f02008a5f20

look at all blast*.loc files; python2.6 compat fix

98:e780606b7c25

import six, codecs
from six.moves import builtins
from os import path
from itertools import repeat
from collections import defaultdict
import argparse
from lxml import objectify
import jinja2

builtin_str = str

            link = template.format(**args)
        except Exception as e:
            warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
            return text if display_nolink else ''

        classattr = 'class="{}" '.format(jinja2.escape(clas)) if clas is not None else ''
        return jinja2.Markup("<a {}href=\"{}\">{}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))


def read_genelinks(dir):
    links = {}
    for f in ('blastdb.loc', 'blastdb_p.loc', 'blastdb_d.loc'):
        try:
            f = open(path.join(dir, f))
            for l in f.readlines():
                if l.strip().startswith('#'):
                    continue

99:8f02008a5f20

import six, codecs
from six.moves import builtins
from os import path
from itertools import repeat
from collections import defaultdict
import glob
import argparse
from lxml import objectify
import jinja2

builtin_str = str

            link = template.format(**args)
        except Exception as e:
            warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
            return text if display_nolink else ''

        classattr = 'class="{0}" '.format(jinja2.escape(clas)) if clas is not None else ''
        return jinja2.Markup("<a {0}href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))


def read_genelinks(dir):
    links = {}
    # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
    # sort reversed, so blastdb.loc will take precedence
    for f in sorted(glob.glob(path.join(dir, 'blastdb*.loc')), reverse=True): 
        try:
            f = open(path.join(dir, f))
            for l in f.readlines():
                if l.strip().startswith('#'):
                    continue