def search(self, what, cat='all'):
        """ Performs search """
        #prepare query
        cat = self.supported_categories[cat.lower()]
        query = "".join((self.url, "/files/?category=", cat, "&subcategory=All&quality=All&seeded=2&external=2&query=", what, "&uid=0&sort=S"))

        data = retrieve_url(query)

        add_res_list = re_compile("/files.*page=[0-9]+")
        torrent_list = re_compile("start torrent list -->(.*)<!-- end torrent", DOTALL)
        data = torrent_list.search(data).group(0)
        list_results = add_res_list.findall(data)

        parser = self.MyHtmlParseWithBlackJack(self.url)
        parser.feed(data)

        del data

        if list_results:
            for search_query in islice((add_res_list.search(result).group(0) for result in list_results[1].split(" | ")), 0, 5):
                response = retrieve_url(self.url + search_query)
                parser.feed(torrent_list.search(response).group(0))
                parser.close()

        return

    def search(self, what, cat='all'):
        """ Performs search """
        connection = https("www.demonoid.pw")

        #prepare query
        cat = self.supported_categories[cat.lower()]
        query = "".join(("/files/?category=", cat, "&subcategory=All&quality=All&seeded=2&external=2&query=", what, "&to=1&uid=0&sort=S"))

        connection.request("GET", query)
        response = connection.getresponse()
        if response.status != 200:
            return

        data = response.read().decode("utf-8")
        add_res_list = re_compile("/files.*page=[0-9]+")
        torrent_list = re_compile("start torrent list -->(.*)<!-- end torrent", DOTALL)
        data = torrent_list.search(data).group(0)
        list_results = add_res_list.findall(data)

        parser = self.MyHtmlParseWithBlackJack(self.url)
        parser.feed(data)

        del data

        if list_results:
            for search_query in islice((add_res_list.search(result).group(0) for result in list_results[1].split(" | ")), 0, 5):
                connection.request("GET", search_query)
                response = connection.getresponse()
                parser.feed(torrent_list.search(response.read().decode('utf-8')).group(0))
                parser.close()

        connection.close()
        return

    def search(self, what, cat="all"):
        """ Performs search """
        query = "".join(
            (
                self.url,
                "/index.php?page=torrents&search=",
                what,
                "&category=",
                self.supported_categories.get(cat, "0"),
                "&active=1",
            )
        )

        get_table = re_compile('(?s)<table\sclass="lista".*>(.*)</table>')
        data = get_table.search(retrieve_url(query)).group(0)
        # extract first ten pages of next results
        next_pages = re_compile('(?m)<option value="(.*)">[0-9]+</option>')
        next_pages = ["".join((self.url, page)) for page in next_pages.findall(data)[:10]]

        parser = self.MyHtmlParseWithBlackJack(self.url)
        parser.feed(data)
        parser.close()

        for page in next_pages:
            parser.feed(get_table.search(retrieve_url(page)).group(0))
            parser.close()

	def __WriteGHDLSection(self, binPath):
		if (self._host.Platform == "Windows"):
			ghdlPath = binPath / "ghdl.exe"
		else:
			ghdlPath = binPath / "ghdl"

		if not ghdlPath.exists():
			raise ConfigurationException("Executable '{0!s}' not found.".format(ghdlPath)) from FileNotFoundError(
				str(ghdlPath))

		# get version and backend
		output = check_output([str(ghdlPath), "-v"], universal_newlines=True)
		version = None
		backend = None
		versionRegExpStr = r"^GHDL (.+?) "
		versionRegExp = re_compile(versionRegExpStr)
		backendRegExpStr = r"(?i).*(mcode|gcc|llvm).* code generator"
		backendRegExp = re_compile(backendRegExpStr)
		for line in output.split('\n'):
			if version is None:
				match = versionRegExp.match(line)
				if match is not None:
					version = match.group(1)

			if backend is None:
				match = backendRegExp.match(line)
				if match is not None:
					backend = match.group(1).lower()

		if ((version is None) or (backend is None)):
			raise ConfigurationException("Version number or back-end name not found in '{0!s} -v' output.".format(ghdlPath))

		self._host.PoCConfig[self._section]['Version'] = version
		self._host.PoCConfig[self._section]['Backend'] = backend

 def __init__(self, *args, **kwargs):
     """
 Parameters
 ----------
 ``*args`` and ``**kwargs``
     Parameters that shall be used for the substitution. Note that you can
     only provide either ``*args`` or ``**kwargs``, furthermore most of the
     methods like `get_sectionsf` require ``**kwargs`` to be provided."""
     if len(args) and len(kwargs):
         raise ValueError("Only positional or keyword args are allowed")
     self.params = args or kwargs
     patterns = {}
     all_sections = self.param_like_sections + self.text_sections
     for section in self.param_like_sections:
         patterns[section] = re_compile(
             '(?<=%s\n%s\n)(?s)(.+?)(?=\n\n\S+|$)' % (
                 section, '-'*len(section)))
     all_sections_patt = '|'.join(
         '%s\n%s\n' % (s, '-'*len(s)) for s in all_sections)
     # examples and see also
     for section in self.text_sections:
         patterns[section] = re_compile(
             '(?<=%s\n%s\n)(?s)(.+?)(?=%s|$)' % (
                 section, '-'*len(section), all_sections_patt))
     self.patterns = patterns

def parse_scorematrix(name, smpath):
    with open(smpath) as fh:
        ws = re_compile(r'\s+')
        comment = re_compile(r'^\s*#')
        S = fh.read().split('\n')
        T = [s.strip() for s in S if not comment.match(s)]
        U = [ws.sub(' ', t).split(' ') for t in T if len(t) > 0]
        V = [u[1:] for u in U[1:]]
        W = [[int(w) for w in v] for v in V]
        lettersX = ''.join(U[0]).upper()
        lettersY = ''.join([u[0] for u in U[1:]]).upper()
        if len(lettersX) >= 20:
            letters = pletters
            klass = ProteinScoreMatrix
        else:
            letters = dletters
            klass = DNAScoreMatrix
        if not set(letters).issubset(set(lettersX + lettersY)):
            msg = "scoring matrix '%s' is insufficiently descriptive" % smpath
            raise RuntimeError(msg)
        if lettersX != lettersY or lettersX[:len(letters)] != letters:
            cols = [lettersX.index(l) for l in letters]
            rows = [lettersY.index(l) for l in letters]
            return klass(name, [[W[i][j] for j in cols] for i in rows])
        else:
            return klass(name, W)

 def __init__(self, configuration=None, name=None):
     SimpleService.__init__(self, configuration=configuration, name=name)
     self.regex = dict(disks=re_compile(r' (?P<array>[a-zA-Z_0-9]+) : active .+\['
                                        r'(?P<total_disks>[0-9]+)/'
                                        r'(?P<inuse_disks>[0-9]+)\]'),
                       status=re_compile(r' (?P<array>[a-zA-Z_0-9]+) : active .+ '
                                         r'(?P<operation>[a-z]+) =[ ]{1,2}'
                                         r'(?P<operation_status>[0-9.]+).+finish='
                                         r'(?P<finish>([0-9.]+))min speed='
                                         r'(?P<speed>[0-9]+)'))

	def setExclude(self, exclude):
		if exclude:
			self._exclude = (
				[re_compile(x) for x in exclude[0]],
				[re_compile(x) for x in exclude[1]],
				[re_compile(x) for x in exclude[2]],
				exclude[3]
			)
		else:
			self._exclude = ([], [], [], [])

	def setInclude(self, include):
		if include:
			self._include = (
				[re_compile(x) for x in include[0]],
				[re_compile(x) for x in include[1]],
				[re_compile(x) for x in include[2]],
				include[3]
			)
		else:
			self._include = ([], [], [], [])

    def getphylo(self, seqs, quiet=True):

        seqs = list(seqs)

        if self.__inputfile is None or not exists(self.__inputfile):
            fd, self.__inputfile = mkstemp()
            close(fd)

        with open(self.__inputfile, "w") as fh:
            SeqIO.write(seqs, fh, "fasta")

        newick_mangle = re_compile(r"[()]")

        id_descs = {}
        mangle = re_compile(r"[^a-zA-Z0-9]+", re_I)
        for r in seqs:
            newid = mangle.sub("_", "_".join((r.id, r.description))).rstrip("_")
            id_descs[newid] = (newick_mangle.sub("_", r.id).strip("_"), r.description)

        self.queuevar("_inputFile", self.__inputfile)
        self.runqueue()

        if not quiet:
            if self.stdout != "":
                print(self.stdout, file=stderr)
            if self.warnings != "":
                print(self.warnings, file=stderr)

        if self.stderr != "":
            raise RuntimeError(self.stderr)

        tree = self.getvar("tree", HyphyInterface.STRING)
        with closing(StringIO(self.getvar("ancestors", HyphyInterface.STRING))) as fh:
            fh.seek(0)
            ancestors = AlignIO.read(fh, "fasta")

        hyphymangling = re_compile(r"_[0-9]+$")

        for r in ancestors:
            key = r.id.rstrip("_unknown_description_").rstrip("_")
            if key not in id_descs:
                key = hyphymangling.sub("", key)
                if key not in id_descs:
                    continue
            # if the key exists, replace
            oldid, olddesc = id_descs[key]
            tree = tree.replace(r.id, oldid)
            r.id = oldid
            r.description = olddesc

        if tree[-1] != ";":
            tree += ";"

        return tree, ancestors

    def valid(record, is_dna=False):
        if is_dna:
            regexp = re_compile(r'[^ACGT]')
        else:
            regexp = re_compile(r'[^ACDEFGHIKLMNPQRSTVWY]')

        seq = regexp.sub('', str(record.seq))

        record.letter_annotations.clear()
        record.seq = Seq(seq, record.seq.alphabet)

        return record

    def pattern(self, format):
        processed_format = ''
        regex_chars = re_compile('([\\\\.^$*+?\\(\\){}\\[\\]|])')
        format = regex_chars.sub('\\\\\\1', format)
        whitespace_replacement = re_compile('\\s+')
        format = whitespace_replacement.sub('\\s+', format)
        while '%' in format:
            directive_index = format.index('%') + 1
            processed_format = '%s%s%s' % (processed_format, format[:directive_index - 1], self[format[directive_index]])
            format = format[directive_index + 1:]

        return '%s%s' % (processed_format, format)

def process_module(rootpath, modulepath):
    """
    build the contents of fname
    """
    mods_to_process = []
    pys_to_process = []
    hidden_py_re = re_compile(r'^__.*__\.py$')
    reg_py_re = re_compile(r'.*\.py$')
    for fname in listdir(modulepath):
        new_mod = join(modulepath, fname)
        if isfile(join(new_mod, '__init__.py')):
            mods_to_process.append(new_mod)
        elif reg_py_re.match(fname) and not hidden_py_re.match(fname):
            pys_to_process.append(new_mod)
    rel_mod_path = relpath(modulepath, rootpath)
    mod_nice_name = rel_mod_path.split(sep)
    new_nice_name = mod_nice_name[-1]
    mod_nice_name = []
    if '_' in new_nice_name and new_nice_name[0] != '_':
        mod_nice_name += new_nice_name.split('_')
    else:
        mod_nice_name.append(new_nice_name)
    mod_nice_name = [x[0].upper()+x[1:] for x in mod_nice_name]
    new_nice_name = ' '.join(mod_nice_name)
    if len(mods_to_process) or len(pys_to_process):
        new_file = open("%s.rst"%(rel_mod_path.replace(sep, '.')), "w")
        new_file.write("""
%s Module
**************************************************************

"""%(new_nice_name))

        if len(mods_to_process):
            new_file.write("""
Contents:

.. toctree::
   :maxdepth: 2

""")
            for new_mod in mods_to_process:
                new_file.write("   "+relpath(new_mod, rootpath).replace(sep, '.')+"\n")
        for new_mod in pys_to_process:
            new_file.write("""
.. automodule:: %s
   :members:
   :private-members:

"""%('.'.join(relpath(new_mod, rootpath).replace(sep, '.').split('.')[1:-1])))
        new_file.close()

	def _infer_i(self):
		from re import compile as re_compile
		pattern = re_compile("\%[0-9]*\.?[0-9]*[uifd]")
		match = pattern.split(self.path_format)
		glob_pattern = '*'.join(match)
		fpaths = glob(os.path.join(self.recording_dir, glob_pattern))

		i_pattern = re_compile('(?<={})[0-9]*(?={})'.format(*match))
		try:
			max_i = max([int(i_pattern.findall(i)[0]) for i in fpaths])
			i = max_i + 1
		except ValueError:
			i = 0
		return i

def preprocess_seqrecords(seqrecords):
    remove_unknown = re_compile(r'[^ACGTUWSMKRYBDHVN]', re_I)
    strip_front = re_compile(r'^[N]+', re_I)
    strip_rear = re_compile(r'[N]+$', re_I)

    for record in seqrecords:
        seq = str(record.seq)
        seq = remove_unknown.sub('', seq)
        seq = strip_front.sub('', seq)
        seq = strip_rear.sub('', seq)

        record.seq = Seq(seq, generic_nucleotide)

    return

	def routeFinished(self, result, retval, extra_args):
		(iface, data, callback) = extra_args
		ipRegexp = '[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}'
		ipPattern = re_compile(ipRegexp)
		ipLinePattern = re_compile(ipRegexp)

		for line in result.splitlines():
			print line[0:7]
			if line[0:7] == "0.0.0.0":
				gateway = self.regExpMatch(ipPattern, line[16:31])
				if gateway:
					data['gateway'] = self.convertIP(gateway)

		self.ifaces[iface] = data
		self.loadNetworkConfig(iface,callback)

 def get_version(self):
     pop = subprocess.Popen( path(self.get_bin_path())/"gcc --version",
                                        stdout=subprocess.PIPE)
     time.sleep(1)
     output = pop.stdout.read()
     reg = re_compile(r"(\d\.\d.\d)")
     return reg.search(output).group(1)

def find_most_recent(guis):
    parser = re_compile(".*?(\d+)(?:\s(\d+)|\.)").match

    # todo
    # This is a mess. Just parse all dates in guis and sort.
    # Then, return list of filenames to backup, filename to rename,
    # and most recent date parsed.
    last_date = 0
    last_version = 1
    latest = None
    others = []
    for g in guis:
        groups = parser(g).groups()
        date = groups[0]
        try:
            n = int(groups[1])
        except IndexError:
            n = None

        idate = int(date)
        if idate > last_date:
            latest = g
            last_date = idate
            last_version = n or 1
        elif idate == last_date:
            if n is not None and n > last_version:
                latest = g
                last_version = n
        else:
            others.append(g)

    return last_version, latest, last_date

def stockholm_rf_ranges(filename):
    hdr = re_compile('^#=GC\s+RF\s+(.+)$', re_I)
    keep = []
    with open(filename) as h:
        for line in h:
            m = hdr.match(line)
            if m:
                keep = [l not in '.-~' for l in m.group(1)]
                break
    ranges = []
    lwr = 0
    val = keep[lwr]
    for i, v in enumerate(keep):
        if v != val:
            # transition T->F, so append range
            if val:
                ranges.append((lwr, i))
            # transition F->T, so update lower bound
            else:
                lwr = i
            # update val
            val = v
    # if we have a terminal val, append final range
    if val:
        ranges.append((lwr, len(keep)))
    return ranges

 def replace_uuids_with_file(self):
     self.vprint('replace UUIDs and remove unused UUIDs')
     uuid_ptn = re_compile('(?<=\s)[0-9A-F]{24}(?=[\s;])')
     for line in fi_input(self.xcode_pbxproj_path, backup='.bak', inplace=1):
         # project.pbxproj is an utf-8 encoded file
         line = line.decode('utf-8')
         uuid_list = uuid_ptn.findall(line)
         if not uuid_list:
             print(line.encode('utf-8'), end='')
         else:
             new_line = line
             # remove line with non-existing element
             if self.__result.get('to_be_removed') and any(
                     i for i in uuid_list if i in self.__result['to_be_removed']):
                 continue
             else:
                 for uuid in uuid_list:
                     new_line = new_line.replace(uuid, self.__result[uuid]['new_key'])
                 print(new_line.encode('utf-8'), end='')
     fi_close()
     tmp_path = self.xcode_pbxproj_path + '.bak'
     if filecmp_cmp(self.xcode_pbxproj_path, tmp_path, shallow=False):
         unlink(self.xcode_pbxproj_path)
         rename(tmp_path, self.xcode_pbxproj_path)
         print('Ignore uniquify, no changes made to', self.xcode_pbxproj_path)
     else:
         unlink(tmp_path)
         print('Uniquify done')