Ejemplo n.º 1
0
    def init_grammar(self):
        """Set up the parsing classes
        Any changes to the grammar of the config file be done here.
        """

        # Some syntax that we need, but don't care about
        SEMICOLON = (Suppress(";"))
        EQUALS = Suppress("=")

        # Top Section
        FILE_NAME = Word(alphas + nums + '-_.')
        alignment_def = Keyword('alignment') + EQUALS\
                        + FILE_NAME + SEMICOLON
        alignment_def.setParseAction(self.set_alignment)

        tree_def = Keyword('user_tree_topology') + EQUALS\
                   + FILE_NAME + SEMICOLON
        tree_def.setParseAction(self.set_user_tree)

        def simple_option(name):
            opt = Keyword(name) + EQUALS +\
                  Word(alphas + nums + '-_') + SEMICOLON
            opt.setParseAction(self.set_simple_option)
            return opt

        branch_def = simple_option('branchlengths')

        MODEL_NAME = Word(alphas + nums + '+' + ' ' + '_')
        model_list = delimitedList(MODEL_NAME)
        model_def = 'models' + EQUALS + model_list + SEMICOLON
        model_def.setParseAction(self.set_models)

        model_selection_def = simple_option("model_selection")
        top_section = alignment_def + Optional(tree_def) + branch_def + \
            model_def + model_selection_def


        # Data Block Parsing
        column = Word(nums)
        block_name = Word(alphas + '_-' + nums)
        block_def = column("start") +\
            Optional(Suppress("-") + column("end")) +\
            Optional(Suppress("\\") + column("step"))
        block_def.setParseAction(self.define_range)

        block_list_def = Group(OneOrMore(Group(block_def)))

        user_subset_def = Optional("charset") + block_name("name") + \
            EQUALS + block_list_def("parts") + SEMICOLON
        user_subset_def.setParseAction(self.define_user_subset)

        block_def_list = OneOrMore(Group(user_subset_def))
        block_section = Suppress("[data_blocks]") + block_def_list
        block_def_list.setParseAction(self.check_blocks)

        # Scheme Parsing
        scheme_name = Word(alphas + '_-' + nums)

        # Make a copy, cos we set a different action on it
        user_subset_ref = block_name.copy()
        user_subset_ref.setParseAction(self.check_block_exists)

        subset = Group(Suppress("(") +
                       delimitedList(user_subset_ref("name")) + Suppress(")"))
        subset.setParseAction(self.define_subset_grouping)

        scheme = Group(OneOrMore(subset))
        scheme_def = scheme_name("name") + \
            EQUALS + scheme("scheme") + SEMICOLON
        scheme_def.setParseAction(self.define_scheme)

        scheme_list = OneOrMore(Group(scheme_def))

        scheme_algo = simple_option("search")
        scheme_section = \
            Suppress("[schemes]") + scheme_algo + Optional(scheme_list)

        # We've defined the grammar for each section.
        # Here we just put it all together
        self.config_parser = (
            top_section + block_section + scheme_section + stringEnd)
Ejemplo n.º 2
0
    def init_grammar(self):
        """Set up the parsing classes
        Any changes to the grammar of the config file be done here.
        """
        # Some syntax that we need, but don't bother looking at
        SEMICOLON = (Suppress(";"))
        EQUALS = Suppress("=")
        OPENB = Suppress("(")
        CLOSEB = Suppress(")")
        BACKSLASH = Suppress("\\")
        DASH = Suppress("-")

        # Top Section
        FILENAME = Word(alphas + nums + '-_.')
        alignmentdef = Keyword('alignment') + EQUALS + FILENAME + SEMICOLON
        alignmentdef.setParseAction(self.set_alignment)

        treedef = Keyword('user_tree_topology') + EQUALS + FILENAME + SEMICOLON
        treedef.setParseAction(self.set_user_tree)

        def simple_option(name):
            opt = Keyword(name) + EQUALS + Word(alphas + nums +
                                                '-_') + SEMICOLON
            opt.setParseAction(self.set_simple_option)
            return opt

        branchdef = simple_option('branchlengths')

        MODELNAME = Word(alphas + nums + '+')
        modellist = delimitedList(MODELNAME)
        modeldef = Keyword("models") + EQUALS + Group(
            (CaselessKeyword("all") | CaselessKeyword("mrbayes")
             | CaselessKeyword("raxml") | CaselessKeyword("beast")
             | CaselessKeyword("all_protein")
             | CaselessKeyword("all_protein_gamma")
             | CaselessKeyword("all_protein_gammaI"))("predefined")
            | Group(modellist)("userlist")) + SEMICOLON
        modeldef.setParseAction(self.set_models)

        modseldef = simple_option("model_selection")
        topsection = alignmentdef + Optional(treedef) + branchdef + \
            modeldef + modseldef

        # Partition Parsing
        column = Word(nums)
        partname = Word(alphas + '_-' + nums)
        partdef = column("start") +\
            Optional(DASH + column("end")) +\
            Optional(BACKSLASH + column("step"))

        partdef.setParseAction(self.define_range)
        partdeflist = Group(OneOrMore(Group(partdef)))
        partition = Optional("charset") + partname("name") + \
            EQUALS + partdeflist("parts") + SEMICOLON
        partition.setParseAction(self.define_partition)
        partlist = OneOrMore(Group(partition))
        partsection = Suppress("[data_blocks]") + partlist

        # Scheme Parsing
        schemename = Word(alphas + '_-' + nums)
        partnameref = partname.copy(
        )  # Make a copy, cos we set a different action on it
        partnameref.setParseAction(self.check_part_exists)

        subset = Group(OPENB + delimitedList(partnameref("name")) + CLOSEB)
        subset.setParseAction(self.define_subset)

        scheme = Group(OneOrMore(subset))
        schemedef = schemename("name") + \
            EQUALS + scheme("scheme") + SEMICOLON
        schemedef.setParseAction(self.define_schema)

        schemelist = OneOrMore(Group(schemedef))

        schemealgo = simple_option("search")
        schemesection = \
            Suppress("[schemes]") + schemealgo + Optional(schemelist)

        # We've defined the grammar for each section. Here we just put it all together
        self.config_parser = (topsection + partsection + schemesection +
                              stringEnd)
Ejemplo n.º 3
0
    def init_grammar(self):
        """Set up the parsing classes
        Any changes to the grammar of the config file be done here.
        """

        # Some syntax that we need, but don't care about
        SEMICOLON = (Suppress(";"))
        EQUALS = Suppress("=")

        # Top Section
        FILE_NAME = Word(alphas + nums + '-_.')
        alignment_def = Keyword('alignment') + EQUALS\
                        + FILE_NAME + SEMICOLON
        alignment_def.setParseAction(self.set_alignment)

        tree_def = Keyword('user_tree_topology') + EQUALS\
                   + FILE_NAME + SEMICOLON
        tree_def.setParseAction(self.set_user_tree)

        def simple_option(name):
            opt = Keyword(name) + EQUALS +\
                  Word(alphas + nums + '-_') + SEMICOLON
            opt.setParseAction(self.set_simple_option)
            return opt

        branch_def = simple_option('branchlengths')

        MODEL_NAME = Word(alphas + nums + '+' + ' ' + '_')
        model_list = delimitedList(MODEL_NAME)
        model_def = 'models' + EQUALS + model_list + SEMICOLON
        model_def.setParseAction(self.set_models)

        model_selection_def = simple_option("model_selection")
        top_section = alignment_def + Optional(tree_def) + branch_def + \
            model_def + model_selection_def

        # Data Block Parsing
        column = Word(nums)
        block_name = Word(alphas + '_-' + nums)
        block_def = column("start") +\
            Optional(Suppress("-") + column("end")) +\
            Optional(Suppress("\\") + column("step"))
        block_def.setParseAction(self.define_range)

        block_list_def = Group(OneOrMore(Group(block_def)))

        user_subset_def = Optional("charset") + block_name("name") + \
            EQUALS + block_list_def("parts") + SEMICOLON
        user_subset_def.setParseAction(self.define_user_subset)

        block_def_list = OneOrMore(Group(user_subset_def))
        block_section = Suppress("[data_blocks]") + block_def_list
        block_def_list.setParseAction(self.check_blocks)

        # Scheme Parsing
        scheme_name = Word(alphas + '_-' + nums)

        # Make a copy, cos we set a different action on it
        user_subset_ref = block_name.copy()
        user_subset_ref.setParseAction(self.check_block_exists)

        subset = Group(
            Suppress("(") + delimitedList(user_subset_ref("name")) +
            Suppress(")"))
        subset.setParseAction(self.define_subset_grouping)

        scheme = Group(OneOrMore(subset))
        scheme_def = scheme_name("name") + \
            EQUALS + scheme("scheme") + SEMICOLON
        scheme_def.setParseAction(self.define_scheme)

        scheme_list = OneOrMore(Group(scheme_def))

        scheme_algo = simple_option("search")
        scheme_section = \
            Suppress("[schemes]") + scheme_algo + Optional(scheme_list)

        # We've defined the grammar for each section.
        # Here we just put it all together
        self.config_parser = (top_section + block_section + scheme_section +
                              stringEnd)
Ejemplo n.º 4
0
    def init_grammar(self):
        """Set up the parsing classes
        Any changes to the grammar of the config file be done here.
        """
        # Some syntax that we need, but don't bother looking at
        SEMICOLON = (Suppress(";"))
        EQUALS = Suppress("=")
        OPENB = Suppress("(")
        CLOSEB = Suppress(")")
        BACKSLASH = Suppress("\\")
        DASH = Suppress("-")

        # Top Section
        FILENAME = Word(alphas + nums + '-_.')
        alignmentdef = Keyword('alignment') + EQUALS + FILENAME + SEMICOLON
        alignmentdef.setParseAction(self.set_alignment)

        treedef = Keyword('user_tree_topology') + EQUALS + FILENAME + SEMICOLON
        treedef.setParseAction(self.set_user_tree)

        def simple_option(name):
            opt = Keyword(name) + EQUALS + Word(alphas + nums + '-_') + SEMICOLON
            opt.setParseAction(self.set_simple_option)
            return opt

        branchdef = simple_option('branchlengths')

        MODELNAME = Word(alphas + nums + '+')
        modellist = delimitedList(MODELNAME)
        modeldef = Keyword("models") + EQUALS + Group(
            (
                CaselessKeyword("all") | CaselessKeyword("mrbayes") | CaselessKeyword("raxml") |
                CaselessKeyword("beast") | CaselessKeyword("all_protein") |
                CaselessKeyword(
                    "all_protein_gamma") | CaselessKeyword("all_protein_gammaI")
            )("predefined") |
            Group(modellist)("userlist")) + SEMICOLON
        modeldef.setParseAction(self.set_models)

        modseldef = simple_option("model_selection")
        topsection = alignmentdef + Optional(treedef) + branchdef + \
            modeldef + modseldef

        # Partition Parsing
        column = Word(nums)
        partname = Word(alphas + '_-' + nums)
        partdef = column("start") +\
            Optional(DASH + column("end")) +\
            Optional(BACKSLASH + column("step"))

        partdef.setParseAction(self.define_range)
        partdeflist = Group(OneOrMore(Group(partdef)))
        partition = Optional("charset") + partname("name") + \
            EQUALS + partdeflist("parts") + SEMICOLON
        partition.setParseAction(self.define_partition)
        partlist = OneOrMore(Group(partition))
        partsection = Suppress("[data_blocks]") + partlist

        # Scheme Parsing
        schemename = Word(alphas + '_-' + nums)
        partnameref = partname.copy(
        )  # Make a copy, cos we set a different action on it
        partnameref.setParseAction(self.check_part_exists)

        subset = Group(OPENB + delimitedList(partnameref("name")) + CLOSEB)
        subset.setParseAction(self.define_subset)

        scheme = Group(OneOrMore(subset))
        schemedef = schemename("name") + \
            EQUALS + scheme("scheme") + SEMICOLON
        schemedef.setParseAction(self.define_schema)

        schemelist = OneOrMore(Group(schemedef))

        schemealgo = simple_option("search")
        schemesection = \
            Suppress("[schemes]") + schemealgo + Optional(schemelist)

        # We've defined the grammar for each section. Here we just put it all together
        self.config_parser = (
            topsection + partsection + schemesection + stringEnd)