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)
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)
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)
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)
