def syntax_checker():
"""
Parse the given variant and render the syntax checker HTML form.
"""
# Backwards compatibility.
if 'variant' in request.args:
return redirect(url_for('.syntax_checker',
description=request.args['variant']),
code=301)
description = request.args.get('description')
if not description:
return render_template('syntax-checker.html')
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request syntaxCheck(%s) from %s'
% (description, request.remote_addr))
stats.increment_counter('syntax-checker/website')
grammar = Grammar(output)
grammar.parse(description)
parse_error = output.getOutput('parseError')
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO',
'Finished request syntaxCheck(%s)' % description)
return render_template('syntax-checker.html',
description=description,
messages=messages,
parse_error=parse_error)
def _parseInput(self, variant):
"""
Parse a variant.
@arg variant: variant description
@type variant: string
@return: parsetree object
@rtype: object
"""
grammar = Grammar(self.__output)
parseTree = grammar.parse(variant)
if not parseTree:
self.__output.addMessage(__file__, 4, "EPARSE",
"Could not parse the given variant")
return None
#if
if not (parseTree.RefSeqAcc or parseTree.LrgAcc):
self.__output.addMessage(
__file__, 4, "EONLYGB",
"Currently we only support GenBank and LRG records")
return None
#if
self.parseTree = parseTree
return parseTree
def syntax_checker():
"""
Parse the given variant and render the syntax checker HTML form.
"""
# Backwards compatibility.
if 'variant' in request.args:
return redirect(url_for('.syntax_checker',
description=request.args['variant']),
code=301)
description = request.args.get('description')
if not description:
return render_template('syntax-checker.html')
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request syntaxCheck(%s) from %s'
% (description, request.remote_addr))
stats.increment_counter('syntax-checker/website')
grammar = Grammar(output)
grammar.parse(description)
parse_error = output.getOutput('parseError')
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO',
'Finished request syntaxCheck(%s)' % description)
return render_template('syntax-checker.html',
description=description,
messages=messages,
parse_error=parse_error)
def _processSyntaxCheck(self, batch_job, cmd, flags):
"""
Process an entry from the Syntax Check, write the results
to the job-file.
Side-effect:
- Output written to outputfile
@arg cmd: The Syntax Checker input
@type cmd:
@arg i: The JobID
@type i:
@arg flags: Flags of the current entry
@type flags:
"""
output = Output(__file__)
grammar = Grammar(output)
output.addMessage(__file__, -1, "INFO",
"Received SyntaxChecker batchvariant " + cmd)
stats.increment_counter('syntax-checker/batch')
skip = self.__processFlags(output, flags)
#Process
if not skip:
parsetree = grammar.parse(cmd)
else:
parsetree = None
if parsetree:
result = "OK"
else:
result = "|".join(output.getBatchMessages(2))
#Output
filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR,
batch_job.result_id)
if not os.path.exists(filename):
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
header = ['Input', 'Status']
handle = io.open(filename, mode='a', encoding='utf-8')
handle.write("%s\n" % "\t".join(header))
#if
else:
handle = io.open(filename, mode='a', encoding='utf-8')
if flags and 'C' in flags:
separator = '\t'
else:
separator = '\n'
handle.write("%s\t%s%s" % (cmd, result, separator))
handle.close()
output.addMessage(__file__, -1, "INFO",
"Finished SyntaxChecker batchvariant " + cmd)
def _processSyntaxCheck(self, batch_job, cmd, flags):
"""
Process an entry from the Syntax Check, write the results
to the job-file.
Side-effect:
- Output written to outputfile
@arg cmd: The Syntax Checker input
@type cmd:
@arg i: The JobID
@type i:
@arg flags: Flags of the current entry
@type flags:
"""
output = Output(__file__)
grammar = Grammar(output)
output.addMessage(__file__, -1, "INFO",
"Received SyntaxChecker batchvariant " + cmd)
stats.increment_counter('syntax-checker/batch')
skip = self.__processFlags(output, flags)
#Process
if not skip :
parsetree = grammar.parse(cmd)
else :
parsetree = None
if parsetree :
result = "OK"
else :
result = "|".join(output.getBatchMessages(2))
#Output
filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
header = ['Input', 'Status']
handle = io.open(filename, mode='a', encoding='utf-8')
handle.write("%s\n" % "\t".join(header))
#if
else :
handle = io.open(filename, mode='a', encoding='utf-8')
if flags and 'C' in flags:
separator = '\t'
else:
separator = '\n'
handle.write("%s\t%s%s" % (cmd, result, separator))
handle.close()
output.addMessage(__file__, -1, "INFO",
"Finished SyntaxChecker batchvariant " + cmd)
def _parseInput(self, variant) :
"""
Parse a variant.
@arg variant: variant description
@type variant: string
@return: parsetree object
@rtype: object
"""
grammar = Grammar(self.__output)
parseTree = grammar.parse(variant)
if not parseTree :
self.__output.addMessage(__file__, 4, "EPARSE",
"Could not parse the given variant")
return None
#if
if not (parseTree.RefSeqAcc or parseTree.LrgAcc):
self.__output.addMessage(__file__, 4, "EONLYGB",
"Currently we only support GenBank and LRG records")
return None
#if
self.parseTree = parseTree
return parseTree
def position_converter():
"""
Position converter.
"""
# Backwards compatibility.
if 'variant' in request.args:
return redirect(url_for('.position_converter',
description=request.args['variant']),
code=301)
assemblies = Assembly.query \
.order_by(*Assembly.order_by_criteria) \
.all()
assembly_name_or_alias = request.args.get('assembly_name_or_alias',
settings.DEFAULT_ASSEMBLY)
description = request.args.get('description')
if not description:
return render_template('position-converter.html',
assemblies=assemblies,
assembly_name_or_alias=assembly_name_or_alias)
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request positionConverter(%s, %s) from %s'
% (assembly_name_or_alias, description,
request.remote_addr))
stats.increment_counter('position-converter/website')
chromosomal_description = None
transcript_descriptions = None
try:
assembly = Assembly.by_name_or_alias(assembly_name_or_alias)
except NoResultFound:
output.addMessage(__file__, 3, 'ENOASSEMBLY',
'Not a valid assembly.')
else:
converter = Converter(assembly, output)
# Convert chromosome name to accession number.
corrected_description = converter.correctChrVariant(description)
if corrected_description:
# Now we're ready to actually do position conversion.
if not(':c.' in corrected_description or
':n.' in corrected_description or
':g.' in corrected_description or
':m.' in corrected_description):
grammar = Grammar(output)
grammar.parse(corrected_description)
if (':c.' in corrected_description or
':n.' in corrected_description):
corrected_description = converter.c2chrom(
corrected_description)
chromosomal_description = corrected_description
if corrected_description and (':g.' in corrected_description or
':m.' in corrected_description):
descriptions = converter.chrom2c(corrected_description, 'dict')
if descriptions is None:
chromosomal_description = None
elif descriptions:
transcript_descriptions = [
'%-10s:\t%s' % (key[:10], '\n\t\t'.join(value))
for key, value in descriptions.items()]
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO',
'Finished request positionConverter(%s, %s)'
% (assembly_name_or_alias, description))
return render_template('position-converter.html',
assemblies=assemblies,
assembly_name_or_alias=assembly_name_or_alias,
description=description,
chromosomal_description=chromosomal_description,
transcript_descriptions=transcript_descriptions,
messages=messages)
def position_converter():
"""
Position converter.
"""
# Backwards compatibility.
if 'variant' in request.args:
return redirect(url_for('.position_converter',
description=request.args['variant']),
code=301)
assemblies = Assembly.query \
.order_by(*Assembly.order_by_criteria) \
.all()
assembly_name_or_alias = request.args.get('assembly_name_or_alias',
settings.DEFAULT_ASSEMBLY)
description = request.args.get('description')
if not description:
return render_template('position-converter.html',
assemblies=assemblies,
assembly_name_or_alias=assembly_name_or_alias)
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request positionConverter(%s, %s) from %s'
% (assembly_name_or_alias, description,
request.remote_addr))
stats.increment_counter('position-converter/website')
chromosomal_description = None
transcript_descriptions = None
try:
assembly = Assembly.by_name_or_alias(assembly_name_or_alias)
except NoResultFound:
output.addMessage(__file__, 3, 'ENOASSEMBLY',
'Not a valid assembly.')
else:
converter = Converter(assembly, output)
# Convert chromosome name to accession number.
corrected_description = converter.correctChrVariant(description)
if corrected_description:
# Now we're ready to actually do position conversion.
if not(':c.' in corrected_description or
':n.' in corrected_description or
':g.' in corrected_description or
':m.' in corrected_description):
grammar = Grammar(output)
grammar.parse(corrected_description)
if (':c.' in corrected_description or
':n.' in corrected_description):
corrected_description = converter.c2chrom(
corrected_description)
chromosomal_description = corrected_description
if corrected_description and (':g.' in corrected_description or
':m.' in corrected_description):
descriptions = converter.chrom2c(corrected_description, 'dict')
if descriptions is None:
chromosomal_description = None
elif descriptions:
transcript_descriptions = [
'%-10s:\t%s' % (key[:10], '\n\t\t'.join(value))
for key, value in descriptions.items()]
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO',
'Finished request positionConverter(%s, %s)'
% (assembly_name_or_alias, description))
return render_template('position-converter.html',
assemblies=assemblies,
assembly_name_or_alias=assembly_name_or_alias,
description=description,
chromosomal_description=chromosomal_description,
transcript_descriptions=transcript_descriptions,
messages=messages)
def _processConversion(self, batch_job, cmd, flags):
"""
Process an entry from the Position Converter, write the results
to the job-file. The Position Converter is wrapped in a try except
block which ensures that he Batch Process keeps running. Errors
are caught and the user will be notified.
Side-effect:
- Output written to outputfile.
@arg cmd: The Syntax Checker input
@type cmd: unicode
@arg i: The JobID
@type i: integer
@arg build: The build to use for the converter
@type build: unicode
@arg flags: Flags of the current entry
@type flags:
"""
O = Output(__file__)
variant = cmd
variants = None
gName = ""
cNames = [""]
O.addMessage(__file__, -1, "INFO",
"Received PositionConverter batchvariant " + cmd)
stats.increment_counter('position-converter/batch')
skip = self.__processFlags(O, flags)
if not skip :
try :
#process
try:
assembly = Assembly.by_name_or_alias(batch_job.argument)
except NoResultFound:
O.addMessage(__file__, 3, 'ENOASSEMBLY',
'Not a valid assembly: ' + batch_job.argument)
raise
converter = Converter(assembly, O)
#Also accept chr accNo
variant = converter.correctChrVariant(variant)
#TODO: Parse the variant and check for c or g. This is ugly
if not(":c." in variant or ":n." in variant or ":g." in variant) :
#Bad name
grammar = Grammar(O)
grammar.parse(variant)
#if
if ":c." in variant or ":n." in variant :
# Do the c2chrom dance
variant = converter.c2chrom(variant)
# NOTE:
# If we received a coding reference convert that to the
# genomic position variant. Use that variant as the input
# of the chrom2c.
# If the input is a genomic variant or if we converted a
# coding variant to a genomic variant we try to find all
# other affected coding variants.
if variant and ":g." in variant :
# Do the chrom2c dance
variants = converter.chrom2c(variant, "dict")
if variants :
gName = variant
# Due to the cyclic behavior of the Position Converter
# we know for a fact that if a correct chrom name is
# generated by the converter.c2chrom that we will at
# least find one variant with chrom2c. Collect the
# variants from a nested lists and store them.
cNames = [cName for cName2 in variants.values() \
for cName in cName2]
except Exception:
#Catch all exceptions related to the processing of cmd
O.addMessage(__file__, 4, "EBATCHU",
"Unexpected error occurred, dev-team notified")
#except
#if
error = "%s" % "|".join(O.getBatchMessages(2))
#Output
filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
header = ['Input Variant',
'Errors',
'Chromosomal Variant',
'Coding Variant(s)']
handle = io.open(filename, mode='a', encoding='utf-8')
handle.write("%s\n" % "\t".join(header))
#if
else :
handle = io.open(filename, mode='a', encoding='utf-8')
if flags and 'C' in flags:
separator = '\t'
else:
separator = '\n'
handle.write("%s\t%s\t%s\t%s%s" % (cmd, error, gName, "\t".join(cNames), separator))
handle.close()
O.addMessage(__file__, -1, "INFO",
"Finisehd PositionConverter batchvariant " + cmd)
def _processConversion(self, batch_job, cmd, flags):
"""
Process an entry from the Position Converter, write the results
to the job-file. The Position Converter is wrapped in a try except
block which ensures that he Batch Process keeps running. Errors
are caught and the user will be notified.
Side-effect:
- Output written to outputfile.
@arg cmd: The Syntax Checker input
@type cmd: unicode
@arg i: The JobID
@type i: integer
@arg build: The build to use for the converter
@type build: unicode
@arg flags: Flags of the current entry
@type flags:
"""
O = Output(__file__)
variant = cmd
variants = None
gName = ""
cNames = [""]
O.addMessage(__file__, -1, "INFO",
"Received PositionConverter batchvariant " + cmd)
stats.increment_counter('position-converter/batch')
skip = self.__processFlags(O, flags)
if not skip:
try:
#process
try:
assembly = Assembly.by_name_or_alias(batch_job.argument)
except NoResultFound:
O.addMessage(__file__, 3, 'ENOASSEMBLY',
'Not a valid assembly: ' + batch_job.argument)
raise
converter = Converter(assembly, O)
#Also accept chr accNo
variant = converter.correctChrVariant(variant)
#TODO: Parse the variant and check for c or g. This is ugly
if not (":c." in variant or ":n." in variant
or ":g." in variant):
#Bad name
grammar = Grammar(O)
grammar.parse(variant)
#if
if ":c." in variant or ":n." in variant:
# Do the c2chrom dance
variant = converter.c2chrom(variant)
# NOTE:
# If we received a coding reference convert that to the
# genomic position variant. Use that variant as the input
# of the chrom2c.
# If the input is a genomic variant or if we converted a
# coding variant to a genomic variant we try to find all
# other affected coding variants.
if variant and ":g." in variant:
# Do the chrom2c dance
variants = converter.chrom2c(variant, "dict")
if variants:
gName = variant
# Due to the cyclic behavior of the Position Converter
# we know for a fact that if a correct chrom name is
# generated by the converter.c2chrom that we will at
# least find one variant with chrom2c. Collect the
# variants from a nested lists and store them.
cNames = [cName for cName2 in variants.values() \
for cName in cName2]
except Exception:
#Catch all exceptions related to the processing of cmd
O.addMessage(__file__, 4, "EBATCHU",
"Unexpected error occurred, dev-team notified")
#except
#if
error = "%s" % "|".join(O.getBatchMessages(2))
#Output
filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR,
batch_job.result_id)
if not os.path.exists(filename):
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
# a list. We need a tab delimited string.
header = [
'Input Variant', 'Errors', 'Chromosomal Variant',
'Coding Variant(s)'
]
handle = io.open(filename, mode='a', encoding='utf-8')
handle.write("%s\n" % "\t".join(header))
#if
else:
handle = io.open(filename, mode='a', encoding='utf-8')
if flags and 'C' in flags:
separator = '\t'
else:
separator = '\n'
handle.write("%s\t%s\t%s\t%s%s" %
(cmd, error, gName, "\t".join(cNames), separator))
handle.close()
O.addMessage(__file__, -1, "INFO",
"Finisehd PositionConverter batchvariant " + cmd)
def setup(self):
super(TestGrammar, self).setup()
self.output = Output(__file__)
self.grammar = Grammar(self.output)
class TestGrammar(MutalyzerTest):
"""
Test the mytalyzer.grammar module.
"""
def setup(self):
super(TestGrammar, self).setup()
self.output = Output(__file__)
self.grammar = Grammar(self.output)
def _parse(self, description):
"""
Parse a variant description.
"""
self.grammar.parse(description)
assert self.output.getOutput('parseError') == []
def test_some_variants(self):
"""
Some example variants.
"""
self._parse('NM_002001.2:c.[12del]')
self._parse('NM_002001.2:c.[(12del)]')
self._parse('NM_002001.2:c.[(12del)?]')
self._parse('NM_002001.2:c.[(12del);(12del)]')
self._parse('NM_002001.2:c.[(12del;12del)]')
self._parse('NM_002001.2:c.[((12del)?;12del)?]')
def test_compound_insertion(self):
"""
Some some compound insertions.
"""
self._parse('NM_002001.2:c.15_16insA')
self._parse('NM_002001.2:c.15_16insATC')
self._parse('NM_002001.2:c.15_16ins[A]')
self._parse('NM_002001.2:c.15_16ins[ATC]')
self._parse('NM_002001.2:c.15_16ins28_39')
self._parse('NM_002001.2:c.15_16ins[28_39]')
self._parse('NM_002001.2:c.15_16ins[28_39;A]')
self._parse('NM_002001.2:c.15_16ins[28_39;ATC]')
self._parse('NM_002001.2:c.15_16ins[28_39;A;ATC]')
self._parse('NM_002001.2:c.15_16ins28_39inv')
self._parse('NM_002001.2:c.15_16ins[28_39inv]')
self._parse('NM_002001.2:c.15_16ins[28_39inv;A]')
self._parse('NM_002001.2:c.15_16ins[28_39inv;ATC]')
self._parse('NM_002001.2:c.15_16ins[28_39inv;A;ATC]')
def test_compound_delins(self):
"""
Some some compound deletion-insertions.
"""
self._parse('NM_002001.2:c.12_17delinsA')
self._parse('NM_002001.2:c.12_17delinsATC')
self._parse('NM_002001.2:c.12_17delins[A]')
self._parse('NM_002001.2:c.12_17delins[ATC]')
self._parse('NM_002001.2:c.12_17delins28_39')
self._parse('NM_002001.2:c.12_17delins[28_39]')
self._parse('NM_002001.2:c.12_17delins[28_39;A]')
self._parse('NM_002001.2:c.12_17delins[28_39;ATC]')
self._parse('NM_002001.2:c.12_17delins[28_39;A;ATC]')
self._parse('NM_002001.2:c.12_17delins28_39inv')
self._parse('NM_002001.2:c.12_17delins[28_39inv]')
self._parse('NM_002001.2:c.12_17delins[28_39inv;A]')
self._parse('NM_002001.2:c.12_17delins[28_39inv;ATC]')
self._parse('NM_002001.2:c.12_17delins[28_39inv;A;ATC]')
def test_protein_variants(self):
"""
Some protein variants.
"""
self._parse('NG_009105.1(OPN1LW):p.=')
self._parse('NG_009105.1(OPN1LW):p.?')
self._parse('NM_000076.2(CDKN1C):p.0')
self._parse('NM_000076.2(CDKN1C):p.0?')
self._parse('NG_009105.1(OPN1LW):p.(=)')
self._parse('NM_000076.2(CDKN1C):p.(Ala123del)')
self._parse('NM_000076.2(CDKN1C):p.(Ala123_Leu126del)')
self._parse('NM_000076.2(CDKN1C):p.(Ala123_Leu126delinsVal)')
self._parse('NM_000076.2(CDKN1C):p.Ala123del')
self._parse('NM_000076.2(CDKN1C):p.Ala123_Leu126del')
self._parse('NM_000076.2(CDKN1C):p.Ala123_Leu126delinsVal')
self._parse('NM_000076.2(CDKN1C):p.Ala123_*317delinsVal')
self._parse('NM_000076.2(CDKN1C):p.Ala123_X317delinsVal')
self._parse('NM_000076.2(CDKN1C):p.Ala123delinsVal')
self._parse('NM_000076.2(CDKN1C):p.Ala123delinsValPro')
self._parse('NM_000076.2(CDKN1C):p.Ala123delinsVP')
self._parse('NM_000076.2(CDKN1C):p.Ala123fs')
self._parse('NM_000076.2(CDKN1C_i001):p.(Glu124Serfs*148)')
self._parse('NM_000076.2(CDKN1C_i001):p.(Glu124SerfsX148)')
self._parse('NM_000076.2(CDKN1C_i001):p.(E124Sfs*148)')
self._parse('NM_000076.2(CDKN1C_i001):p.(E124SfsX148)')
self._parse('NG_009105.1(OPN1LW):p.Met1Leu')
self._parse('NP_064445.1(OPN1LW):p.Met1?')
self._parse('NP_064445.1(OPN1LW):p.M1?')
self._parse('NP_064445.1:p.Gln16del')
self._parse('NP_064445.1:p.Gln16dup')
self._parse('NP_064445.1:p.Gln3del')
self._parse('NP_064445.1:p.Q16del')
self._parse('NP_064445.1:p.Q16dup')
self._parse('NP_064445.1:p.Q16*')
self._parse('NP_064445.1:p.Q16X')
self._parse('NG_009105.1:p.Gln3Leu')
self._parse('NG_009105.1(OPN1LW):p.Gln3Leu')
self._parse('NG_009105.1(OPN1LW_i1):p.Gln3Leu')
self._parse('NG_009105.1(OPN1LW_v1):p.Gln3Leu')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Gln4insLeu')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Gln4insGln')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Gln4dup')
self._parse('NG_009105.1(OPN1LW):p.Q3_Q4insQ')
self._parse('NG_009105.1(OPN1LW):p.Q3_Q4insQQ')
self._parse('NG_009105.1(OPN1LW):p.Q3_Q4dup')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7del')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7delinsValLeu')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7delinsValPro')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7delinsGlnGlnTrpSerLeu')
self._parse('NG_009105.1(OPN1LW):p.Q3_L7delinsGlnGlnTrpSerLeu')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7delinsQQWSL')
#self._parse('NG_009105.1(OPN1LW):p.Met1AlaextMet-1')
#self._parse('NG_009105.1(OPN1LW):p.M1AextM-1')
#self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7[3]')
self._parse('NG_009105.1(OPN1LW):p.Gln3_Leu7(1_6)')
self._parse('NG_009105.1(OPN1LW):p.Gln3Leu')
self._parse('NG_009105.1(OPN1LW):p.Gln3Leu')
#self._parse('NM_000076.2(CDKN1C_i001):p.(*317Trpext*3)')
self._parse('NM_000076.2(CDKN1C_i001):p.(*317TrpextX3)')
#self._parse('NM_000076.2(CDKN1C_i001):p.(*317Cysext*1)')
self._parse('NM_000076.2(CDKN1C_i001):p.(*317CysextX1)')
#self._parse('NM_000076.2(CDKN1C_i001):p.(*317Cext*1)')
self._parse('NM_000076.2(CDKN1C_i001):p.(*317CextX1)')
#self._parse('t(X;17)(DMD:p.Met1_Val1506; SGCA:p.Val250_*387)')
def test_minus_in_gene_symbol(self):
"""
Gene symbol is allowed to contain a minus character.
"""
self._parse('UD_132464528477(KRTAP2-4_v001):c.100del')
def grammar(output):
return Grammar(output)
