def _converter(self, assembly_name_or_alias):
"""
Create a Converter instance for a given genome assembly.
"""
assembly = Assembly.query \
.filter(or_(Assembly.name == assembly_name_or_alias,
Assembly.alias == assembly_name_or_alias)) \
.one()
return Converter(assembly, self.output)
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 lovd_variant_info():
"""
The chromosomal to coding and vice versa conversion interface for LOVD.
Search for an NM number in the database, if the version number matches,
get the start and end positions in a variant and translate these positions
to chromosomal notation if the variant is in coding notation and vice
versa.
- If no end position is present, the start position is assumed to be the
end position.
- If the version number is not found in the database, an error message is
generated and a suggestion for an other version is given.
- If the reference sequence is not found at all, an error is returned.
- If no variant is present, the transcription start and end and CDS end
in coding notation is returned.
- If the variant is not accepted by the nomenclature parser, a parse error
will be printed.
Get variant info and return the result as plain text.
Parameters:
LOVD_ver
The version of the calling LOVD.
build
The human genome build (hg19 assumed).
acc
The accession number (NM number).
var
A description of the variant.
Returns:
start_main
The main coordinate of the start position in I{c.} (non-star) notation.
start_offset
The offset coordinate of the start position in I{c.} notation (intronic
position).
end_main
The main coordinate of the end position in I{c.} (non-star) notation.
end_offset
The offset coordinate of the end position in I{c.} notation (intronic
position).
start_g
The I{g.} notation of the start position.
end_g
The I{g.} notation of the end position.
type
The mutation type.
Returns (alternative):
trans_start
Transcription start in I{c.} notation.
trans_stop
Transcription stop in I{c.} notation.
CDS_stop
CDS stop in I{c.} notation.
"""
lovd_version = request.args['LOVD_ver']
build = request.args['build']
accession = request.args['acc']
description = request.args.get('var')
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request variantInfo(%s:%s (LOVD_ver %s, '
'build %s)) from %s'
% (accession, description, lovd_version, build,
request.remote_addr))
try:
assembly = Assembly.by_name_or_alias(build)
except NoResultFound:
response = make_response('invalid build')
response.headers['Content-Type'] = 'text/plain; charset=utf-8'
return response
converter = Converter(assembly, output)
result = ''
# If no variant is given, return transcription start, transcription
# end and CDS stop in c. notation.
if description:
ret = converter.mainMapping(accession, description)
else:
ret = converter.giveInfo(accession)
if ret:
result = '%i\n%i\n%i' % ret
if not result and not getattr(ret, 'startmain', None):
out = output.getOutput('LOVDERR')
if out:
result = out[0]
else:
result = 'Unknown error occured'
output.addMessage(__file__, -1, 'INFO',
'Finished request variantInfo(%s:%s (LOVD_ver %s, '
'build %s))'
% (accession, description, lovd_version, build))
if not result and getattr(ret, 'startmain', None):
result = '%i\n%i\n%i\n%i\n%i\n%i\n%s' % (
ret.startmain, ret.startoffset, ret.endmain, ret.endoffset,
ret.start_g, ret.end_g, ret.mutationType)
# Todo: Obsoleted error messages, remove soon.
if lovd_version == '2.0-23':
response = re.sub('^Error \(.*\):', 'Error:', result)
response = make_response(result)
response.headers['Content-Type'] = 'text/plain; charset=utf-8'
return response
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 lovd_variant_info():
"""
The chromosomal to coding and vice versa conversion interface for LOVD.
Search for an NM number in the database, if the version number matches,
get the start and end positions in a variant and translate these positions
to chromosomal notation if the variant is in coding notation and vice
versa.
- If no end position is present, the start position is assumed to be the
end position.
- If the version number is not found in the database, an error message is
generated and a suggestion for an other version is given.
- If the reference sequence is not found at all, an error is returned.
- If no variant is present, the transcription start and end and CDS end
in coding notation is returned.
- If the variant is not accepted by the nomenclature parser, a parse error
will be printed.
Get variant info and return the result as plain text.
Parameters:
LOVD_ver
The version of the calling LOVD.
build
The human genome build (hg19 assumed).
acc
The accession number (NM number).
var
A description of the variant.
Returns:
start_main
The main coordinate of the start position in I{c.} (non-star) notation.
start_offset
The offset coordinate of the start position in I{c.} notation (intronic
position).
end_main
The main coordinate of the end position in I{c.} (non-star) notation.
end_offset
The offset coordinate of the end position in I{c.} notation (intronic
position).
start_g
The I{g.} notation of the start position.
end_g
The I{g.} notation of the end position.
type
The mutation type.
Returns (alternative):
trans_start
Transcription start in I{c.} notation.
trans_stop
Transcription stop in I{c.} notation.
CDS_stop
CDS stop in I{c.} notation.
"""
lovd_version = request.args['LOVD_ver']
build = request.args['build']
accession = request.args['acc']
description = request.args.get('var')
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received request variantInfo(%s:%s (LOVD_ver %s, '
'build %s)) from %s'
% (accession, description, lovd_version, build,
request.remote_addr))
try:
assembly = Assembly.by_name_or_alias(build)
except NoResultFound:
response = make_response('invalid build')
response.headers['Content-Type'] = 'text/plain; charset=utf-8'
return response
converter = Converter(assembly, output)
result = ''
# If no variant is given, return transcription start, transcription
# end and CDS stop in c. notation.
if description:
ret = converter.mainMapping(accession, description)
else:
ret = converter.giveInfo(accession)
if ret:
result = '%i\n%i\n%i' % ret
if not result and not getattr(ret, 'startmain', None):
out = output.getOutput('LOVDERR')
if out:
result = out[0]
else:
result = 'Unknown error occured'
output.addMessage(__file__, -1, 'INFO',
'Finished request variantInfo(%s:%s (LOVD_ver %s, '
'build %s))'
% (accession, description, lovd_version, build))
if not result and getattr(ret, 'startmain', None):
result = '%i\n%i\n%i\n%i\n%i\n%i\n%s' % (
ret.startmain, ret.startoffset, ret.endmain, ret.endoffset,
ret.start_g, ret.end_g, ret.mutationType)
# Todo: Obsoleted error messages, remove soon.
if lovd_version == '2.0-23':
response = re.sub('^Error \(.*\):', 'Error:', result)
response = make_response(result)
response.headers['Content-Type'] = 'text/plain; charset=utf-8'
return response
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)
