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 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)