def write(self, raw_data, filename) :
"""
Write raw LRG data to a file. The data is parsed before writing,
if a parse error occurs None is returned.
@arg raw_data: The data
@type raw_data: byte string
@arg filename: The intended name of the file
@type filename: unicode
@return:
- filename ; The full path and name of the file written
- None ; In case of an error
@rtype: unicode
"""
# Dirty way to test if a file is valid,
# Parse the file to see if it's a real LRG file.
try:
lrg.create_record(raw_data)
except DOMException:
self._output.addMessage(__file__, 4, "ERECPARSE",
"Could not parse file.")
return None # Explicit return on Error
return self._write(raw_data, filename) #returns full path
def write(self, raw_data, filename) :
"""
Write raw LRG data to a file. The data is parsed before writing,
if a parse error occurs None is returned.
@arg raw_data: The data
@type raw_data: byte string
@arg filename: The intended name of the file
@type filename: unicode
@return:
- filename ; The full path and name of the file written
- None ; In case of an error
@rtype: unicode
"""
# Dirty way to test if a file is valid,
# Parse the file to see if it's a real LRG file.
try:
lrg.create_record(raw_data)
except DOMException:
self._output.addMessage(__file__, 4, "ERECPARSE",
"Could not parse file.")
return None # Explicit return on Error
return self._write(raw_data, filename) #returns full path
def loadrecord(self, identifier):
"""
Load and parse a LRG file based on the identifier.
:arg unicode identifier: The name of the LRG file to read.
:returns: GenRecord.Record of LRG file or None in case of failure.
:rtype: object
"""
# Make a filename based upon the identifier.
filename = self._name_to_file(identifier)
if not os.path.isfile(filename):
# We can't find the file.
filename = self.fetch(identifier)
if filename is None:
# Notify batch to skip all instance of identifier.
self._output.addOutput('BatchFlags', ('S1', identifier))
# return None in case of error.
return None
# Now we have the file, so we can parse it.
file_handle = bz2.BZ2File(filename, 'r')
# Create GenRecord.Record from LRG file.
record = lrg.create_record(file_handle.read())
file_handle.close()
# We don't create LRGs from other sources, so id is always the same
# as source_id.
record.id = identifier
record.source_id = identifier
return record
def loadrecord(self, identifier):
"""
Load and parse a LRG file based on the identifier.
:arg unicode identifier: The name of the LRG file to read.
:returns: GenRecord.Record of LRG file or None in case of failure.
:rtype: object
"""
# Make a filename based upon the identifier.
filename = self._name_to_file(identifier)
if not os.path.isfile(filename):
# We can't find the file.
filename = self.fetch(identifier)
if filename is None:
# Notify batch to skip all instance of identifier.
self._output.addOutput('BatchFlags', ('S1', identifier))
# return None in case of error.
return None
# Now we have the file, so we can parse it.
file_handle = bz2.BZ2File(filename, 'r')
# Create GenRecord.Record from LRG file.
record = lrg.create_record(file_handle.read())
file_handle.close()
# We don't create LRGs from other sources, so id is always the same
# as source_id.
record.id = identifier
record.source_id = identifier
return record
def test_lrg_multiple_transcripts(settings, references):
"""
"""
accession = references[0].accession
filename = os.path.join(settings.CACHE_DIR, '%s.xml.bz2' % accession)
file_handle = bz2.BZ2File(filename, 'r')
record = create_record(file_handle.read())
file_handle.close()
assert len(record.geneList[0].transcriptList) == 2
def test_lrg_basic(settings, references):
"""
"""
accession = references[0].accession
filename = os.path.join(settings.CACHE_DIR, '%s.xml.bz2' % accession)
file_handle = bz2.BZ2File(filename, 'r')
record = create_record(file_handle.read())
file_handle.close()
assert [g.name for g in record.geneList] == ['COL1A1']
assert record.geneList[0].transcriptList[0].name == '1'
assert len(record.geneList[0].transcriptList) == 1
assert record.geneList[0].transcriptList[0].CDS is not None
assert record.organism == 'H**o sapiens'
def write(self, raw_data, filename):
"""
Write raw LRG data to a file. The data is parsed before writing,
if a parse error occurs None is returned.
:arg str raw_data: The data.
:arg unicode filename: The intended name of the file.
:returns: The full path and name of the file written, None in case of
an error.
:rtype: unicode
"""
# Dirty way to test if a file is valid,
# Parse the file to see if it's a real LRG file.
try:
lrg.create_record(raw_data)
except DOMException:
self._output.addMessage(__file__, 4, 'ERECPARSE',
'Could not parse file.')
# Explicit return on Error.
return None
# Returns full path.
return self._write(raw_data, filename)
def write(self, raw_data, filename):
"""
Write raw LRG data to a file. The data is parsed before writing,
if a parse error occurs None is returned.
:arg str raw_data: The data.
:arg unicode filename: The intended name of the file.
:returns: The full path and name of the file written, None in case of
an error.
:rtype: unicode
"""
# Dirty way to test if a file is valid,
# Parse the file to see if it's a real LRG file.
try:
lrg.create_record(raw_data)
except DOMException:
self._output.addMessage(
__file__, 4, 'ERECPARSE', 'Could not parse file.')
# Explicit return on Error.
return None
# Returns full path.
return self._write(raw_data, filename)
def loadrecord(self, identifier):
"""
Load and parse a LRG file based on the identifier
@arg identifier: The name of the LRG file to read
@type identifier: unicode
@return: record ; GenRecord.Record of LRG file
None ; in case of failure
@rtype:
"""
# Make a filename based upon the identifier.
filename = self._nametofile(identifier)
if not os.path.isfile(filename) : # We can't find the file.
filename = self.fetch(identifier)
if filename is None: # return None in case of error
#Notify batch to skip all instance of identifier
self._output.addOutput("BatchFlags", ("S1", identifier))
return None
# Now we have the file, so we can parse it.
file_handle = bz2.BZ2File(filename, "r")
#create GenRecord.Record from LRG file
record = lrg.create_record(file_handle.read())
file_handle.close()
# We don't create LRGs from other sources, so id is always the same
# as source_id.
record.id = identifier
record.source_id = identifier
return record
def loadrecord(self, identifier):
"""
Load and parse a LRG file based on the identifier
@arg identifier: The name of the LRG file to read
@type identifier: unicode
@return: record ; GenRecord.Record of LRG file
None ; in case of failure
@rtype:
"""
# Make a filename based upon the identifier.
filename = self._nametofile(identifier)
if not os.path.isfile(filename) : # We can't find the file.
filename = self.fetch(identifier)
if filename is None: # return None in case of error
#Notify batch to skip all instance of identifier
self._output.addOutput("BatchFlags", ("S1", identifier))
return None
# Now we have the file, so we can parse it.
file_handle = bz2.BZ2File(filename, "r")
#create GenRecord.Record from LRG file
record = lrg.create_record(file_handle.read())
file_handle.close()
# We don't create LRGs from other sources, so id is always the same
# as source_id.
record.id = identifier
record.source_id = identifier
return record
