def setup(self):
super(TestMutator, self).setup()
self.gb_parser = genbank.GBparser()
def loadrecord(self, accession):
"""
Load a RefSeq record and return it.
The record is found by trying the following options in order:
1. Returned from the cache if it is there.
2. Re-created (if it was created by slicing) or re-downloaded (if it
was created by URL) if we have information on its source in the
database.
3. Fetched from the NCBI.
:arg unicode accession: A RefSeq accession number.
:returns: A parsed RefSeq record or `None` if no record could be found
for the given accession.
:rtype: object
"""
reference = Reference.query.filter_by(accession=accession).first()
if reference is None:
# We don't know it, fetch it from NCBI.
filename = self.fetch(accession)
else:
# We have seen it before.
filename = self._name_to_file(reference.accession)
if os.path.isfile(filename):
# It is still in the cache, so filename is valid.
pass
elif reference.source == 'ncbi_slice':
# It was previously created by slicing.
cast_orientation = {None: None, 'forward': 1, 'reverse': 2}
(slice_accession, slice_start, slice_stop,
slice_orientation) = reference.source_data.split(':')
slice_start = int(slice_start)
slice_stop = int(slice_stop)
slice_orientation = cast_orientation[slice_orientation]
if not self.retrieveslice(slice_accession, slice_start,
slice_stop, slice_orientation):
filename = None
elif reference.source == 'url':
# It was previously created by URL.
if not self.downloadrecord(reference.source_data):
filename = None
elif reference.source == 'ncbi':
# It was previously fetched from NCBI.
filename = self.fetch(reference.accession)
else:
# It was previously created by uploading.
self._output.addMessage(__file__, 4, 'ERETR',
'Please upload this sequence again.')
filename = None
# If filename is None, we could not retrieve the record.
if filename is None:
# Notify batch job to skip all instance of identifier.
self._output.addOutput('BatchFlags', ('S1', accession))
return None
# Now we have the file, so we can parse it.
genbank_parser = genbank.GBparser()
record = genbank_parser.create_record(filename)
if reference:
record.id = reference.accession
else:
record.id = record.source_id
# Todo: This will change once we support protein references.
if isinstance(record.seq.alphabet, ProteinAlphabet):
self._output.addMessage(
__file__, 4, 'ENOTIMPLEMENTED',
'Protein reference sequences are not supported.')
return None
return record
def loadrecord(self, identifier):
"""
Load a RefSeq record and return it.
The record is found by trying the following options in order:
1. Returned from the cache if it is there.
2. Re-created (if it was created by slicing) or re-downloaded (if it
was created by URL) if we have information on its source in the
database.
3. Fetched from the NCBI.
:arg identifier: A RefSeq accession number or geninfo identifier (GI).
:type identifier: unicode
:return: A parsed RefSeq record or `None` if no record could be found
for the given identifier.
:rtype: mutalyzer.GenRecord.Record
"""
if identifier[0].isdigit():
# This is a GI number (geninfo identifier).
reference = Reference.query \
.filter_by(geninfo_identifier=identifier) \
.first()
else:
# This is a RefSeq accession number.
reference = Reference.query \
.filter_by(accession=identifier) \
.first()
if reference is None:
# We don't know it, fetch it from NCBI.
filename = self.fetch(identifier)
else:
# We have seen it before.
filename = self._nametofile(reference.accession)
if os.path.isfile(filename):
# It is still in the cache, so filename is valid.
pass
elif reference.slice_accession:
# It was previously created by slicing.
cast_orientation = {None: None,
'forward': 1,
'reverse': 2}
if not self.retrieveslice(reference.slice_accession,
reference.slice_start,
reference.slice_stop,
cast_orientation[reference.slice_orientation]):
filename = None
elif reference.download_url:
# It was previously created by URL.
if not self.downloadrecord(reference.download_url):
filename = None
elif reference.geninfo_identifier:
# It was previously fetched from NCBI.
filename = self.fetch(reference.accession)
else:
# It was previously created by uploading.
self._output.addMessage(__file__, 4, 'ERETR',
'Please upload this sequence again.')
filename = None
# If filename is None, we could not retrieve the record.
if filename is None:
# Notify batch job to skip all instance of identifier.
self._output.addOutput('BatchFlags', ('S1', identifier))
return None
# Now we have the file, so we can parse it.
GenBankParser = genbank.GBparser()
record = GenBankParser.create_record(filename)
if reference:
record.id = reference.accession
else:
record.id = record.source_id
# Todo: This will change once we support protein references.
if isinstance(record.seq.alphabet, ProteinAlphabet):
self._output.addMessage(
__file__, 4, 'ENOTIMPLEMENTED',
'Protein reference sequences are not supported.')
return None
return record