def test_1_theoretical_ion_space_step(self):
print("test_1_theoretical_ion_space_step")
ms_digest = MSDigestParameters.parse(self.protein_prospector_file)
theo_ions = entry_point.generate_theoretical_ion_space(
self.ms1_matching_output_file, self.glycosylation_sites_file,
ms_digest.constant_modifications, ms_digest.variable_modifications,
ms_digest.enzyme, self.num_procs)
self.assertTrue(os.path.exists(theo_ions))
self.theoretical_ion_space_file = theo_ions
theoretical_ions = SqliteDict(theo_ions, tablename="theoretical_search_space")
sequence_set = theoretical_ions.itervalues()
peptide_sequences = [
sequence.Sequence(s["Seq_with_mod"]) for s in sequence_set]
peptide_mods = set()
for seq in peptide_sequences:
for resid, mod in seq:
peptide_mods.update((m.rule for m in mod))
print(peptide_mods)
class FindingsDatabase(object):
def __init__(self, db_file):
self._findings_db = SqliteDict(db_file,
tablename="findings",
autocommit=True,
decode=legacy_decode)
def close(self):
self._findings_db.close()
def get_findings(self, finding_filter) -> Iterable[Finding]:
for result in self._findings_db.itervalues():
if finding_filter(result):
yield result
def create(self, commit, secret):
finding = Finding(commit, secret)
self._findings_db[finding.id] = finding
return finding
def update(self, finding):
self._findings_db[finding.id] = finding
class Cache(object):
def __init__(self, **kwargs):
self.name = kwargs.get('name', DEFAULT_DATABASE_NAME)
self._db = SqliteDict('./%s.sqlite' % self.name,
encode=cache_encode,
decode=cache_decode,
autocommit=True)
logger.info('name=%s size=%s', self.name, len(self._db))
def close(self):
self._db.close()
def __del__(self):
pass # self.close()
def __iter__(self):
return self._db.__iter__()
def iteritems(self):
return self._db.iteritems()
def iterkeys(self):
return self._db.iterkeys()
def itervalues(self):
return self._db.itervalues()
def items(self):
return self.iteritems()
def __getitem__(self, key):
return self._db.__getitem__(key)
def get(self, key, default=None):
try:
return self.__getitem__(key)
except KeyError:
return default
def __setitem__(self, key, value):
return self._db.__setitem__(key, value)
def set(self, key, value):
return self.__setitem__(key, value)
def __len__(self):
return len(self._db)
def __contains__(self, key):
return key in self._db
def __delitem__(self, key):
if key in self._db:
del self._db[key]
def list(self, limit=None):
logger.info('list')
keys = []
for key in self:
keys.append(key)
if limit is not None and len(keys) == limit: break
return keys
