def setUp(self):
self.nodeDB = {}
tmp = testutil.TempDir('graphshelve-test')
filename = tmp.subfile() # needs a random name each time
self.datagraph = mapping.Graph(sourceDB=self.nodeDB,
targetDB=self.nodeDB,
filename=filename, intKeys=True)
def setUp(self, worldbasePath=None, **kwargs):
# overwrite the WORLDBASEPATH environment variable
self.tempdir = testutil.TempDir('pygrdata')
if worldbasePath is None:
worldbasePath = self.tempdir.path
worldbase.update(worldbasePath, **kwargs)
# handy shortcuts
self.EQ = self.assertEqual
def setUp(self, pygrDataPath=None, **kwargs):
# overwrite the WORLDBASEPATH environment variable
self.tempdir = testutil.TempDir('pygrdata')
if pygrDataPath is None:
pygrDataPath = self.tempdir.path
pygr.Data.clear_cache() # make sure no old data loaded
pygr.Data.update(pygrDataPath, **kwargs) # use this path
# handy shortcuts
self.EQ = self.assertEqual
def setUp(self, worldbasePath=None, **kwargs):
# overwrite the WORLDBASEPATH environment variable
self.tempdir = testutil.TempDir('pygrdata')
if worldbasePath is None:
worldbasePath = self.tempdir.path
self.metabase = metabase.MetabaseList(worldbasePath, **kwargs)
self.pygrData = self.metabase.Data
self.schema = self.metabase.Schema
# handy shortcuts
self.EQ = self.assertEqual
def populate_swissprot():
"Populate the current worldbase with swissprot data"
# build BlastDB out of the sequences
sp_hbb1 = testutil.datafile('sp_hbb1')
sp = seqdb.BlastDB(sp_hbb1)
sp.__doc__ = 'little swissprot'
worldbase.Bio.Seq.Swissprot.sp42 = sp
# also store a fragment
hbb = sp['HBB1_TORMA']
ival = hbb[10:35]
ival.__doc__ = 'fragment'
worldbase.Bio.Seq.frag = ival
# build a mapping to itself
m = mapping.Mapping(sourceDB=sp, targetDB=sp)
trypsin = sp['PRCA_ANAVA']
m[hbb] = trypsin
m.__doc__ = 'map sp to itself'
worldbase.Bio.Seq.spmap = m
# create an annotation database and bind as exons attribute
worldbase.schema.Bio.Seq.spmap = metabase.OneToManyRelation(
sp, sp, bindAttrs=('buddy', ))
annoDB = seqdb.AnnotationDB({1: ('HBB1_TORMA', 10, 50)},
sp,
sliceAttrDict=dict(id=0, start=1, stop=2))
exon = annoDB[1]
# generate the names where these will be stored
tempdir = testutil.TempDir('exonAnnot')
filename = tempdir.subfile('cnested')
nlmsa = cnestedlist.NLMSA(filename,
'w',
pairwiseMode=True,
bidirectional=False)
nlmsa.addAnnotation(exon)
nlmsa.build()
annoDB.__doc__ = 'a little annotation db'
nlmsa.__doc__ = 'a little map'
worldbase.Bio.Annotation.annoDB = annoDB
worldbase.Bio.Annotation.map = nlmsa
worldbase.schema.Bio.Annotation.map = \
metabase.ManyToManyRelation(sp, annoDB, bindAttrs=('exons', ))
def setUp(self):
tmp = testutil.TempDir('graphshelve-test')
filename = tmp.subfile() # needs a random name each time
self.datagraph = mapping.Graph(filename=filename, intKeys=True)