def setUp(self):
class Annotation(object):
def __init__(self, **kwargs):
self.__dict__.update(kwargs)
slicedb = dict(annot1=Annotation(id='seq', start=0, stop=10),
annot2=Annotation(id='seq', start=5, stop=9))
sequence_dict = dict(seq = Sequence('ATGGGGCCGATTG', 'seq'))
self.db = AnnotationDB(slicedb, sequence_dict)
#!user/bin/env python
import pygr.Data
from pygr.seqdb import BlastDB, AnnotationDB
seqdb = BlastDB('/somepath/hg18.fa')
exon_slices = pygr.Data.Collection(path='exon_slices.db',mode='c',writeback=False) # Store on disk
exon_db = AnnotationDB(exon_slices, seqdb,sliceAttrDict=dict(id=0, exon_id=1, orientation=2, gene_id=3, start=4, stop=5))
from pygr.cnestedlist import NLMSA
nlmsa = NLMSA('exonAnnot','w',use_virtual_lpo=True,bidirectional=False)
ifile = file('exonslice.txt')
for line in ifile:
row = [x for x in line.split()] # CONVERT TO LIST SO MUTABLE
row[1] = int(row[1]) # CONVERT FROM STRING TO INTEGER
exon_slices[row[1]] = row
exon = exon_db[row[1]] # GET THE ANNOTATION OBJECT FOR THIS EXON
nlmsa.addAnnotation(exon) # SAVE IT TO GENOME MAPPING
exon_db.clear()
nlmsa.build() # FINALIZE GENOME ALIGNMENT INDEXES
ifile.close()
class AnnotationDB_Test(unittest.TestCase):
"""
Test for all of the basic dictionary functions on 'AnnotationDB'.
"""
def setUp(self):
class Annotation(object):
def __init__(self, **kwargs):
self.__dict__.update(kwargs)
slicedb = dict(annot1=Annotation(id='seq', start=0, stop=10),
annot2=Annotation(id='seq', start=5, stop=9))
sequence_dict = dict(seq = Sequence('ATGGGGCCGATTG', 'seq'))
self.db = AnnotationDB(slicedb, sequence_dict)
def test_keys(self):
"AnnotationDB keys"
k = self.db.keys()
k.sort()
assert k == ['annot1', 'annot2'], k
def test_contains(self):
"AnnotationDB contains"
assert 'annot1' in self.db, self.db.keys()
assert 'annot2' in self.db
assert 'foo' not in self.db
def test_has_key(self):
"AnnotationDB has key"
assert self.db.has_key('annot1')
assert self.db.has_key('annot2')
assert not self.db.has_key('foo')
def test_get(self):
"AnnotationDB get"
assert self.db.get('foo') is None
assert self.db.get('annot1') is not None
assert str(self.db.get('annot1').sequence).startswith('ATGGGGC')
assert self.db.get('annot2') is not None
assert str(self.db.get('annot2').sequence).startswith('GCCG')
def test_items(self):
"AnnotationDB items"
i = [ k for (k,v) in self.db.items() ]
i.sort()
assert i == ['annot1', 'annot2']
def test_iterkeys(self):
"AnnotationDB iterkeys"
kk = self.db.keys()
kk.sort()
ik = list(self.db.iterkeys())
ik.sort()
assert kk == ik
def test_itervalues(self):
"AnnotationDB itervalues"
kv = self.db.values()
kv.sort()
iv = list(self.db.itervalues())
iv.sort()
assert kv[0] == iv[0]
assert kv == iv, (kv, iv)
def test_iteritems(self):
"AnnotationDB iteritems"
ki = self.db.items()
ki.sort()
ii = list(self.db.iteritems())
ii.sort()
assert ki == ii, (ki, ii)
def test_readonly(self):
"AnnotationDB readonly"
try:
self.db.copy() # what should 'copy' do on AD?
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try: # what should 'setdefault' do on AD?
self.db.setdefault('foo')
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try: # what should 'update' do on AD?
self.db.update({})
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.clear()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.pop()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.popitem()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
def test_equality(self):
"AnnotationDB equality"
# Check that separately generated annotation objects test equal"
key = 'annot1'
db = self.db
x = db.sliceAnnotation(key, db.sliceDB[key])
y = db.sliceAnnotation(key, db.sliceDB[key])
assert x == y
def test_bad_seqdict(self):
"AnnotationDB bad seqdict"
class Annotation(object):
def __init__(self, **kwargs):
self.__dict__.update(kwargs)
slicedb = dict(annot1=Annotation(id='seq', start=0, stop=10),
annot2=Annotation(id='seq', start=5, stop=9))
foo_dict = dict(foo=Sequence('ATGGGGCCGATTG', 'foo'))
try:
db = AnnotationDB(slicedb, foo_dict)
assert 0, "incorrect seqdb; key error should be raised"
except KeyError:
pass