def test_interval_index_file():
ix = Indexes()
chrs = []
for i in range( 5 ):
intervals = []
name = "seq%d" % i
max = random.randint( 0, interval_index_file.MAX )
# print name, "size", max
for i in range( 500 ):
start = random.randint( 0, max )
end = random.randint( 0, max )
if end < start:
end, start = start, end
ix.add( name, start, end, i, max=interval_index_file.MAX )
intervals.append( ( start, end, i ) )
chrs.append( intervals )
fname = mktemp()
f = open( fname, "w" )
ix.write( f )
f.close()
del ix
ix = Indexes( fname )
for i in range( 5 ):
intervals = chrs[i]
name = "seq%d" % i
for i in range( 100 ):
start = random.randint( 0, max )
end = random.randint( 0, max )
if end < start:
end, start = start, end
query_intervals = set()
for ( s, e, i ) in intervals:
if e > start and s < end:
query_intervals.add( ( s, e, i ) )
result = ix.find( name, start, end )
for inter in result:
assert inter in query_intervals
def test_interval_index_file():
ix = Indexes()
chrs = []
for i in range( 5 ):
intervals = []
name = "seq%d" % i
max = random.randint( 0, interval_index_file.MAX )
# print name, "size", max
for i in range( 500 ):
start = random.randint( 0, max )
end = random.randint( 0, max )
if end < start:
end, start = start, end
ix.add( name, start, end, i, max=interval_index_file.MAX )
intervals.append( ( start, end, i ) )
chrs.append( intervals )
fname = mktemp()
f = open( fname, "w" )
ix.write( f )
f.close()
del ix
ix = Indexes( fname )
for i in range( 5 ):
intervals = chrs[i]
name = "seq%d" % i
for i in range( 100 ):
start = random.randint( 0, max )
end = random.randint( 0, max )
if end < start:
end, start = start, end
query_intervals = set()
for ( s, e, i ) in intervals:
if e > start and s < end:
query_intervals.add( ( s, e, i ) )
result = ix.find( name, start, end )
for inter in result:
assert inter in query_intervals
def test_zero():
ix = Indexes()
ix.add("t.idx", 0, 0, 1, 123)