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#!/usr/bin/env python
import unittest
from cogent.core.location import Map, Span
from cogent.core.annotation import _Annotatable, Feature, _Feature
from cogent import LoadSeqs, DNA
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",
"Matthew Wakefield"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def SimpleAnnotation(parent, locations, Name):
return Feature(parent, '', Name, locations)
def annotate(parent, start, end, Name):
annot = parent.addAnnotation(SimpleAnnotation, locations=[(start, end)], Name=Name)
return annot
def structure(a, depth=0):
annots = [structure(annot, depth+1) for annot in a.annotations]
if not isinstance(a, _Feature):
return ('seq', len(a), annots)
elif annots:
return (a.Name, repr(a.map), annots)
else:
return (a.Name, repr(a.map))
class MapTest(unittest.TestCase):
"""Testing annotation of and by maps"""
def test_spans(self):
# a simple two part map of length 10
map = Map([(0,5), (5,10)], parent_length=10)
# try different spans on the above map
for ((start, end), expected) in [
((0, 4), "[0:4]"),
((0, 5), "[0:5]"),
((0, 6), "[0:5, 5:6]"),
((5, 10), "[5:10]"),
((-1, 10), "[-1-, 0:5, 5:10]"),
((5, 11), "[5:10, -1-]"),
((0, 10), "[0:5, 5:10]"),
((10, 0), "[10:5, 5:0]"),
]:
r = repr(Span(start, end, Reverse=start>end).remapWith(map))
#print (start, end), r,
if r != expected:
self.fail(repr((r, expected)))
def test_maps_on_maps(self):
seq = DNA.makeSequence('ATCGATCGAT' * 5, Name='base')
feat1 = annotate(seq, 10, 20, 'fake')
feat2 = annotate(feat1, 3, 5, 'fake2')
feat3 = annotate(seq, 1, 3, 'left')
seq2 = seq[5:]
self.assertEqual(structure(seq), ('seq', 50,
[('fake', '[10:20]/50',
[('fake2', '[3:5]/10')]),
('left', '[1:3]/50')])
)
self.assertEqual(structure(seq2), ('seq', 45,
[('fake', '[5:15]/45',
[('fake2', '[3:5]/10')])])
)
def test_getByAnnotation(self):
seq = DNA.makeSequence('ATCGATCGAT' * 5, Name='base')
seq.addAnnotation(Feature, 'test_type', 'test_label', [(5,10)])
seq.addAnnotation(Feature, 'test_type', 'test_label2', [(15,18)])
answer = list(seq.getByAnnotation('test_type'))
self.assertEqual( len(answer), 2)
self.assertEqual( str(answer[0]), 'TCGAT')
self.assertEqual( str(answer[1]), 'TCG')
answer = list(seq.getByAnnotation('test_type', 'test_label'))
self.assertEqual( len(answer), 1)
self.assertEqual( str(answer[0]), 'TCGAT')
# test ignoring of a partial annotation
sliced_seq = seq[:17]
answer = list(sliced_seq.getByAnnotation('test_type', ignore_partial=True))
self.assertEqual(len(answer), 1)
self.assertEqual( str(answer[0]), 'TCGAT')
def test_getBySequenceAnnotation(self):
aln = LoadSeqs(data={
'a': 'ATCGAAATCGAT',
'b': 'ATCGA--TCGAT'})
b = aln.getSeq('b')
b.addAnnotation(Feature, 'test_type', 'test_label', [(4,6)])
answer = aln.getBySequenceAnnotation('b', 'test_type')[0].todict()
self.assertEqual(answer, {'b':'A--T', 'a':'AAAT'})
if 0: # old, needs fixes
# Maps
a = Map([(10,20)], parent_length=100)
for (desc, map, expected) in [
('a ', a, "Map([10:20] on base)"),
('i ', a.inverse(), "Map([-10-, 0:10, -80-] on Map([10:20] on base))"),
('1 ', a[5:], "Map([5:10] on Map([10:20] on base))"),
('1r', a[5:].relative_to(b), "Map([15:20] on base)"),
('2 ', a[:5], "Map([0:5] on Map([10:20] on base))"),
('2r', a[:5].relative_to(b), "Map([10:15] on base)"),
('r ', a.relative_to(a[5:]), "Map([-5-, 0:5] on Map([5:10] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6]), "Map([0:2] on Map([2:6] on Map([10:20] on base)))"),
('r ', a[2:4].relative_to(a[2:6][0:3]), "Map([0:2] on Map([0:3] on Map([2:6] on Map([10:20] on base))))")]:
print desc, repr(map),
if repr(map) == expected:
print
else:
print ' <--- ', expected
bad = True
if __name__ == '__main__':
unittest.main()
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