def test_combine_hits_overlap():
"""If the overlap removal is working correctly, the combined length of the coordinates
should be 3 * the total length of the query (6 bp less than combined length of subjects"""
results = [{'qstart': 1, 'qend': 5, 'sstart': 1, 'send': 15, 'strand': 1},
{'qstart': 4, 'qend': 8, 'sstart': 21, 'send': 35, 'strand': 1}]
coords = combine_hits(results)
print coords
assert coords[0][1]-coords[0][0]+1 + coords[1][1]-coords[1][0]+1 == (results[1]['qend'] - results[0]['qstart'] + 1) * 3
def test_combine_hits():
"""this will ensure that all pairs of coordinates are in the correct order (lowest to
highest for + strand hits; highest to lowest for - strand hits"""
args = parse_args((os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
results = top_query(args)
for result in results:
coords = combine_hits(result)
print coords
if coords[0][0] < coords[0][1]:
for x in range(len(coords)-1):
assert coords[x][0] > coords[x+1][0]
else:
for x in range(len(coords)-1):
assert coords[x][0] < coords[x+1][0]
