def main(args):
"""
Use analyzeAlphaHelices to get a collection of alpha helix reads analyzed
and print the results.
@param args: Command line arguments as returned by the C{argparse}
C{parse_args} method.
"""
if args.pdb:
readClass = SSAARead
readsClass = SSFastaReads
else:
readClass = AARead
readsClass = FastaReads
reads = readsClass(sys.stdin, readClass=readClass, checkAlphabet=0)
if args.minSequenceLength:
reads = reads.filter(minLength=args.minSequenceLength)
analysis = analyzeAlphaHelices(reads)
print('Processed %d alpha helices.' % len(reads))
for key in ('length', 'extremaCount', 'initial', 'final',
'consecutivePeaks', 'consecutiveTroughs', 'noExtremaLength'):
if analysis[key]:
print(analysis[key])
else:
print('No values recorded for', key)
def testFourDifferingHelices(self):
"""
The analysis of four differing alpha helices must be as expected.
"""
reads = Reads()
reads.add(AARead('id1', 'GGFFFRRFFFG'))
reads.add(AARead('id2', 'GRRFFFFGGGRRRGRGRGGFFGGG'))
reads.add(AARead('id3', 'RRGRRRFFGFFGGGRRR'))
reads.add(AARead('id4', 'GGG'))
self.assertEqual(
{
'length': [11, 24, 17, 3],
'initial': [2, 1, 0],
'final': [1, 3, 0],
'extremaCount': [8, 13, 12, 0],
'consecutivePeaks': [
3,
3, # id1
4,
2, # id2
4
], # id3
'consecutiveTroughs': [
2, # id1
2,
5, # id2
5,
3
], # id3
'noExtremaLength': [3], # id4
},
analyzeAlphaHelices(reads))
def testResultDictValuesAreStatsInstances(self):
"""
In the values analysis C{dict} returned by analyzeAlphaHelices, all
values must be C{Stats} instances.
"""
reads = Reads()
for value in analyzeAlphaHelices(reads).values():
self.assertIsInstance(value, Stats)
def testNoHelices(self):
"""
The analysis of an empty set of alpha helices must be as expected.
"""
reads = Reads()
self.assertEqual(
{
'length': [],
'initial': [],
'final': [],
'extremaCount': [],
'consecutivePeaks': [],
'consecutiveTroughs': [],
'noExtremaLength': [],
}, analyzeAlphaHelices(reads))
def testNoExtrema(self):
"""
The analysis of a helix with no extrema must be correct.
"""
reads = Reads()
reads.add(AARead('id', 'GG'))
self.assertEqual(
{
'length': [2],
'initial': [],
'final': [],
'extremaCount': [0],
'consecutivePeaks': [],
'consecutiveTroughs': [],
'noExtremaLength': [2],
}, analyzeAlphaHelices(reads))
def testOneHelix(self):
"""
The analysis of a single alpha helix must be as expected.
"""
reads = Reads()
reads.add(AARead('id', 'F'))
self.assertEqual(
{
'length': [1],
'initial': [0],
'final': [0],
'extremaCount': [1],
'consecutivePeaks': [1],
'consecutiveTroughs': [],
'noExtremaLength': [],
}, analyzeAlphaHelices(reads))
def testTwoDifferingHelices(self):
"""
The analysis of two differing alpha helices must be as expected.
"""
reads = Reads()
reads.add(AARead('id', 'FG'))
reads.add(AARead('id', 'GRR'))
self.assertEqual(
{
'length': [2, 3],
'initial': [0, 1],
'final': [1, 0],
'extremaCount': [1, 2],
'consecutivePeaks': [1],
'consecutiveTroughs': [2],
'noExtremaLength': [],
}, analyzeAlphaHelices(reads))
def testTwoIdenticalHelices(self):
"""
The analysis of two identical alpha helices must be as expected.
"""
reads = Reads()
reads.add(AARead('id', 'F'))
reads.add(AARead('id', 'F'))
self.assertEqual(
{
'length': [1, 1],
'initial': [0, 0],
'final': [0, 0],
'extremaCount': [1, 1],
'consecutivePeaks': [1, 1],
'consecutiveTroughs': [],
'noExtremaLength': [],
}, analyzeAlphaHelices(reads))
