def testFindAllClasses(self):
"""
The find function should be able to find all trig point classes by
name.
"""
for klass in ALL_TRIG_CLASSES:
self.assertIs(klass, findTrigPoint(klass.NAME))
def extractNonPairFeatures(self):
"""
Find all non-pair features in the template.
@raise ValueError: If a line contains an unknown landmark or trig
point name or if the sequence for a feature does not match the
overall full sequence given in the first line of the template
for the subject/query.
@return: A generator that yields 2-tuples containing:
1. A C{str} feature name
2. A C{light.features.Landmark} or a C{light.features.TrigPoint}
instance
as they are found in the template lines.
"""
for line in self.noPipes[1:]:
if line.find(',') != -1:
# There is a comma on the line, so this is a pair of
# features from the matched region. Ignore it as it will be
# processed in extractPairedFeatures.
continue
featureName = line[:self.indentLength].strip()
featureStr = line[self.indentLength:]
landmark = findLandmark(featureName)
if landmark is None:
trigPoint = findTrigPoint(featureName)
if trigPoint is None:
raise ValueError('Unknown feature name %r found in %s '
'template' % (featureName, self.TYPE))
for match in _NONWHITE_REGEXP.finditer(featureStr):
offset = match.start()
length = match.end() - offset
sequence = featureStr[offset:offset + length]
if sequence != self.read.sequence[offset:offset + length]:
raise ValueError(
'%s feature sequence %r found in %s template (offset '
'%d, length %d) does not match the full sequence for '
'the %s at those offsets' %
(featureName, sequence, self.TYPE, offset, length,
self.TYPE))
if landmark:
yield (featureName,
Landmark(landmark.NAME, landmark.SYMBOL, offset,
length))
else:
yield (featureName,
TrigPoint(trigPoint.NAME, trigPoint.SYMBOL, offset))
def __init__(self,
landmarks=None,
trigPoints=None,
limitPerLandmark=None,
maxDistance=None,
minDistance=None,
distanceBase=None,
featureLengthBase=None,
randomLandmarkDensity=None,
randomTrigPointDensity=None,
acAlphaHelixFilename=None,
acAlphaHelix310Filename=None,
acAlphaHelixCombinedFilename=None,
acAlphaHelixPiFilename=None,
acExtendedStrandFilename=None):
# First set the simple scalar parameters.
self.limitPerLandmark = (self.DEFAULT_LIMIT_PER_LANDMARK
if limitPerLandmark is None else
limitPerLandmark)
self.maxDistance = (self.DEFAULT_MAX_DISTANCE
if maxDistance is None else maxDistance)
self.minDistance = (self.DEFAULT_MIN_DISTANCE
if minDistance is None else minDistance)
self.distanceBase = (self.DEFAULT_DISTANCE_BASE
if distanceBase is None else distanceBase)
if self.distanceBase <= 0:
raise ValueError('distanceBase must be > 0.')
self.featureLengthBase = (self.DEFAULT_FEATURE_LENGTH_BASE
if featureLengthBase is None else
featureLengthBase)
if self.featureLengthBase <= 0:
raise ValueError('featureLengthBase must be > 0.')
self.randomLandmarkDensity = (self.DEFAULT_RANDOM_LANDMARK_DENSITY
if randomLandmarkDensity is None else
randomLandmarkDensity)
self.randomTrigPointDensity = (self.DEFAULT_RANDOM_TRIG_POINT_DENSITY
if randomTrigPointDensity is None else
randomTrigPointDensity)
self.acAlphaHelixFilename = (self.DEFAULT_AC_ALPHAHELIX_FILENAME
if acAlphaHelixFilename is None else
acAlphaHelixFilename)
self.acAlphaHelix310Filename = (
self.DEFAULT_AC_ALPHAHELIX_3_10_FILENAME
if acAlphaHelix310Filename is None else acAlphaHelix310Filename)
self.acAlphaHelixCombinedFilename = (
self.DEFAULT_AC_ALPHAHELIX_COMBINED_FILENAME
if acAlphaHelixCombinedFilename is None else
acAlphaHelixCombinedFilename)
self.acAlphaHelixPiFilename = (self.DEFAULT_AC_ALPHAHELIX_PI_FILENAME
if acAlphaHelixPiFilename is None else
acAlphaHelixPiFilename)
self.acExtendedStrandFilename = (
self.DEFAULT_AC_EXTENDED_STRAND_FILENAME
if acExtendedStrandFilename is None else acExtendedStrandFilename)
if landmarks is None:
landmarkClasses = DEFAULT_LANDMARK_CLASSES
else:
landmarkClasses = set()
for landmark in landmarks:
if isinstance(landmark, string_types):
cls = findLandmark(landmark)
if cls:
landmarkClasses.add(cls)
else:
raise ValueError(
'Could not find landmark finder class %r.' %
landmark)
else:
# Assume this is already a landmark class.
landmarkClasses.add(landmark)
if trigPoints is None:
trigPointClasses = DEFAULT_TRIG_CLASSES
else:
trigPointClasses = set()
for trigPoint in trigPoints:
if isinstance(trigPoint, string_types):
cls = findTrigPoint(trigPoint)
if cls:
trigPointClasses.add(cls)
else:
raise ValueError(
'Could not find trig point finder class %r.' %
trigPoint)
else:
# Assume this is already a trig point class.
trigPointClasses.add(trigPoint)
# The finders instantiated here are not used in this file. They are
# used by the backend. We make sorted lists of them so we're guaranteed
# to always process them in the same order (in printing, in checksums,
# etc).
self.landmarkFinders = sorted(cls(self) for cls in landmarkClasses)
self.trigPointFinders = sorted(cls(self) for cls in trigPointClasses)
def extractPairedFeatures(self):
"""
Find all paired features in the template.
@raise ValueError: If a line contains an unknown landmark or trig
point name or doesn't have exactly one comma (separating the two
names).
@return: A generator that yields 4-tuples containing
1. A C{str} landmark feature name
2. A C{light.features.Landmark} instance
3. A C{str} trig point feature name (this may actually be a
landmark, but we typically call it a trig point).
4. A C{light.features.TrigPoint} instance (may actuall be a
C{light.features.Landmark} instance)
as they are found in the template lines.
"""
for line in self.noPipes[1:]:
if line.find(',') == -1:
# This line contains non-paired features (it has just one
# feature name - implied by the lack of a comma). Ignore it
# as it will be processed in extractNonPairFeatures.
continue
if line.count(',') != 1:
raise ValueError('%s template line %r contains multiple '
'commas' % (self.TYPE, line))
landmarkName, secondFeatureName = map(
str.strip, line[:self.indentLength].split(','))
featureStr = line[self.indentLength:]
landmark = findLandmark(landmarkName)
# The first feature of a matched pair must be a landmark.
if landmark is None:
raise ValueError('Unknown landmark name %r found in %s '
'template line %r' %
(landmarkName, self.TYPE, line))
# The second feature of a matched pair can be a trig point or
# another landmark.
landmark2 = findLandmark(secondFeatureName)
if landmark2 is None:
trigPoint = findTrigPoint(secondFeatureName)
if trigPoint is None:
raise ValueError('Unknown feature name %r found in %s '
'template' % (secondFeatureName,
self.TYPE))
for count, match in enumerate(
_NONWHITE_REGEXP.finditer(featureStr)):
if count > 1:
raise ValueError(
'More than two features found in matched region pair '
'line in %s template. Line was %r' % (self.TYPE, line))
first = count == 0
offset = match.start()
length = match.end() - offset
sequence = featureStr[offset:offset + length]
if sequence != self.read.sequence[offset:offset + length]:
if first:
raise ValueError(
'%s feature sequence %r found in %s template '
'(offset %d, length %d) does not match the full '
'sequence for the %s at those offsets' %
(landmarkName, sequence, self.TYPE, offset, length,
self.TYPE))
else:
raise ValueError(
'%s feature sequence %r found in %s template '
'(offset %d, length %d) does not match the full '
'sequence for the %s at those offsets' %
(secondFeatureName, sequence, self.TYPE, offset,
length, self.TYPE))
if first:
landmarkFeature = Landmark(landmark.NAME, landmark.SYMBOL,
offset, length)
else:
if landmark2:
secondFeature = Landmark(landmark2.NAME,
landmark2.SYMBOL, offset,
length)
else:
secondFeature = TrigPoint(trigPoint.NAME,
trigPoint.SYMBOL, offset)
yield (landmarkName, landmarkFeature,
secondFeatureName, secondFeature)
def testFindDevTrigPoint(self):
"""
The find function should be able to find development trig point
classes.
"""
self.assertIs(RandomTrigPoint, findTrigPoint('RandomTrigPoint'))
def testFindTrigPointFails(self):
"""
The find function should return C{None} if asked to find a trig
point class that doesn't exist.
"""
self.assertIs(None, findTrigPoint('silly'))