def getComponents(matches, max_distance=0, min_overlap=0, by_query=False):
"""return overlapping matches.
max_distance
allow reads to be joined if they are # residues apart.
Adjacent reads are 1 residue apart, overlapping reads are 0 residues
apart
min_overlap
require at least # residues to be overlapping
"""
addAlignments(matches, by_query=by_query)
components = Components.IComponents()
for x in range(0, len(matches)):
components.add(x, x)
if min_overlap > 0 and max_distance > 0:
raise ValueError(
"both min_overlap (%i) and max_distance (%i) > 0" % (min_overlap, max_distance))
if by_query:
if min_overlap > 0:
f = lambda x, y: alignlib_lite.py_getAlignmentOverlap(
matches[x].mMapQuery2Target,
matches[y].mMapQuery2Target,
alignlib_lite.py_RR) >= min_overlap
else:
f = lambda x, y: alignlib_lite.py_getAlignmentShortestDistance(
matches[x].mMapQuery2Target,
matches[y].mMapQuery2Target,
alignlib_lite.py_RR) <= max_distance
else:
if min_overlap > 0:
f = lambda x, y: alignlib_lite.py_getAlignmentOverlap(
matches[x].mMapTarget2Query,
matches[y].mMapTarget2Query,
alignlib_lite.py_RR) >= min_overlap
else:
f = lambda x, y: alignlib_lite.py_getAlignmentShortestDistance(
matches[x].mMapTarget2Query,
matches[y].mMapTarget2Query,
alignlib_lite.py_RR) <= max_distance
for x in range(len(matches)):
for y in range(0, x):
if f(x, y):
components.add(x, y)
return components.getComponents()
def getComponents(matches, max_distance=0, min_overlap=0, by_query=False):
"""return overlapping matches.
max_distance
allow reads to be joined if they are # residues apart.
Adjacent reads are 1 residue apart, overlapping reads are 0 residues
apart
min_overlap
require at least # residues to be overlapping
"""
addAlignments(matches, by_query=by_query)
components = Components.IComponents()
for x in range(0, len(matches)):
components.add(x, x)
if min_overlap > 0 and max_distance > 0:
raise ValueError(
"both min_overlap (%i) and max_distance (%i) > 0" % (min_overlap, max_distance))
if by_query:
if min_overlap > 0:
f = lambda x, y: alignlib_lite.py_getAlignmentOverlap(
matches[x].mMapQuery2Target,
matches[y].mMapQuery2Target,
alignlib_lite.py_RR) >= min_overlap
else:
f = lambda x, y: alignlib_lite.py_getAlignmentShortestDistance(
matches[x].mMapQuery2Target,
matches[y].mMapQuery2Target,
alignlib_lite.py_RR) <= max_distance
else:
if min_overlap > 0:
f = lambda x, y: alignlib_lite.py_getAlignmentOverlap(
matches[x].mMapTarget2Query,
matches[y].mMapTarget2Query,
alignlib_lite.py_RR) >= min_overlap
else:
f = lambda x, y: alignlib_lite.py_getAlignmentShortestDistance(
matches[x].mMapTarget2Query,
matches[y].mMapTarget2Query,
alignlib_lite.py_RR) <= max_distance
for x in range(len(matches)):
for y in range(0, x):
if f(x, y):
components.add(x, y)
return components.getComponents()
def compareChains( pairs1, pairs2 ):
'''compare chains in pairs1 versus those in pairs2'''
result = {}
for key1, chain1 in pairs1.iteritems():
E.debug( "comparing %s" % str(key1) )
ntotal = chain1.getNumAligned()
if key1 not in pairs2:
result[ key1 ] = DiffResult._make( (ntotal, 0, 0, ntotal) )
continue
chain2 = pairs2[key1]
nsame = alignlib_lite.py_getAlignmentIdentity( chain1, chain2, alignlib_lite.py_RR )
noverlap = alignlib_lite.py_getAlignmentOverlap( chain1, chain2, alignlib_lite.py_RR )
ndifferent = noverlap - nsame
nunique = ntotal - noverlap
result[ key1 ] = DiffResult._make( (ntotal, nsame, ndifferent, nunique ) )
return result
def compareChains(pairs1, pairs2):
'''compare chains in pairs1 versus those in pairs2'''
result = {}
for key1, chain1 in pairs1.iteritems():
E.debug("comparing %s" % str(key1))
ntotal = chain1.getNumAligned()
if key1 not in pairs2:
result[key1] = DiffResult._make((ntotal, 0, 0, ntotal))
continue
chain2 = pairs2[key1]
nsame = alignlib_lite.py_getAlignmentIdentity(chain1, chain2,
alignlib_lite.py_RR)
noverlap = alignlib_lite.py_getAlignmentOverlap(
chain1, chain2, alignlib_lite.py_RR)
ndifferent = noverlap - nsame
nunique = ntotal - noverlap
result[key1] = DiffResult._make((ntotal, nsame, ndifferent, nunique))
return result