def mafIsHardExtracted(name, outblocks, maf):
blockSet = set()
for b in outblocks:
blockSet.add(b.hashify())
f = open(maf)
lastLine = mtt.processHeader(f)
r = mtt.extractBlockStr(f, lastLine)
observedBlocks = set()
while r is not None:
b = rawBlockToObj(r)
if b is not None:
if b.hashify() not in blockSet:
print '\n[%s]' % name
print 'dang, hashed output contains'
print b.hashify()
print 'not in hashed expected output'
print blockSet
f.close()
return False
else:
observedBlocks.add(b.hashify())
r = mtt.extractBlockStr(f)
for b in blockSet:
if b not in observedBlocks:
print '\n[%s]' % name
print 'dang, expected hashed output block'
print b
print 'not observed in hashed output blocks'
for block in observedBlocks:
print block
f.close()
return False
f.close()
return True
def mafIsSorted(maf):
f = open(maf)
lastLine = mtt.processHeader(f)
observedNonTargetBlocks = []
expectedNonTargetBlocks = list(g_nonTargetBlocks)
for i in xrange(0, len(expectedNonTargetBlocks)):
observedNonTargetBlocks.append(mtt.extractBlockStr(f, lastLine).replace(" ", ""))
lastLine = None
expectedNonTargetBlocks[i] = expectedNonTargetBlocks[i].replace(" ", "")
if observedNonTargetBlocks != expectedNonTargetBlocks:
f.close()
print "\nnon-target block failure observed:"
print "".join(observedNonTargetBlocks)
print "!= expected:"
print "".join(expectedNonTargetBlocks)
return False
sortedBlocks = []
expectedTargetBlocks = list(g_targetBlocks)
for i in xrange(0, len(expectedTargetBlocks)):
sortedBlocks.append(mtt.extractBlockStr(f).replace(" ", ""))
expectedTargetBlocks[i] = expectedTargetBlocks[i].replace(" ", "")
for i in xrange(0, len(sortedBlocks)):
if sortedBlocks[i] != expectedTargetBlocks[i]:
f.close()
print "\nsorted block failure"
print sortedBlocks[i]
print "!="
print expectedTargetBlocks[i]
print "observed "
print sortedBlocks
print "!= expected "
print expectedTargetBlocks
return False
f.close()
return True
def mafIsExtracted(maf):
f = open(maf)
lastLine = mtt.processHeader(f)
for i in xrange(0, len(g_overlappingBlocks)):
b = mtt.extractBlockStr(f, lastLine)
lastLine = None
if b not in g_overlappingBlocks:
print 'dang'
print b
print '!='
print g_overlappingBlocks
return False
return True
def mafIsExtracted(maf):
f = open(maf)
lastLine = mtt.processHeader(f)
for i in xrange(0, len(g_overlappingBlocks)):
b = mtt.extractBlockStr(f, lastLine)
lastLine = None
if hashStr(b) not in g_overlappingBlocksHashed:
print 'dang, block'
print b
print 'is not in set of expected output'
print g_overlappingBlocks
f.close()
return False
f.close()
return True
def mafIsFiltered(maf, blockList):
f = open(maf)
lastLine = mtt.processHeader(f)
for i in xrange(0, len(blockList)):
# walk through the maf, assessing the equivalence to the blockList items
b = mtt.extractBlockStr(f, lastLine)
lastLine = None
if b != blockList[i]:
print 'dang'
print 'observed:'
print b
print '!='
print 'expected:'
print blockList[i]
return False
return True
def mafIsFiltered(maf, blockList):
f = open(maf)
lastLine = mtt.processHeader(f)
for i in xrange(0, len(blockList)):
# walk through the maf, assessing the equivalence to the blockList items
b = mtt.extractBlockStr(f, lastLine)
lastLine = None
if b != blockList[i]:
print 'dang'
print 'observed:'
print b
print '!='
print 'expected:'
print blockList[i]
return False
return True
def mafIsCoerced(filename, expected):
f = open(filename)
lastLine = mtt.processHeader(f)
# walk through the maf, assessing the equivalence to the blockList items
b = mtt.extractBlockStr(f, lastLine)
maf = ''
while (b is not None):
lastLine = None
maf += b
b = mtt.extractBlockStr(f, lastLine)
if hashify(maf) != hashify(expected):
print '\ndang'
print 'observed:'
print maf
print '!='
print 'expected:'
print expected
return False
return True
def mafIsCorrect(filename, expected):
f = open(filename)
lastLine = mtt.processHeader(f)
# walk through the maf, assessing the equivalence to the blockList items
b = mtt.extractBlockStr(f, lastLine)
maf = ''
while (b is not None):
lastLine = None
maf += b
b = mtt.extractBlockStr(f, lastLine)
if hashify(maf) != hashify(expected):
print '\ndang'
print 'observed:'
print maf
print '!='
print 'expected:'
print expected
return False
return True
def mafIsFiltered(filename, expected, header):
f = open(filename)
lastLine = mtt.processHeader(f)
maf = ''
b = mtt.extractBlockStr(f, lastLine)
while (b is not None):
lastLine = None
maf += b
b = mtt.extractBlockStr(f, lastLine)
if maf != expected:
print 'dang'
print 'observed:'
print maf
print '!='
print 'expected:'
print expected
f.close()
return False
f.close()
return True
def mafIsOrdered(filename, expected, header):
f = open(filename)
lastLine = mtt.processHeader(f)
maf = ''
b = mtt.extractBlockStr(f, lastLine)
while (b is not None):
lastLine = None
maf += b
b = mtt.extractBlockStr(f, lastLine)
if hashify(maf) != hashify(expected):
print 'dang'
print 'observed:'
print maf
print '!='
print 'expected:'
print expected
f.close()
return False
f.close()
return True
def mafIsClosed(maf, outList):
if not os.path.exists(maf):
return False
f = open(maf)
lastLine = mtt.processHeader(f)
block = mtt.extractBlockStr(f, lastLine)
if block is None:
return False
while block is not None:
lastLine = None
block = block.strip()
block = block.split('\n')
block = block[1:] # throw away alignment line
for line in block:
line = line.strip()
if line == '':
continue
if line not in outList:
return False
block = mtt.extractBlockStr(f, lastLine)
f.close()
return True
def mafIsClosed(maf, outList):
if not os.path.exists(maf):
return False
f = open(maf)
lastLine = mtt.processHeader(f)
block = mtt.extractBlockStr(f, lastLine)
if block is None:
return False
while block is not None:
lastLine = None
block = block.strip()
block = block.split('\n')
block = block[1:] # throw away alignment line
for line in block:
line = line.strip()
if line == '':
continue
if line not in outList:
return False
block = mtt.extractBlockStr(f, lastLine)
f.close()
return True
def mafIsSorted(maf):
f = open(maf)
lastLine = mtt.processHeader(f)
observedNonTargetBlocks = []
expectedNonTargetBlocks = list(g_nonTargetBlocks)
for i in xrange(0, len(expectedNonTargetBlocks)):
observedNonTargetBlocks.append(
mtt.extractBlockStr(f, lastLine).replace(' ', ''))
lastLine = None
expectedNonTargetBlocks[i] = expectedNonTargetBlocks[i].replace(
' ', '')
if observedNonTargetBlocks != expectedNonTargetBlocks:
f.close()
print '\nnon-target block failure observed:'
print ''.join(observedNonTargetBlocks)
print '!= expected:'
print ''.join(expectedNonTargetBlocks)
return False
sortedBlocks = []
expectedTargetBlocks = list(g_targetBlocks)
for i in xrange(0, len(expectedTargetBlocks)):
sortedBlocks.append(mtt.extractBlockStr(f).replace(' ', ''))
expectedTargetBlocks[i] = expectedTargetBlocks[i].replace(' ', '')
for i in xrange(0, len(sortedBlocks)):
if sortedBlocks[i] != expectedTargetBlocks[i]:
f.close()
print '\nsorted block failure'
print sortedBlocks[i]
print '!='
print expectedTargetBlocks[i]
print 'observed '
print sortedBlocks
print '!= expected '
print expectedTargetBlocks
return False
f.close()
return True