def readFastaChunks(self):
numChunks = self.scale or 1
if self.seq is not None and len(self.seq) >= (
(numChunks - 1) *
chunkSize) + 1: #at least on character in the last chunk
return
self.seq = ''
self.length = len(self.seq)
partialSequences = []
for index, chunkStart in enumerate(
range(self.start, self.start + numChunks * chunkSize,
chunkSize)):
tempState = self.copy()
tempState.start = chunkStart
chunk = readFile(tempState)
if chunk is None:
break
else:
partialSequences.append(chunk)
self.seq = "".join(partialSequences)
if self.scale >= 10:
print "Done reading files"
self.length = len(self.seq)
def readAndAppendNextChunk(self, addPadding=False):
assert StorageRequestHandler.GetFastaFilePath(self.specimen, self.chromosome,
1) is not None, "Specimen and Chromosome is not in the database"
startBackup = self.start
if not self.seq:
self.seq = '' #ensure that seq is at least a string object
self.start = self.start + len(self.seq) # jump to the end of the current sequence (+ chunkSize)
#print "Requesting",self.specimen, self.chromosome, self.start
sequence = readFile(self)# see if there's a file that begins where you end, this will stop on a partial file
if sequence is not None:
self.seq = self.seq + sequence #append two sequences together
elif addPadding:
self.seq = self.seq + ('N' * chunkSize)
self.start = startBackup
self.length = len(self.seq)
return self
def readFastaChunks(self):
numChunks = self.scale or 1
if self.seq is not None and len(self.seq) >= (
(numChunks - 1) * chunkSize) + 1: #at least on character in the last chunk
return
self.seq = ''
self.length = len(self.seq)
partialSequences = [None] * numChunks
for index, chunkStart in enumerate(range(self.start, self.start + numChunks * chunkSize, chunkSize)):
tempState = self.copy()
tempState.start = chunkStart
partialSequences[index] = readFile(tempState)
if partialSequences[index] is None:
partialSequences[index] = ''
self.seq = ''.join(partialSequences)
if self.scale >= 10:
print "Done reading files"
self.length = len(self.seq)
def readAndAppendNextChunk(self, addPadding=False):
assert StorageRequestHandler.GetFastaFilePath(
self.specimen, self.chromosome,
1) is not None, "Specimen and Chromosome is not in the database"
startBackup = self.start
if not self.seq:
self.seq = '' #ensure that seq is at least a string object
self.start = self.start + len(
self.seq) # jump to the end of the current sequence (+ chunkSize)
#print "Requesting",self.specimen, self.chromosome, self.start
sequence = readFile(
self
) # see if there's a file that begins where you end, this will stop on a partial file
if sequence is not None:
self.seq = self.seq + sequence #append two sequences together
elif addPadding:
self.seq = self.seq + ('N' * chunkSize)
self.start = startBackup
self.length = len(self.seq)
return self
