def convertIdsToTxIds(errorIds):
"""read the sequence from a file in fasta format"""
txList = list()
for record in fasta.fasta_itr(three_utr_combined_file):
header = record.header
geneId, transcriptId, geneName = header.split('|')
txList.append(transcriptId);
for list1 in itertools.izip(errorIds):
print list1
for list2 in itertools.izip(list1[0]):
idx = list2[0]
print txList[idx]
return txList;
def constructFromFile(self, fileName, **args) :
print 'reading from', fileName
headerHandler = fastaHeaderHandler
if 'headerHandler' in args :
headerHandler = args['headerHandler']
numPatterns = fasta.fasta_count(fileName)
self.container.__init__(self, numPatterns)
patternIDs = []
L = []
for record in fasta.fasta_itr(fileName) :
self.addPattern(record.sequence)
patternID, label = headerHandler(record.header)
patternIDs.append(patternID)
if label is not None :
L.append(label)
self.attachLabels(Labels(L, patternID = patternIDs, **args))
def constructFromFile(self, fileName, **args):
print 'reading from', fileName
headerHandler = fastaHeaderHandler
if 'headerHandler' in args:
headerHandler = args['headerHandler']
numPatterns = fasta.fasta_count(fileName)
self.container.__init__(self, numPatterns)
patternIDs = []
L = []
for record in fasta.fasta_itr(fileName):
self.addPattern(record.sequence)
patternID, label = headerHandler(record.header)
patternIDs.append(patternID)
if label is not None:
L.append(label)
self.attachLabels(Labels(L, patternID=patternIDs, **args))
def fasta_read(file_name) :
"""read the sequence from a file in fasta format"""
return [record.sequence for record in fasta.fasta_itr(file_name)]
def fasta_read(file_name):
"""read the sequence from a file in fasta format"""
return [record.sequence for record in fasta.fasta_itr(file_name)]