def MakeReference(self):
if not os.path.isfile(self.strRefFile):
with open(self.strBarcodeFile) as Barcode, \
open(self.strTargetSeqFile) as Target, \
open(self.strReferenceSeqFile) as Ref, \
open(self.strRefFile, 'w') as Output:
listBarcode = Helper.RemoveNullAndBadKeyword(Barcode)
listTarget = Helper.RemoveNullAndBadKeyword(Target)
listRef = Helper.RemoveNullAndBadKeyword(Ref)
## defensive
assert len(listBarcode) == len(listTarget) == len(listRef), 'Barcode, Target and Reference must be a same row number.'
listName = []
for strBar, strTar in zip(listBarcode, listTarget):
strBar = strBar.replace('\n', '').replace('\r', '').strip().upper()
strTar = strTar.replace('\n', '').replace('\r', '').strip().upper()
Helper.CheckIntegrity(self.strBarcodeFile, strBar) ## defensive
Helper.CheckIntegrity(self.strBarcodeFile, strTar) ## defensive
listName.append(strBar + ':' + strTar + '\n')
for i, strRow in enumerate(listRef):
strRow = strRow.replace('\r', '').strip().upper()
Output.write('>' + listName[i] + strRow + '\n')
def MakeReference(self):
with open(self.strBarcodeFile) as Barcode, \
open(self.strReferenceSeqFile) as Ref, \
open(self.strRefFile, 'w') as Output:
listBarcode = Helper.RemoveNullAndBadKeyword(Barcode)
listRef = Helper.RemoveNullAndBadKeyword(Ref)
## defensive
assert len(listBarcode) == len(
listRef), 'Barcode and Reference must be a same row number.'
dictBarcode = {}
for strBarcode in listBarcode:
strBarcode = strBarcode.replace('\n', '').replace('\r',
'').upper()
Helper.CheckIntegrity(self.strBarcodeFile,
strBarcode) ## defensive
listBarcode = strBarcode.split(':')
strBarSample = listBarcode[0]
strBarcode = listBarcode[1]
dictBarcode[strBarSample] = strBarcode
for strRef in listRef:
strRef = strRef.replace('\n', '').replace('\r', '').upper()
Helper.CheckIntegrity(self.strBarcodeFile,
strRef) ## defensive
listRef = strRef.split(':')
strRefSample = listRef[0]
strRef = listRef[1]
try:
sBarcode = dictBarcode[strRefSample]
Output.write('%s\t%s\t%s\n' %
(strRefSample, sBarcode, strRef))
except KeyError:
logging.error('no matching')
logging.error(strRefSample, strRef)