def chemistryBarcodeTriple(self):
"""
The chemistry barcode triple consists of (BindingKit,
SequencingKit, SoftwareVersion) and is written on the
instrument to the bax file as of primary version 2.1. Prior
to that, it was only written in the metadata.xml.
If the triple is not found in the bas file, we look in the
metadata.xml---throwing an exception if the xml file is not
found or can't be parsed.
"""
try:
bindingKit = self.file["/ScanData/RunInfo"].attrs["BindingKit"]
sequencingKit = self.file["/ScanData/RunInfo"].attrs[
"SequencingKit"]
# version string in bas file looks like "2.1.1.1.x", we have to extract
# the "2.1.1"
tmp = self.file["/PulseData/BaseCalls"].attrs["ChangeListID"]
swVersion = ".".join(tmp.split(".")[0:2])
return (bindingKit, sequencingKit, swVersion)
except:
movieName = self.movieName
_up = op.dirname(op.dirname(self.filename))
metadataLocation = op.join(_up, movieName + ".metadata.xml")
triple = tripleFromMetadataXML(metadataLocation)
return triple
def chemistryBarcodeTriple(self):
"""
The chemistry barcode triple consists of (BindingKit,
SequencingKit, SoftwareVersion) and is written on the
instrument to the bax file as of primary version 2.1. Prior
to that, it was only written in the metadata.xml.
If the triple is not found in the bas file, we look in the
metadata.xml---throwing an exception if the xml file is not
found or can't be parsed.
"""
try:
bindingKit = self.file["/ScanData/RunInfo"].attrs["BindingKit"]
sequencingKit = self.file["/ScanData/RunInfo"].attrs["SequencingKit"]
# version string in bas file looks like "2.1.1.1.x", we have to extract
# the "2.1.1"
tmp = self.file["/PulseData/BaseCalls"].attrs["ChangeListID"]
swVersion= ".".join(tmp.split(".")[0:2])
return (bindingKit, sequencingKit, swVersion)
except:
movieName = self.movieName
_up = op.dirname(op.dirname(self.filename))
metadataLocation = op.join(_up, movieName + ".metadata.xml")
triple = tripleFromMetadataXML(metadataLocation)
return triple
def _chemistryBarcodeTripleFromMetadataXML(self):
try:
movieName = self.movieName
_up = op.dirname(op.dirname(self.filename))
metadataLocation = op.join(_up, movieName + ".metadata.xml")
triple = tripleFromMetadataXML(metadataLocation)
return triple
except ChemistryLookupError:
return None
def _chemistryBarcodeTripleFromMetadataXML(self):
try:
movieName = self.movieName
_up = op.dirname(op.dirname(self.filename))
metadataLocation = op.join(_up, movieName + ".metadata.xml")
triple = tripleFromMetadataXML(metadataLocation)
return triple
except ChemistryLookupError:
return None
