def parseStats(filename):
url = urlparse(filename)
fileType = url.scheme
fileLocation = url.path.strip()
if url.netloc:
fileLocation = url.netloc
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record["tag"] = "SummaryStats"
whitelist = [
"ShortInsertFraction",
"AdapterDimerFraction",
"MedianInsertDist",
"ProdDist",
"ReadTypeDist",
"ReadLenDist",
"ReadQualDist",
"InsertReadQualDist",
"InsertReadLenDist",
"ControlReadQualDist",
"ControlReadLenDist",
"NumSequencingZmws",
]
stats.pruneChildrenTo(whitelist)
return stats
def parseStats(filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record['tag'] = 'SummaryStats'
return stats
def parseStats(filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record['tag'] = 'SummaryStats'
return stats
def parseStats(filename):
url = urlparse(filename)
fileLocation = url.path.strip()
if url.netloc:
fileLocation = url.netloc
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record['tag'] = 'SummaryStats'
return stats
def parseStats(filename):
url = urlparse(filename)
fileLocation = url.path.strip()
if url.netloc:
fileLocation = url.netloc
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record['tag'] = 'SummaryStats'
return stats
def parseStats(filename):
url = urlparse(filename)
fileType = url.scheme
fileLocation = url.path.strip()
if url.netloc:
fileLocation = url.netloc
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record['tag'] = 'SummaryStats'
whitelist = ['ShortInsertFraction', 'AdapterDimerFraction',
'NumSequencingZmws'] + DISTLIST
stats.pruneChildrenTo(whitelist)
return stats
def parseStats(filename):
url = urlparse(filename)
fileType = url.scheme
fileLocation = url.path.strip()
if url.netloc:
fileLocation = url.netloc
tree = ET.parse(fileLocation)
root = tree.getroot()
root = _updateStats(root)
stats = StatsMetadata(_eleToDictList(root))
stats.record['tag'] = 'SummaryStats'
whitelist = [
'ShortInsertFraction', 'AdapterDimerFraction', 'MedianInsertDist',
'ProdDist', 'ReadTypeDist', 'ReadLenDist', 'ReadQualDist',
'InsertReadQualDist', 'InsertReadLenDist', 'ControlReadQualDist',
'ControlReadLenDist', 'NumSequencingZmws'
]
stats.pruneChildrenTo(whitelist)
return stats
