def __init__(self, base_dir):
self._dir = base_dir
self._configuration = IlluminaConfiguration(base_dir)
self._metrics_path = os.path.join(base_dir, "Data", "reports",
"Summary")
assert os.path.exists(
self._metrics_path
), "The RTA QC metrics folder %s does not exist" % self._metrics_path
# Assert that the readN.xml qc metrics files exist
self._metric_files = []
for read in self._configuration.reads().keys():
qc_file = os.path.join(self._metrics_path, "read%s.xml" % read)
assert os.path.exists(
qc_file), "The RTA QC metrics file %s does not exist" % qc_file
self._metric_files.append(qc_file)
# Parse the XML files
self.readSummaries()
def __init__(self, base_dir):
self._dir = base_dir
self._configuration = IlluminaConfiguration(base_dir)
self._metrics_path = os.path.join(base_dir,"Data","reports","Summary")
assert os.path.exists(self._metrics_path), "The RTA QC metrics folder %s does not exist" % self._metrics_path
# Assert that the readN.xml qc metrics files exist
self._metric_files = []
for read in self._configuration.reads().keys():
qc_file = os.path.join(self._metrics_path,"read%s.xml" % read)
assert os.path.exists(qc_file), "The RTA QC metrics file %s does not exist" % qc_file
self._metric_files.append(qc_file)
# Parse the XML files
self.readSummaries()
class RTAQCMetrics:
def __init__(self, base_dir):
self._dir = base_dir
self._configuration = IlluminaConfiguration(base_dir)
self._metrics_path = os.path.join(base_dir,"Data","reports","Summary")
assert os.path.exists(self._metrics_path), "The RTA QC metrics folder %s does not exist" % self._metrics_path
# Assert that the readN.xml qc metrics files exist
self._metric_files = []
for read in self._configuration.reads().keys():
qc_file = os.path.join(self._metrics_path,"read%s.xml" % read)
assert os.path.exists(qc_file), "The RTA QC metrics file %s does not exist" % qc_file
self._metric_files.append(qc_file)
# Parse the XML files
self.readSummaries()
@staticmethod
def metrics():
return [
['error_rate', 'ErrRatePhiX', False],
['error_rate_sd', 'ErrRatePhiXSD', False],
['raw_cluster_dens', 'ClustersRaw', True],
['raw_cluster_dens_sd', 'ClustersRawSD', True],
['prc_cluster_pf', 'PrcPFClusters', False],
['prc_cluster_pf_sd', 'PrcPFClustersSD', False],
['pf_cluster_dens', 'ClustersPF', True],
['pf_cluster_dens_sd', 'ClustersPFSD', True],
['phasing', 'Phasing', False],
['prephasing', 'Prephasing', False],
['prc_aligned', 'PrcAlign', False],
['prc_aligned_sd', 'PrcAlignSD', False]
]
def configuration(self):
return self._configuration
# getQCstats() is probably the method you usually want to call
def getQCstats(self):
qc_stats = {}
for metric in self.metrics():
qc_stats[metric[0]] = self.getAllLaneMetrics(metric[1],metric[2])
return qc_stats
def readSummaries(self):
self._qc_roots = {}
for qc_file in self._metric_files:
tree = ET.parse(qc_file)
root = tree.getroot()
if root is not None:
read = root.get("Read","0")
self._qc_roots[read] = root
def getAllSingleLaneMetric(self, metric, lane, clu_dens = False):
metrics = {}
for read, root in self._qc_roots.items():
metrics["read%s" % read] = self.getSingleLaneMetric(root, metric, lane, clu_dens)
return metrics
def getSingleLaneMetric(self, root, metric, lane, clu_dens = False):
m = self.getLaneMetric(root, metric, clu_dens, lane)
return m[lane]
def getAllLaneMetrics(self, metric, clu_dens):
metrics = {}
for read, root in self._qc_roots.items():
metrics["read%s" % read] = self.getLaneMetric(root, metric, clu_dens)
return metrics
def getLaneMetric(self, root, metric, clu_dens, lane=None):
if clu_dens: densRatio = float(root.get("densityRatio"))
lanes = root.findall("Lane")
m = {}
for l in lanes:
k = l.get("key")
if lane is not None and k != str(lane):
continue
val = float(l.get(metric))
m[k] = val
if clu_dens:
m[k] = str(int(round((densRatio * val)/1000))) + 'K'
return m
class RTAQCMetrics:
def __init__(self, base_dir):
self._dir = base_dir
self._configuration = IlluminaConfiguration(base_dir)
self._metrics_path = os.path.join(base_dir, "Data", "reports",
"Summary")
assert os.path.exists(
self._metrics_path
), "The RTA QC metrics folder %s does not exist" % self._metrics_path
# Assert that the readN.xml qc metrics files exist
self._metric_files = []
for read in self._configuration.reads().keys():
qc_file = os.path.join(self._metrics_path, "read%s.xml" % read)
assert os.path.exists(
qc_file), "The RTA QC metrics file %s does not exist" % qc_file
self._metric_files.append(qc_file)
# Parse the XML files
self.readSummaries()
@staticmethod
def metrics():
return [['error_rate', 'ErrRatePhiX', False],
['error_rate_sd', 'ErrRatePhiXSD', False],
['raw_cluster_dens', 'ClustersRaw', True],
['raw_cluster_dens_sd', 'ClustersRawSD', True],
['prc_cluster_pf', 'PrcPFClusters', False],
['prc_cluster_pf_sd', 'PrcPFClustersSD', False],
['pf_cluster_dens', 'ClustersPF', True],
['pf_cluster_dens_sd', 'ClustersPFSD', True],
['phasing', 'Phasing', False],
['prephasing', 'Prephasing', False],
['prc_aligned', 'PrcAlign', False],
['prc_aligned_sd', 'PrcAlignSD', False]]
def configuration(self):
return self._configuration
# getQCstats() is probably the method you usually want to call
def getQCstats(self):
qc_stats = {}
for metric in self.metrics():
qc_stats[metric[0]] = self.getAllLaneMetrics(metric[1], metric[2])
return qc_stats
def readSummaries(self):
self._qc_roots = {}
for qc_file in self._metric_files:
tree = ET.parse(qc_file)
root = tree.getroot()
if root is not None:
read = root.get("Read", "0")
self._qc_roots[read] = root
def getAllSingleLaneMetric(self, metric, lane, clu_dens=False):
metrics = {}
for read, root in self._qc_roots.items():
metrics["read%s" % read] = self.getSingleLaneMetric(
root, metric, lane, clu_dens)
return metrics
def getSingleLaneMetric(self, root, metric, lane, clu_dens=False):
m = self.getLaneMetric(root, metric, clu_dens, lane)
return m[lane]
def getAllLaneMetrics(self, metric, clu_dens):
metrics = {}
for read, root in self._qc_roots.items():
metrics["read%s" % read] = self.getLaneMetric(
root, metric, clu_dens)
return metrics
def getLaneMetric(self, root, metric, clu_dens, lane=None):
if clu_dens: densRatio = float(root.get("densityRatio"))
lanes = root.findall("Lane")
m = {}
for l in lanes:
k = l.get("key")
if lane is not None and k != str(lane):
continue
val = float(l.get(metric))
m[k] = val
if clu_dens:
m[k] = str(int(round((densRatio * val) / 1000))) + 'K'
return m
