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 _addFile(dset, filename):
handledTypes = {'xml': _addXmlFile,
'bam': _addGenericFile,
'fofn': _addFofnFile,
'': _addUnknownFile,
'file': _addUnknownFile}
fileType = uri2scheme(filename)
fileLocation = uri2fn(filename)
handledTypes[fileType](dset, fileLocation)
def _addFile(dset, filename):
handledTypes = {'xml': _addXmlFile,
'bam': _addGenericFile,
'fofn': _addFofnFile,
'': _addUnknownFile,
'file': _addUnknownFile}
fileType = uri2scheme(filename)
fileLocation = uri2fn(filename)
handledTypes[fileType](dset, fileLocation)
def resolveLocation(fname, possibleRelStart=None):
"""Find the absolute path of a file that exists relative to
possibleRelStart."""
fname = uri2fn(fname)
if (possibleRelStart is not None and os.path.exists(possibleRelStart)
and os.path.exists(os.path.join(possibleRelStart, fname))):
return os.path.abspath(os.path.join(possibleRelStart, fname))
if os.path.exists(fname):
return os.path.abspath(fname)
log.error("Including unresolved file: {f}".format(f=fname))
return fname
def __parseMetadata(xsd_name, tag_name, return_type, filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
dsm_tag = (".//{http://pacificbiosciences.com/" + xsd_name + "}" +
tag_name)
try:
metadata = _eleToDictList(tree.getroot().find(dsm_tag))
except AttributeError:
# the tag wasn't found, we're trying to do something with None
raise InvalidDataSetIOError("Unable to parse metadata from "
"{f}".format(f=filename))
return return_type(metadata)
def __parseMetadata(xsd_name, tag_name, return_type, filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
dsm_tag = (".//{http://pacificbiosciences.com/" + xsd_name + "}" +
tag_name)
try:
metadata = _eleToDictList(tree.getroot().find(dsm_tag))
except AttributeError:
# the tag wasn't found, we're trying to do something with None
raise InvalidDataSetIOError("Unable to parse metadata from "
"{f}".format(f=filename))
return return_type(metadata)
def resolveLocation(fname, possibleRelStart=None):
"""Find the absolute path of a file that exists relative to
possibleRelStart."""
fname = uri2fn(fname)
if (possibleRelStart is not None and
os.path.exists(possibleRelStart) and
os.path.exists(os.path.join(possibleRelStart, fname))):
return os.path.abspath(os.path.join(possibleRelStart, fname))
if os.path.exists(fname):
return os.path.abspath(fname)
log.error("Including unresolved file: {f}".format(f=fname))
return fname
def parseMetadata(filename):
fileLocation = uri2fn(filename)
tree = ET.parse(fileLocation)
dsm_tag = (".//{http://pacificbiosciences.com/PacBioDatasets.xsd}"
"DataSetMetadata")
try:
metadata = _parseXmlDataSetMetadata(tree.getroot().find(dsm_tag))
except AttributeError:
# the tag wasn't found, we're trying to do something with None
raise InvalidDataSetIOError("Unable to parse metadata from "
"{f}".format(f=filename))
return metadata