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###############################################################################
# Copyright (c) 2011-2016, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
###############################################################################
# Author: Martin D. Smith
import os
import logging
log = logging.getLogger(__name__)
def fileType(fname):
"""Get the extension of fname (with h5 type)"""
remainder, ftype = os.path.splitext(fname)
if ftype == '.h5':
_, prefix = os.path.splitext(remainder)
ftype = prefix + ftype
elif ftype == '.index':
_, prefix = os.path.splitext(remainder)
if prefix == '.contig':
ftype = prefix + ftype
ftype = ftype.strip('.')
return ftype
def getDataSetUuid(xmlfile):
"""
Quickly retrieve the uuid from the root element of a dataset XML file,
using a streaming parser to avoid loading the entire dataset into memory.
Returns None if the parsing fails.
"""
try:
import xml.etree.cElementTree as ET
for event, element in ET.iterparse(xmlfile, events=("start",)):
return element.get("UniqueId")
except Exception:
return None
def getDataSetMetaType(xmlfile):
"""
Quickly retrieve the MetaType from the root element of a dataset XML file,
using a streaming parser to avoid loading the entire dataset into memory.
Returns None if the parsing fails.
"""
try:
import xml.etree.cElementTree as ET
for event, element in ET.iterparse(xmlfile, events=("start",)):
return element.get("MetaType")
except Exception:
return None
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