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#################################################################################
# Copyright (c) 2011-2015, 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,g 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.
#################################################################################
# Authors: David Alexander
from pbcore.io.base import getFileHandle
from os.path import dirname, isabs, join, abspath, expanduser
import xml.etree.ElementTree as ET
__all__ = [ "readFofn",
"readInputXML",
"enumeratePulseFiles" ]
def readFofn(f):
"""
Return iterator over filenames in a FOFN ("file-of-filenames")
file or file-like object.
If f is a path to a true FOFN on disk, any paths listed in the
FOFN that are relative (i.e., do not contain a leading '/') will
be reckoned from the directory containing the FOFN.
"""
if isinstance(f, basestring):
fofnRoot = dirname(abspath(expanduser(f)))
else:
fofnRoot = None
for line in getFileHandle(f):
path = line.rstrip()
if not path:
continue # skip empty lines
elif isabs(path):
yield path
elif fofnRoot is not None:
yield join(fofnRoot, path)
else:
raise IOError, "Cannot handle relative paths in StringIO FOFN"
def readInputXML(fname):
tree = ET.parse(fname)
root = tree.getroot()
for elt in root.iter():
if elt.tag=="location":
yield elt.text
def enumeratePulseFiles(fname):
"""
A pulse file is a file with suffix .bax.h5, .plx.h5, or bas.h5
fname is either a name of a pulse file, a list of names of pulse
files, a FOFN (file of file names) listing pulse files, or an
input.xml file.
This is a generalization of readFofn for the case where fname is
of type fofn|pulse, provided for convenience for tools that accept
such an argument.
"""
if isinstance(fname, list):
for fname_ in fname:
yield fname_
elif fname.endswith(".fofn"):
for pls in readFofn(fname):
yield pls
elif fname.endswith(".xml"):
for pls in readInputXML(fname):
yield pls
else:
yield fname
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