1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
# Authors: David Alexander
from __future__ import absolute_import
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
|
