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#!/usr/bin/env python
import os
import sys
from pbcore.util.ToolRunner import PBToolRunner
from operator import xor
import h5py
# Version info
__version__ = "1.1"
def validateFile(p):
if os.path.isfile(p):
return os.path.abspath(p)
else:
raise IOError("Unable to find {p}.".format(p=p))
class CopyIpdSummaryDatasets(PBToolRunner):
"""
Copy IpdRatio datasets from infile:/ref0000x to outfile:/ref000x/Kinetics/IpdRatio
or from infile:/ref0000x to mergefile:/ref000x (Dataset)
"""
def __init__(self):
super(
CopyIpdSummaryDatasets,
self).__init__(
CopyIpdSummaryDatasets.__doc__)
self.parser.add_argument('--infile',
required=True,
type=validateFile,
dest='infile',
help='Input cmp.h5 filename')
self.parser.add_argument('--outfile',
type=validateFile,
required=False,
help='Output cmp.h5 filename')
self.parser.add_argument('--mergefile',
type=validateFile,
required=False,
help='Filename of output h5 file for merging')
def validateArgs(self):
if not xor(bool(self.args.mergefile), bool(self.args.outfile)):
raise Exception(
"Exactly one of --outfile, --mergefile is required")
def getVersion(self):
return __version__
def copyToCmpH5(self):
inFile = h5py.File(self.args.infile, mode='r')
outFile = h5py.File(self.args.outfile, mode='r+')
for refDataset in inFile.items():
(name, ds) = refDataset
if '/' + name in outFile:
targetGroup = outFile['/' + name]
if 'Kinetics' in targetGroup:
kinGroup = targetGroup['Kinetics']
else:
kinGroup = targetGroup.create_group('Kinetics')
if 'IpdRatio' in kinGroup:
del kinGroup['IpdRatio']
h5py.h5o.copy(inFile.id, name, kinGroup.id, 'IpdRatio')
def copyToMergeFile(self):
inFile = h5py.File(self.args.infile, mode='r')
mergeFile = h5py.File(self.args.mergefile, mode='r+')
for refDataset in inFile.items():
(name, ds) = refDataset
h5py.h5o.copy(inFile.id, name, mergeFile.id, name)
def run(self):
if self.args.outfile:
self.copyToCmpH5()
else:
self.copyToMergeFile()
return 0
def main():
kt = CopyIpdSummaryDatasets()
rcode = kt.start()
return rcode
if __name__ == "__main__":
sys.exit(main())
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