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#!/usr/bin/python3
import glob
import os
import shutil
import sys
import shasta
# Get from the arguments the list of input fasta files and check that they all exist.
helpMessage = "This script restores a run to memory from directory DataOnDisk."
if not len(sys.argv)==1:
print(helpMessage)
exit(1)
if not os.path.lexists('Data'):
raise Exception('Missing: Data. Use SetupRunDirectory.py to set up the run directory.')
if not os.path.lexists('DataOnDisk'):
raise Exception('Missing: DataOnDisk.')
if glob.glob('Data/*'):
raise Exception('The Data directory is not empty. Nothing was restored.')
# Copy the Data directory.
# We cannot use regular copy commands because
# this is on the huge page filesystem.
inputFileNames = glob.glob('DataOnDisk/*')
for inputFileName in inputFileNames:
lastSlashPosition = inputFileName.rfind('/')
outputFileName = 'Data/' + inputFileName[lastSlashPosition+1:]
shasta.mappedCopy(inputFileName, outputFileName)
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