def __getInput(self, pdag, fspec):
"""Get an input file. If fspec can be None, File or FileIn, or any
object that can be converted to a string. Return the appropriate PIn
object, None, or a string. Adds decompression process if needed."""
if fspec == None:
return None
if isinstance(fspec, File):
fspec = FileIn(fspec)
if not isinstance(fspec, FileIn):
return str(fspec)
# handle File object, include arg prefix
path = fspec.file.getInPath()
if fileOps.isCompressed(path) and fspec.autoDecompress:
pdev = Pipeline.Pipe()
pdag.create((fileOps.decompressCmd(path), path), stdout=pdev)
return Pipeline.PIn(pdev, fspec.prefix)
else:
return Pipeline.PIn(Pipeline.File(path), fspec.prefix)
