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if we run out of storage space while writing we should throw a useful error #246
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Should we maybe abstract File IO into a stand-alone module? |
That would be useful, yep!
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Maybe create a checklist of functionalities to be abstracted?
Ram On Thu, Jan 23, 2014 at 2:37 PM, Michael R. Crusoe <[email protected]
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There are a couple I/O related issues that should be worked on together. #247 "don't infinite loop when reading truncated hash files" |
Thank you. This helps a lot. I'll prepare signatures for generic read-write functions. These should Ram On Thu, Jan 23, 2014 at 4:34 PM, Michael R. Crusoe <[email protected]
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Can psutil (https://code.google.com/p/psutil/) be used to check disk space or do we have other standards that we already use? |
We only support Linux and OS X so the os.statvfs function is good enough. http://docs.python.org/2/library/os.html#os.statvfs
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Cool. Next up - how do we estimate python object size (to compare with free disk space) - can we use this piece of code? http://code.activestate.com/recipes/546530/ |
We don't, not directly. Since the whole point of khmer is to operate on a (Also that code is huge and complex. Using it would be a great burden to The exception to this are writing out the hashtables to disk. Those we can We could issue a warning based upon the input file size. It seems risky to
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That is a reasonable (not to mention amazing) way to approximate required space, @mr-c ! Will do. As of now, the methods in the new API are:
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@mr-c How do we determine the size of the hashtable? I'm unable to understand the C part of the implementation :( |
Both normalize-by-median and load-into-counting output messages with the --t On Sat, Jan 25, 2014 at 04:22:00PM -0800, Ram RS wrote:
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Got it. And should I double check to make sure that any script creating a ht afresh does indeed consume CMD line args via build_construct_args() and not directly via add_argument()? |
Oh, Ok. Thanks! |
Fixed by #333, closing |
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