[Bioperl-l] storing/retrieving a large hash on file system?

Ben Bimber bimber at wisc.edu
Tue May 18 15:28:06 UTC 2010


this question is more of a general perl one than bioperl specific, so
I hope it is appropriate for this list:

I am writing code that has two steps.  the first generates a large,
complex hash describing mutations.  it takes a fair amount of time to
run this step.  the second step uses this data to perform downstream
calculations.  for the purposes of writing/debugging this downstream
code, it would save me a lot of time if i could run the first step
once, then store this hash in something like the file system.  this
way I could quickly load it, when debugging the downstream code
without waiting for the hash to be recreated.

is there a 'best practice' way to do something like this?  I could
save a tab-delimited file, which is human readable, but does not
represent the structure of the hash, so I would need code to re-parse
it.  I assume I could probably do something along the lines of dumping
a JSON string, then read/decode it.  this is easy, but not so
human-readable.  is there another option i'm not thinking of?  what do
others do in this sort of situation?

thanks in advance.

-Ben



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