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

[Spiros Denaxas]

Hello,

it all really depends on your definition of readable. YAML is readable
but requires a parser ; XML is readable but is bloated and requires a
code and a parser.

You can directly dump the output from Data::Dumper and then eval() it
back in a hash. I would think this is the cleanest way if you
specifically want to dump a hash and re-generate it with no additional
code.

You can set the $Data::Dumper::Indent flag to control how readable the hash is.

hope this helps,

Spiros

On Tue, May 18, 2010 at 4:28 PM, Ben Bimber <bimber at wisc.edu> wrote:
> 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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